Starting phenix.real_space_refine on Fri Mar 15 02:31:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncg_12265/03_2024/7ncg_12265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncg_12265/03_2024/7ncg_12265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncg_12265/03_2024/7ncg_12265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncg_12265/03_2024/7ncg_12265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncg_12265/03_2024/7ncg_12265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncg_12265/03_2024/7ncg_12265.pdb" } resolution = 3.43 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: 4 Type Number sf(0) Gaussians C 3180 2.51 5 N 876 2.21 5 O 996 1.98 5 H 5376 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L PHE 94": "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: 10428 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "G" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 4.93, per 1000 atoms: 0.47 Number of scatterers: 10428 At special positions: 0 Unit cell: (131.1, 78.66, 46.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 996 8.00 N 876 7.00 C 3180 6.00 H 5376 1.00 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=0, symmetry=0 Time building additional restraints: 8.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 57.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 52 removed outlier: 8.929A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N SER E 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLY A 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N THR E 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N LYS A 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N GLU E 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS A 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL E 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N HIS E 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY A 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N LEU A 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLY F 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL A 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N LYS F 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N SER A 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N LYS F 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR A 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N GLY F 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU A 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N VAL F 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY F 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N HIS A 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LEU F 38 " --> pdb=" O TYR K 39 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLY K 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL F 40 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 10.756A pdb=" N LYS K 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N SER F 42 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N LYS K 45 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR F 44 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLY K 47 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU F 46 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N VAL K 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL F 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY K 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N HIS F 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR J 39 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL K 40 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY J 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER K 42 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS J 43 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR K 44 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS J 45 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL K 52 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR L 39 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL J 40 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY L 41 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER J 42 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS L 43 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR J 44 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS L 45 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL J 52 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 55 through 57 removed outlier: 6.712A pdb=" N ALA A 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA J 56 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 66 removed outlier: 6.797A pdb=" N GLU E 61 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU A 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR F 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL F 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN A 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU F 61 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR K 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL K 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN F 65 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU K 61 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU J 61 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR L 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL J 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL L 66 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN J 65 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 70 through 82 removed outlier: 6.639A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLY E 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR