Starting phenix.real_space_refine on Mon Mar 11 18:30:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/03_2024/8sbd_40305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/03_2024/8sbd_40305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/03_2024/8sbd_40305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/03_2024/8sbd_40305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/03_2024/8sbd_40305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/03_2024/8sbd_40305.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 S 96 5.16 5 C 2912 2.51 5 N 720 2.21 5 O 856 1.98 5 H 4280 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8864 Number of models: 1 Model: "" Number of chains: 32 Chain: "p" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "o" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "n" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "m" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "l" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "k" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "j" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "i" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "h" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "g" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "f" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "e" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "d" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "c" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "b" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "a" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "O" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "N" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "M" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "L" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "K" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "J" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "I" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "B" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 4.16, per 1000 atoms: 0.47 Number of scatterers: 8864 At special positions: 0 Unit cell: (75.53, 95.45, 56.44, 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 96 16.00 O 856 8.00 N 720 7.00 C 2912 6.00 H 4280 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS p 7 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS p 19 " - pdb=" SG CYS P 20 " distance=2.03 Simple disulfide: pdb=" SG CYS o 7 " - pdb=" SG CYS O 7 " distance=2.03 Simple disulfide: pdb=" SG CYS o 19 " - pdb=" SG CYS O 20 " distance=2.03 Simple disulfide: pdb=" SG CYS n 7 " - pdb=" SG CYS N 7 " distance=2.03 Simple disulfide: pdb=" SG CYS n 19 " - pdb=" SG CYS N 20 " distance=2.03 Simple disulfide: pdb=" SG CYS m 7 " - pdb=" SG CYS M 7 " distance=2.03 Simple disulfide: pdb=" SG CYS m 19 " - pdb=" SG CYS M 20 " distance=2.03 Simple disulfide: pdb=" SG CYS l 7 " - pdb=" SG CYS L 7 " distance=2.03 Simple disulfide: pdb=" SG CYS l 19 " - pdb=" SG CYS L 20 " distance=2.03 Simple disulfide: pdb=" SG CYS k 7 " - pdb=" SG CYS K 7 " distance=2.03 Simple disulfide: pdb=" SG CYS k 19 " - pdb=" SG CYS K 20 " distance=2.03 Simple disulfide: pdb=" SG CYS j 7 " - pdb=" SG CYS J 7 " distance=2.03 Simple disulfide: pdb=" SG CYS j 19 " - pdb=" SG CYS J 20 " distance=2.03 Simple disulfide: pdb=" SG CYS i 7 " - pdb=" SG CYS I 7 " distance=2.03 Simple disulfide: pdb=" SG CYS i 19 " - pdb=" SG CYS I 20 " distance=2.03 Simple disulfide: pdb=" SG CYS h 7 " - pdb=" SG CYS H 7 " distance=2.03 Simple disulfide: pdb=" SG CYS h 19 " - pdb=" SG CYS H 20 " distance=2.03 Simple disulfide: pdb=" SG CYS g 7 " - pdb=" SG CYS G 7 " distance=2.03 Simple disulfide: pdb=" SG CYS g 19 " - pdb=" SG CYS G 20 " distance=2.03 Simple disulfide: pdb=" SG CYS f 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS f 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS e 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS e 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS d 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS c 7 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS c 19 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS b 7 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS b 19 " - pdb=" SG CYS B 20 " distance=2.03 Simple disulfide: pdb=" SG CYS a 7 " - pdb=" SG CYS A 7 " distance=2.03 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS A 20 " distance=2.03 Simple disulfide: pdb=" SG CYS P 6 " - pdb=" SG CYS P 11 " distance=2.03 Simple disulfide: pdb=" SG CYS O 6 " - pdb=" SG CYS O 11 " distance=2.03 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 11 " distance=2.03 Simple disulfide: pdb=" SG CYS M 6 " - pdb=" SG CYS M 11 " distance=2.03 Simple disulfide: pdb=" SG CYS L 6 " - pdb=" SG