E 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N VAL E 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N GLN E 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N ALA A 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N THR E 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N LYS A 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA F 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA F 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN A 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS F 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL F 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL K 74 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR F 75 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA K 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 77 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA K 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN F 79 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS K 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR F 81 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL K 82 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL J 70 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLY K 73 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR J 72 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR K 75 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL J 74 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N VAL K 77 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ALA J 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N GLN K 79 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N ALA J 78 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR K 81 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N LYS J 80 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL L 74 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR J 75 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA L 76 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL J 77 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA L 78 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN J 79 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS L 80 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR J 81 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL L 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.778A pdb=" N VAL A 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL J 95 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 50 removed outlier: 8.924A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU D 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY B 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU D 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N GLY H 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N VAL D 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N LYS H 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N SER D 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N LYS H 45 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 44 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLY H 47 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU D 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL H 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY H 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N HIS D 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR I 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL G 40 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY I 41 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER G 42 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS I 43 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR G 44 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS I 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 52 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.655A pdb=" N ALA B 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA G 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 66 removed outlier: 6.791A pdb=" N GLU C 61 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU B 61 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU D 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR H 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL D 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL H 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN D 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU H 61 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU G 61 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 70 through 82 removed outlier: 6.515A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLY C 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR B 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N VAL C 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N THR C 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N LYS B 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 75 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA D 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA D 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN B 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS D 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 75 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA H 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA H 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN D 79 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS H 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR D 81 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL H 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY H 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR G 72 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR H 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N GLN H 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ALA G 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR H 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N LYS G 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL I 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR G 75 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA I 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL G 77 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA I 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN G 79 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS I 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR G 81 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL I 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 95 through 96 removed outlier: 6.796A pdb=" N VAL B 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL G 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 279 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: 3.22 Time building geometry restraints manager: 8.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 0.96: 110 0.96 - 1.11: 5266 1.11 - 1.26: 864 1.26 - 1.41: 1016 1.41 - 1.56: 3196 Bond restraints: 10452 Sorted by residual: bond pdb=" N ALA H 56 " pdb=" H ALA H 56 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE2 PHE C 94 " pdb=" HE2 PHE C 94 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N PHE G 94 " pdb=" H PHE G 94 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N THR D 75 " pdb=" H THR D 75 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS H 50 " pdb=" HE1 HIS H 50 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 10447 not shown) Histogram of bond angle deviations from ideal: 102.98 - 108.13: 3433 108.13 - 113.29: 9780 113.29 - 118.44: 2175 118.44 - 123.60: 3047 123.60 - 128.75: 597 Bond angle restraints: 19032 Sorted by residual: angle pdb=" CA PHE A 94 " pdb=" CB PHE A 94 " pdb=" CG PHE A 94 " ideal model delta sigma weight residual 113.80 120.82 -7.02 1.00e+00 1.00e+00 4.93e+01 angle pdb=" CA PHE C 94 " pdb=" CB PHE C 94 " pdb=" CG PHE C 94 " ideal model delta sigma weight residual 113.80 120.77 -6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" CA PHE E 94 " pdb=" CB PHE E 94 " pdb=" CG PHE E 94 " ideal model delta sigma weight residual 113.80 120.15 -6.35 1.00e+00 1.00e+00 4.03e+01 angle pdb=" N THR F 59 " pdb=" CA THR F 59 " pdb=" C THR F 59 " ideal model delta sigma weight residual 110.41 117.37 -6.96 1.23e+00 6.61e-01 3.21e+01 angle pdb=" CA PHE F 94 " pdb=" CB PHE F 94 " pdb=" CG PHE F 94 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 4179 15.81 - 31.62: 199 31.62 - 47.42: 91 47.42 - 63.23: 258 63.23 - 79.04: 61 Dihedral angle restraints: 4788 sinusoidal: 2664 harmonic: 2124 Sorted by residual: dihedral pdb=" CA VAL G 74 " pdb=" C VAL G 74 " pdb=" N THR G 75 " pdb=" CA THR G 75 " ideal model delta harmonic sigma weight residual 180.00 155.12 24.88 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA VAL H 74 " pdb=" C VAL H 74 " pdb=" N THR H 75 " pdb=" CA THR H 75 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA VAL L 74 " pdb=" C VAL L 74 " pdb=" N THR L 75 " pdb=" CA THR L 75 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 4785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 402 0.053 - 0.105: 305 0.105 - 0.158: 164 0.158 - 0.211: 36 0.211 - 0.263: 5 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA LYS K 45 " pdb=" N LYS K 45 " pdb=" C LYS K 45 " pdb=" CB LYS K 45 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LYS B 45 " pdb=" N LYS B 45 " pdb=" C LYS B 45 " pdb=" CB LYS B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LYS C 58 " pdb=" N LYS C 58 " pdb=" C LYS C 58 " pdb=" CB LYS C 58 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 909 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 94 " -0.053 2.00e-02 2.50e+03 3.97e-02 4.73e+01 pdb=" CG PHE L 94 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE L 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE L 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE L 94 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE L 94 " 0.031 2.00e-02 2.50e+03 pdb=" CZ PHE L 94 " -0.021 2.00e-02 2.50e+03 pdb=" HD1 PHE L 94 " 0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE L 94 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE L 94 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE L 94 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE L 94 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 65 " 0.035 2.00e-02 2.50e+03 4.85e-02 3.52e+01 pdb=" CG ASN H 65 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN H 65 " -0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN H 65 " 0.046 2.00e-02 2.50e+03 pdb="HD21 ASN H 65 " -0.077 2.00e-02 2.50e+03 pdb="HD22 ASN H 65 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.086 2.00e-02 2.50e+03 3.42e-02 3.51e+01 pdb=" CG PHE C 94 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE C 94 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE C 94 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE C 94 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE C 94 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE C 94 " 0.034 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.28: 1355 2.28 - 2.84: 20520 2.84 - 3.39: 24437 3.39 - 3.95: 32774 3.95 - 4.50: 46164 Nonbonded interactions: 125250 Sorted by model distance: nonbonded pdb=" OE1 GLU B 61 " pdb=" HZ1 LYS D 96 " model vdw 1.729 1.850 