CYS L 11 " distance=2.03 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 11 " distance=2.03 Simple disulfide: pdb=" SG CYS J 6 " - pdb=" SG CYS J 11 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 11 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 11 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 11 " distance=2.03 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 811.4 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'n' and resid 15 through 17 removed outlier: 6.137A pdb=" N TYR p 16 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR l 16 " --> pdb=" O LEU f 17 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR h 16 " --> pdb=" O LEU b 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'm' and resid 12 through 19 removed outlier: 6.503A pdb=" N VAL o 12 " --> pdb=" O GLU m 13 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU m 15 " --> pdb=" O VAL o 12 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA o 14 " --> pdb=" O LEU m 15 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU m 17 " --> pdb=" O ALA o 14 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR o 16 " --> pdb=" O LEU m 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS m 19 " --> pdb=" O TYR o 16 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL o 18 " --> pdb=" O CYS m 19 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL k 12 " --> pdb=" O GLU i 13 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LEU i 15 " --> pdb=" O VAL k 12 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA k 14 " --> pdb=" O LEU i 15 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU i 17 " --> pdb=" O ALA k 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR k 16 " --> pdb=" O LEU i 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS i 19 " --> pdb=" O TYR k 16 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL k 18 " --> pdb=" O CYS i 19 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU k 13 " --> pdb=" O ALA e 14 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR e 16 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU k 15 " --> pdb=" O TYR e 16 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL e 18 " --> pdb=" O LEU k 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU k 17 " --> pdb=" O VAL e 18 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL g 12 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N LEU e 15 " --> pdb=" O VAL g 12 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA g 14 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU e 17 " --> pdb=" O ALA g 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR g 16 " --> pdb=" O LEU e 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS e 19 " --> pdb=" O TYR g 16 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL g 18 " --> pdb=" O CYS e 19 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL c 12 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU a 15 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA c 14 " --> pdb=" O LEU a 15 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU a 17 " --> pdb=" O ALA c 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR c 16 " --> pdb=" O LEU a 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS a 19 " --> pdb=" O TYR c 16 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL c 18 " --> pdb=" O CYS a 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'm' and resid 24 through 25 removed outlier: 6.417A pdb=" N PHE o 24 " --> pdb=" O PHE i 25 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE k 24 " --> pdb=" O PHE e 25 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE g 24 " --> pdb=" O PHE a 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 15 through 19 removed outlier: 6.721A pdb=" N LEU P 16 " --> pdb=" O GLU J 17 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR J 19 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN P 18 " --> pdb=" O TYR J 19 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU L 16 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR F 19 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN L 18 " --> pdb=" O TYR F 19 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU H 16 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR B 19 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN H 18 " --> pdb=" O TYR B 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 15 through 16 removed outlier: 6.433A pdb=" N GLN O 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN K 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN G 15 " --> pdb=" O LEU A 16 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4280 1.04 - 1.23: 184 1.23 - 1.43: 1864 1.43 - 1.63: 2512 1.63 - 1.82: 96 Bond restraints: 8936 Sorted by residual: bond pdb=" N VAL J 3 " pdb=" CA VAL J 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.31e+00 bond pdb=" N VAL D 3 " pdb=" CA VAL D 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.21e+00 bond pdb=" N VAL H 3 " pdb=" CA VAL H 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.20e+00 bond pdb=" N VAL L 3 " pdb=" CA VAL L 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.20e+00 bond pdb=" N VAL P 3 " pdb=" CA VAL P 3 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.15e+00 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 106.04 - 111.10: 9408 111.10 - 116.17: 1794 116.17 - 121.24: 2652 121.24 - 126.31: 2012 126.31 - 131.37: 86 Bond angle restraints: 15952 Sorted by residual: angle pdb=" N VAL g 18 " pdb=" CA VAL g 18 " pdb=" C VAL g 18 " ideal model delta sigma weight residual 106.53 111.16 -4.63 1.41e+00 5.03e-01 1.08e+01 angle pdb=" N VAL m 18 " pdb=" CA VAL m 18 " pdb=" C VAL m 18 " ideal model delta sigma weight residual 106.53 111.15 -4.62 1.41e+00 5.03e-01 1.08e+01 angle pdb=" N VAL k 18 " pdb=" CA VAL k 18 " pdb=" C VAL k 18 " ideal model delta sigma weight residual 106.53 111.15 -4.62 1.41e+00 5.03e-01 1.07e+01 angle pdb=" N VAL e 18 " pdb=" CA VAL e 18 " pdb=" C VAL e 18 " ideal model delta sigma weight residual 106.53 111.14 -4.61 1.41e+00 5.03e-01 1.07e+01 angle pdb=" N VAL c 18 " pdb=" CA VAL c 18 " pdb=" C VAL c 18 " ideal model delta sigma weight residual 106.53 111.13 -4.60 1.41e+00 5.03e-01 1.07e+01 ... (remaining 15947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 3653 11.63 - 23.26: 451 23.26 - 34.89: 176 34.89 - 46.52: 96 46.52 - 58.15: 24 Dihedral angle restraints: 4400 sinusoidal: 2272 harmonic: 2128 Sorted by residual: dihedral pdb=" CA THR N 8 " pdb=" C THR N 8 " pdb=" N SER N 9 " pdb=" CA SER N 9 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA THR B 8 " pdb=" C THR B 8 " pdb=" N SER B 9 " pdb=" CA SER B 9 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA THR J 8 " pdb=" C THR J 8 " pdb=" N SER J 9 " pdb=" CA SER J 9 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 434 0.028 - 0.056: 178 0.056 - 0.084: 59 0.084 - 0.111: 55 0.111 - 0.139: 10 Chirality restraints: 736 Sorted by residual: chirality pdb=" CA THR L 8 " pdb=" N THR L 8 " pdb=" C THR L 8 " pdb=" CB THR L 8 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA THR P 8 " pdb=" N THR P 8 " pdb=" C THR P 8 " pdb=" CB THR P 8 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA THR H 8 " pdb=" N THR H 8 " pdb=" C THR H 8 " pdb=" CB THR H 8 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 733 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS D 7 " -0.003 2.00e-02 2.50e+03 5.96e-03 3.56e-01 pdb=" C CYS D 7 " 0.010 2.00e-02 2.50e+03 pdb=" O CYS D 7 " -0.004 2.00e-02 2.50e+03 pdb=" N THR D 8 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 7 " -0.003 2.00e-02 2.50e+03 5.94e-03 3.53e-01 pdb=" C CYS B 7 " 0.010 2.00e-02 2.50e+03 pdb=" O CYS B 7 " -0.004 2.00e-02 2.50e+03 pdb=" N THR B 8 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 7 " -0.003 2.00e-02 2.50e+03 5.92e-03 3.51e-01 pdb=" C CYS J 7 " 0.010 2.00e-02 2.50e+03 pdb=" O CYS J 7 " -0.004 2.00e-02 2.50e+03 pdb=" N THR J 8 " -0.003 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 1356 2.25 - 2.84: 21353 2.84 - 3.43: 23171 3.43 - 4.01: 35173 4.01 - 4.60: 50315 Nonbonded interactions: 131368 Sorted by model distance: nonbonded pdb="HE21 GLN N 15 " pdb=" OE1 GLU N 17 " model vdw 1.666 1.850 nonbonded pdb="HE21 GLN B 15 " pdb=" OE1 GLU B 17 " model vdw 1.666 1.850 nonbonded pdb="HE21 GLN J 15 " pdb=" OE1 GLU J 17 " model vdw 1.666 1.850 nonbonded pdb="HE21 GLN H 15 " pdb=" OE1 GLU H 17 " model vdw 1.667 1.850 nonbonded pdb="HE21 GLN P 15 " pdb=" OE1 GLU P 17 " model vdw 1.667 1.850 ... (remaining 131363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.130 Extract box with map and model: 2.390 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 31.490 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 : 0.003 0.020 4656 Z= 0.206 Angle : 0.725 4.629 6280 Z= 0.437 Chirality : 0.043 0.139 736 Planarity : 0.002 0.006 760 Dihedral : 12.978 52.500 1576 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.97 % Allowed : 8.96 % Favored : 85.07 % 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: -4.19 (0.24), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS b 10 PHE 0.007 0.002 PHE m 24 TYR 0.007 0.001 TYR i 16 ARG 0.001 0.000 ARG o 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 0.825 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: H 8 THR cc_start: 0.8017 (t) cc_final: 0.7790 (m) REVERT: B 8 THR cc_start: 0.7919 (t) cc_final: 0.7518 (m) outliers start: 32 outliers final: 15 residues processed: 109 average time/residue: 0.1737 time to fit residues: 29.4650 Evaluate side-chains 78 