nonbonded pdb=" HZ3 LYS G 96 " pdb=" OE1 GLU H 61 " model vdw 1.753 1.850 nonbonded pdb=" OE1 GLU A 61 " pdb=" HZ1 LYS F 96 " model vdw 1.758 1.850 nonbonded pdb=" OE1 GLU F 61 " pdb=" HZ1 LYS K 96 " model vdw 1.762 1.850 nonbonded pdb=" O GLU C 83 " pdb=" HG SER C 87 " model vdw 1.767 1.850 ... (remaining 125245 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.710 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: 0.180 Extract box with map and model: 3.890 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 36.100 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.012 0.042 5076 Z= 0.846 Angle : 2.196 7.783 6864 Z= 1.439 Chirality : 0.084 0.263 912 Planarity : 0.009 0.039 840 Dihedral : 10.992 79.035 1716 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -1.51 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS A 50 PHE 0.064 0.018 PHE C 94 TYR 0.051 0.014 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.812 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: A 43 LYS cc_start: 0.8262 (mttt) cc_final: 0.8005 (mttm) REVERT: A 83 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6690 (mt-10) REVERT: B 43 LYS cc_start: 0.8011 (mttt) cc_final: 0.7691 (mtpp) REVERT: B 80 LYS cc_start: 0.8635 (tttt) cc_final: 0.8385 (tttm) REVERT: B 83 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6734 (mt-10) REVERT: C 43 LYS cc_start: 0.7733 (mttt) cc_final: 0.6933 (mmmt) REVERT: C 46 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6925 (mm-30) REVERT: D 43 LYS cc_start: 0.8564 (mttt) cc_final: 0.8213 (mtpp) REVERT: E 43 LYS cc_start: 0.8264 (mttt) cc_final: 0.7524 (mmmt) REVERT: E 46 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7713 (mt-10) REVERT: G 80 LYS cc_start: 0.8509 (tttt) cc_final: 0.8296 (tttm) REVERT: H 46 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7666 (mt-10) REVERT: J 45 LYS cc_start: 0.8276 (mttt) cc_final: 0.8020 (mptt) REVERT: J 80 LYS cc_start: 0.8513 (tttt) cc_final: 0.8300 (tttm) REVERT: K 46 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7580 (mt-10) REVERT: K 60 LYS cc_start: 0.7097 (mttt) cc_final: 0.6701 (mtmt) REVERT: K 61 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6939 (mp0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.5522 time to fit residues: 69.4851 Evaluate side-chains 75 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6869 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5076 Z= 0.203 Angle : 0.584 4.976 6864 Z= 0.341 Chirality : 0.052 0.139 912 Planarity : 0.002 0.012 840 Dihedral : 5.934 16.125 732 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.16 % Allowed : 6.40 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 50 PHE 0.021 0.004 PHE A 94 TYR 0.005 0.001 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.800 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: A 43 LYS cc_start: 0.8042 (mttt) cc_final: 0.7686 (mtpp) REVERT: B 43 LYS cc_start: 0.8221 (mttt) cc_final: 0.7946 (mtpp) REVERT: B 80 LYS cc_start: 0.8778 (tttt) cc_final: 0.8454 (tttm) REVERT: C 43 LYS cc_start: 0.7945 (mttt) cc_final: 0.6986 (mmmt) REVERT: C 46 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7003 (mm-30) REVERT: D 43 LYS cc_start: 0.8524 (mttt) cc_final: 0.8146 (mtpp) REVERT: E 43 LYS cc_start: 0.8271 (mttt) cc_final: 0.7280 (mmmt) REVERT: G 45 LYS cc_start: 0.8307 (mttt) cc_final: 0.7972 (mtpp) REVERT: G 60 LYS cc_start: 0.7061 (mttt) cc_final: 0.6736 (mtpt) REVERT: G 80 LYS cc_start: 0.8628 (tttt) cc_final: 0.8416 (tttm) REVERT: H 43 LYS cc_start: 0.8280 (mttt) cc_final: 0.8009 (mtpt) REVERT: J 43 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8109 (mttm) REVERT: J 60 LYS cc_start: 0.7192 (mttt) cc_final: 0.6939 (mttp) REVERT: K 43 LYS cc_start: 0.8254 (mttt) cc_final: 0.7763 (mtpp) REVERT: K 46 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7683 (mt-10) outliers start: 6 outliers final: 6 residues processed: 92 average time/residue: 0.6710 time to fit residues: 72.1940 Evaluate side-chains 81 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.6971 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5076 Z= 0.263 Angle : 0.591 4.661 6864 Z= 0.344 Chirality : 0.053 0.136 912 Planarity : 0.002 0.011 840 Dihedral : 5.648 14.821 732 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.13 % Allowed : 7.36 % Favored : 90.50 % 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: -2.66 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS L 50 PHE 0.018 0.004 PHE A 94 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.849 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: A 60 LYS cc_start: 0.7325 (mttt) cc_final: 0.7093 (mtpt) REVERT: B 43 LYS cc_start: 0.8366 (mttt) cc_final: 0.8116 (mttm) REVERT: B 80 LYS cc_start: 0.8779 (tttt) cc_final: 0.8424 (tttm) REVERT: C 43 LYS cc_start: 0.8064 (mttt) cc_final: 0.7789 (mtpp) REVERT: D 43 LYS cc_start: 0.8599 (mttt) cc_final: 0.8176 (mtpp) REVERT: E 43 LYS cc_start: 0.8268 (mttt) cc_final: 0.7282 (mmmt) REVERT: E 83 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6713 (mp0) REVERT: F 43 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8257 (mtpp) REVERT: G 45 LYS cc_start: 0.8254 (mttt) cc_final: 0.7969 (mtpp) REVERT: G 60 LYS cc_start: 0.7402 (mttt) cc_final: 0.7170 (mttt) REVERT: H 43 LYS cc_start: 0.8350 (mttt) cc_final: 0.8078 (mtpt) REVERT: J 60 LYS cc_start: 0.7285 (mttt) cc_final: 0.6959 (mttp) REVERT: J 83 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6017 (mp0) REVERT: K 43 LYS cc_start: 0.8286 (mttt) cc_final: 0.7972 (mtpt) REVERT: K 45 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7653 (mtpp) outliers start: 11 outliers final: 11 residues processed: 92 average time/residue: 