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 7 CYS Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain h residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain B residue 6 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4656 Z= 0.175 Angle : 0.575 4.581 6280 Z= 0.312 Chirality : 0.044 0.136 736 Planarity : 0.002 0.008 760 Dihedral : 8.605 55.084 633 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.41 % Allowed : 15.49 % Favored : 79.10 % 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: -4.14 (0.24), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.18), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS j 10 PHE 0.004 0.001 PHE g 24 TYR 0.008 0.001 TYR i 16 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 59 time to evaluate : 0.808 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 outliers start: 29 outliers final: 21 residues processed: 83 average time/residue: 0.1714 time to fit residues: 22.2884 Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain h residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain B residue 6 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4656 Z= 0.235 Angle : 0.601 5.935 6280 Z= 0.322 Chirality : 0.045 0.116 736 Planarity : 0.002 0.015 760 Dihedral : 8.485 56.009 630 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 6.53 % Allowed : 17.91 % Favored : 75.56 % 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: -4.18 (0.25), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS l 10 PHE 0.008 0.002 PHE o 24 TYR 0.012 0.002 TYR K 19 ARG 0.003 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 52 time to evaluate : 0.816 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: j 7 CYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6462 (m) outliers start: 35 outliers final: 24 residues processed: 81 average time/residue: 0.1715 time to fit residues: 21.9571 Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 7 CYS Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain h residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 5 GLN N 18 ASN M 5 GLN K 5 GLN I 5 GLN E 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4656 Z= 0.385 Angle : 0.706 7.284 6280 Z= 0.377 Chirality : 0.049 0.127 736 Planarity : 0.003 0.013 760 Dihedral : 9.164 58.284 630 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 30.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer: Outliers : 6.34 % Allowed : 20.90 % Favored : 72.76 % 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: -4.19 (0.25), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS m 10 PHE 0.015 0.003 PHE k 24 TYR 0.020 0.003 TYR k 16 ARG 0.002 0.000 ARG m 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 54 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 28 residues processed: 82 average time/residue: 0.1746 time to fit residues: 22.3340 Evaluate side-chains 76 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 48 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 7 CYS Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 9 SER Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 24 PHE Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain h residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN E 5 GLN D 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4656 Z= 0.284 Angle : 0.656 7.353 6280 Z= 0.349 Chirality : 0.046 0.118 736 Planarity : 0.002 0.015 760 Dihedral : 8.913 59.344 630 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 27.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.46 % Favored : 86.54 % Rotamer: Outliers : 5.41 % Allowed : 23.69 % Favored : 70.90 % 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: -4.19 (0.25), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS l 10 PHE 0.007 0.001 PHE k 24 TYR 0.012 0.002 TYR k 16 ARG 0.001 0.000 ARG m 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 52 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 22 residues processed: 77 average time/residue: 0.1713 time to fit residues: 20.6546 Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN G 5 GLN C 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4656 Z= 0.543 Angle : 0.816 9.652 6280 Z= 0.431 Chirality : 0.053 0.175 736 Planarity : 0.004 0.014 760 Dihedral : 9.411 59.893 629 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 36.