0.6382 time to fit residues: 68.3175 Evaluate side-chains 91 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.6975 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5076 Z= 0.200 Angle : 0.532 4.621 6864 Z= 0.308 Chirality : 0.053 0.130 912 Planarity : 0.002 0.007 840 Dihedral : 5.395 13.134 732 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.52 % Allowed : 8.53 % Favored : 88.95 % 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: -2.65 (0.24), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 50 PHE 0.015 0.003 PHE A 94 TYR 0.006 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.868 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: A 60 LYS cc_start: 0.7361 (mttt) cc_final: 0.7154 (mtpt) REVERT: B 43 LYS cc_start: 0.8368 (mttt) cc_final: 0.8066 (mtpt) REVERT: C 43 LYS cc_start: 0.8134 (mttt) cc_final: 0.7840 (mtpp) REVERT: D 43 LYS cc_start: 0.8648 (mttt) cc_final: 0.8365 (mtpp) REVERT: E 43 LYS cc_start: 0.8239 (mttt) cc_final: 0.7169 (mmmt) REVERT: G 45 LYS cc_start: 0.8166 (mttt) cc_final: 0.7787 (mtpp) REVERT: J 43 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8335 (mttm) REVERT: J 60 LYS cc_start: 0.7291 (mttt) cc_final: 0.6969 (mttp) REVERT: J 83 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5884 (mp0) outliers start: 13 outliers final: 13 residues processed: 85 average time/residue: 0.6425 time to fit residues: 63.8727 Evaluate side-chains 87 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5076 Z= 0.203 Angle : 0.528 4.596 6864 Z= 0.305 Chirality : 0.053 0.138 912 Planarity : 0.002 0.013 840 Dihedral : 5.237 12.775 732 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.29 % Allowed : 9.50 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 50 PHE 0.014 0.003 PHE A 94 TYR 0.007 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.845 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: B 43 LYS cc_start: 0.8401 (mttt) cc_final: 0.8081 (mtpt) REVERT: C 43 LYS cc_start: 0.8137 (mttt) cc_final: 0.7847 (mtpp) REVERT: D 43 LYS cc_start: 0.8657 (mttt) cc_final: 0.8371 (mttm) REVERT: D 60 LYS cc_start: 0.7151 (mttt) cc_final: 0.6715 (mttm) REVERT: E 43 LYS cc_start: 0.8178 (mttt) cc_final: 0.7374 (mmmt) REVERT: E 83 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6715 (mp0) REVERT: G 45 LYS cc_start: 0.7843 (mttt) cc_final: 0.7627 (mtpp) REVERT: H 43 LYS cc_start: 0.8355 (mttt) cc_final: 0.8124 (mtpt) REVERT: H 58 LYS cc_start: 0.7819 (mttt) cc_final: 0.7585 (mttt) REVERT: I 83 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6138 (mp0) REVERT: J 43 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8282 (mttm) REVERT: J 60 LYS cc_start: 0.7294 (mttt) cc_final: 0.6945 (mttp) outliers start: 17 outliers final: 16 residues processed: 91 average time/residue: 0.6037 time to fit residues: 64.5032 Evaluate side-chains 96 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.6992 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5076 Z= 0.173 Angle : 0.510 4.602 6864 Z= 0.294 Chirality : 0.053 0.132 912 Planarity : 0.001 0.012 840 Dihedral : 5.052 12.379 732 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.91 % Allowed : 10.08 % Favored : 87.02 % 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: -2.51 (0.27), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.012 0.003 PHE A 94 TYR 0.006 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.831 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: B 43 LYS cc_start: 0.8423 (mttt) cc_final: 0.8120 (mtpt) REVERT: C 43 LYS cc_start: 0.8134 (mttt) cc_final: 0.7854 (mtpp) REVERT: D 43 LYS cc_start: 0.8686 (mttt) cc_final: 0.8407 (mtpp) REVERT: D 60 LYS cc_start: 0.7121 (mttt) cc_final: 0.6679 (mttp) REVERT: E 43 LYS cc_start: 0.8153 (mttt) cc_final: 0.7358 (mmmt) REVERT: E 83 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6770 (mp0) REVERT: H 58 LYS cc_start: 0.7901 (mttt) cc_final: 0.7655 (mttt) REVERT: I 83 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6077 (mp0) REVERT: J 60 LYS cc_start: 0.7289 (mttt) cc_final: 0.6932 (mttp) REVERT: J 83 GLU cc_start: 0.6487 (mt-10) cc_final: 0.5921 (mp0) REVERT: K 43 LYS cc_start: 0.8338 (mttt) cc_final: 0.7995 (mtpp) outliers start: 15 outliers final: 15 residues processed: 90 average time/residue: 0.6255 time to fit residues: 66.6081 Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7010 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5076 Z= 0.197 Angle : 0.517 4.593 6864 Z= 0.299 Chirality : 0.053 0.139 912 Planarity : 0.002 0.012 840 Dihedral : 5.054 12.186 732 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 3.68 % Allowed : 10.08 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.27), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 50 PHE 0.011 0.003 PHE G 94 TYR 0.007 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.837 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: A 60 LYS cc_start: 0.7437 (mtpt) cc_final: 0.7237 (mtpt) REVERT: A 83 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6839 (mt-10) REVERT: B 43 LYS cc_start: 0.8440 (mttt) cc_final: 0.7931 (mtpp) REVERT: C 43 LYS cc_start: 0.8165 (mttt) cc_final: 0.7851 (mtpp) REVERT: D 43 LYS cc_start: 0.8674 (mttt) cc_final: 0.8354 (mttm) REVERT: E 43 LYS cc_start: 0.8198 (mttt) cc_final: 0.7399 (mmmt) REVERT: F 60 LYS cc_start: 0.7747 (mttt) cc_final: 0.7276 (mttm) REVERT: H 43 LYS cc_start: 0.8486 (mttt) cc_final: 0.8227 (mtpt) REVERT: H 58 LYS cc_start: 0.7908 (mttt) cc_final: 0.7680 (mttt) REVERT: I 83 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6176 (mp0) REVERT: J 60 LYS cc_start: 0.7210 (mttt) cc_final: 0.6857 (mttp) REVERT: J 83 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6048 (mp0) REVERT: K 43 LYS cc_start: 0.8354 (mttt) cc_final: 0.8002 (mtpp) outliers start: 19 outliers final: 18 residues processed: 93 average time/residue: 0.6113 time to fit residues: 66.9616 Evaluate side-chains 102 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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: 0.6988 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5076 Z= 0.149 Angle : 0.487 4.614 6864 Z= 0.281 Chirality : 0.053 0.135 912 Planarity : 0.001 0.013 840 Dihedral : 4.860 12.252 732 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.10 % Allowed : 10.47 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.27), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.008 0.002 PHE A 94 TYR 0.006 0.001 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.834 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: C 43 LYS cc_start: 0.8159 (mttt) cc_final: 0.7880 (mtpp) REVERT: E 43 LYS cc_start: 0.8239 (mttt) cc_final: 0.7412 (mmmt) REVERT: E 83 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6657 (mp0) REVERT: F 60 LYS cc_start: 0.7742 (mttt) cc_final: 0.7340 (mttm) REVERT: H 43 LYS cc_start: 0.8397 (mttt) cc_final: 0.8124 (mtpt) REVERT: H 58 LYS cc_start: 0.7908 (mttt) cc_final: 0.7656 (mttt) REVERT: I 83 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6149 (mp0) REVERT: J 60 LYS cc_start: 0.7271 (mttt) cc_final: 0.6923 (mtpt) REVERT: J 83 GLU cc_start: 0.6467 (mt-10) cc_final: 0.5939 (mp0) REVERT: K 43 LYS cc_start: 0.8380 (mttt) cc_final: 0.8022 (mtpp) outliers start: 16 outliers final: 16 residues processed: 88 average time/residue: 0.5997 time to fit residues: 62.0683 Evaluate side-chains 94 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.6984 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5076 Z= 0.147 Angle : 0.488 4.647 6864 Z= 0.281 Chirality : 0.053 0.135 912 Planarity : 0.001 0.020 840 Dihedral : 4.778 11.821 732 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.10 % Allowed : 11.05 % Favored : 85.85 % 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: -2.25 (0.28), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 50 PHE 0.009 0.002 PHE G 94 TYR 0.005 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.754 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: A 83 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6226 (mp0) REVERT: B 43 LYS cc_start: 0.8441 (mttt) cc_final: 0.8016 (mtpp) REVERT: C 43 LYS cc_start: 0.8204 (mttt) cc_final: 0.7854 (mtpp) REVERT: D 43 LYS cc_start: 0.8697 (mttt) cc_final: 0.8351 (mtpp) REVERT: D 60 LYS cc_start: 0.7348 (mttt) cc_final: 0.6884 (mttm) REVERT: E 43 LYS cc_start: 0.8260 (mttt) cc_final: 0.7447 (mmmt) REVERT: E 83 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6755 (mp0) REVERT: F 60 LYS cc_start: 0.7724 (mttt) cc_final: 0.7301 (mttm) REVERT: I 83 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6165 (mp0) REVERT: J 60 LYS cc_start: 0.7221 (mttt) cc_final: 0.6892 (mtpt) REVERT: J 83 GLU cc_start: 0.6484 (mt-10) cc_final: 0.5966 (mp0) REVERT: K 43 LYS cc_start: 0.8459 (mttt) cc_final: 0.8115 (mtpp) outliers start: 16 outliers final: 15 residues processed: 89 average time/residue: 0.5954 time to fit residues: 62.5816 Evaluate side-chains 96 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 overall best weight: 0.7638 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5076 Z= 0.163 Angle : 0.495 4.653 6864 Z= 0.286 Chirality : 0.053 0.134 912 Planarity : 0.002 0.020 840 Dihedral : 4.785 11.595 732 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.49 % Allowed : 11.43 % Favored : 85.08 % 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: -2.23 (0.28), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.010 0.002 PHE A 94 TYR 0.005 0.001 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.863 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: A 83 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6277 (mp0) REVERT: B 43 LYS cc_start: 0.8449 (mttt) cc_final: 0.8149 (mtpp) REVERT: C 43 LYS cc_start: 0.8214 (mttt) cc_final: 0.7234 (mmmt) REVERT: D 58 LYS cc_start: 0.8280 (mttt) cc_final: 0.8067 (mttm) REVERT: D 60 LYS cc_start: 0.7667 (mttt) cc_final: 0.7181 (mttp) REVERT: E 43 LYS cc_start: 0.8283 (mttt) cc_final: 0.7472 (mmmt) REVERT: F 60 LYS cc_start: 0.7704 (mttt) cc_final: 0.7295 (mttm) REVERT: H 43 LYS cc_start: 0.8409 (mttt) cc_final: 0.8119 (mtpt) REVERT: I 83 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6193 (mp0) REVERT: J 60 LYS cc_start: 0.7198 (mttt) cc_final: 0.6901 (mtpt) REVERT: J 83 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5932 (mp0) REVERT: K 43 LYS cc_start: 0.8469 (mttt) cc_final: 0.8121 (mtpp) outliers start: 18 outliers final: 17 residues processed: 93 average time/residue: 0.6006 time to fit residues: 66.2669 Evaluate side-chains 100 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.0030 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.173206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.141712 restraints weight = 18881.279| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.90 r_work: 0.4150 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5076 Z= 0.135 Angle : 0.475 4.652 6864 Z= 0.273 Chirality : 0.053 0.134 912 Planarity : 0.001 0.015 840 Dihedral : 4.622 11.768 732 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.10 % Allowed : 11.63 % Favored : 85.27 % 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: -2.07 (0.28), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 50 PHE 0.007 0.002 PHE F 94 TYR 0.004 0.001 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3304.45 seconds wall clock time: 58 minutes 41.17 seconds (3521.17 seconds total)