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.23 % Favored : 80.77 % Rotamer: Outliers : 6.90 % Allowed : 27.24 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.25), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 10 PHE 0.018 0.003 PHE k 24 TYR 0.023 0.004 TYR k 16 ARG 0.001 0.000 ARG a 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 58 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 32 residues processed: 90 average time/residue: 0.1843 time to fit residues: 25.5465 Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 52 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 7 CYS Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 24 PHE Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4656 Z= 0.198 Angle : 0.651 7.354 6280 Z= 0.344 Chirality : 0.046 0.128 736 Planarity : 0.002 0.018 760 Dihedral : 8.521 59.906 629 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.66 % Allowed : 29.85 % Favored : 65.49 % 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: -4.26 (0.26), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.20), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS j 5 PHE 0.005 0.001 PHE a 25 TYR 0.009 0.001 TYR J 14 ARG 0.002 0.001 ARG c 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 47 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 24 residues processed: 68 average time/residue: 0.1859 time to fit residues: 19.9443 Evaluate side-chains 68 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 44 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain N residue 18 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4656 Z= 0.303 Angle : 0.673 8.058 6280 Z= 0.355 Chirality : 0.047 0.126 736 Planarity : 0.002 0.010 760 Dihedral : 8.742 59.656 629 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 4.85 % Allowed : 30.41 % Favored : 64.74 % 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 (0.26), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.20), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS l 10 PHE 0.009 0.002 PHE k 24 TYR 0.014 0.002 TYR J 14 ARG 0.001 0.000 ARG o 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 46 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 25 residues processed: 68 average time/residue: 0.1823 time to fit residues: 19.5816 Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 46 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain N residue 18 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7114 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4656 Z= 0.233 Angle : 0.639 7.308 6280 Z= 0.338 Chirality : 0.046 0.126 736 Planarity : 0.002 0.012 760 Dihedral : 8.529 59.599 629 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 26.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 4.85 % Allowed : 30.41 % Favored : 64.74 % 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: -4.26 (0.26), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.20), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS l 10 PHE 0.006 0.001 PHE k 24 TYR 0.015 0.002 TYR N 19 ARG 0.001 0.000 ARG c 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 24 residues processed: 68 average time/residue: 0.1779 time to fit residues: 19.0834 Evaluate side-chains 69 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 45 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7027 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4656 Z= 0.158 Angle : 0.583 5.543 6280 Z= 0.311 Chirality : 0.044 0.122 736 Planarity : 0.002 0.015 760 Dihedral : 8.127 59.995 629 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 4.29 % Allowed : 30.41 % Favored : 65.30 % 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: -4.14 (0.27), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.20), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS h 10 PHE 0.004 0.001 PHE a 25 TYR 0.008 0.001 TYR c 26 ARG 0.001 0.000 ARG a 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 22 residues processed: 65 average time/residue: 0.1680 time to fit residues: 17.4740 Evaluate side-chains 66 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5400 r_free = 0.5400 target = 0.407630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.5862 r_free = 0.5862 target = 0.324269 restraints weight = 17471.988| |-----------------------------------------------------------------------------| r_work (start): 0.5268 rms_B_bonded: 2.11 r_work: 0.5751 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.5694 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work (final): 0.5694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4656 Z= 0.253 Angle : 0.630 6.817 6280 Z= 0.333 Chirality : 0.046 0.121 736 Planarity : 0.002 0.009 760 Dihedral : 8.413 59.614 629 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 4.66 % Allowed : 30.04 % Favored : 65.30 % 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: -4.19 (0.27), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.20), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS j 5 PHE 0.007 0.001 PHE k 24 TYR 0.011 0.002 TYR K 19 ARG 0.001 0.000 ARG e 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2749.54 seconds wall clock time: 49 minutes 4.23 seconds (2944.23 seconds total)