Starting phenix.real_space_refine on Wed Nov 15 11:19:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/11_2023/6ofh_20046_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/11_2023/6ofh_20046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/11_2023/6ofh_20046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/11_2023/6ofh_20046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/11_2023/6ofh_20046_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/11_2023/6ofh_20046_neut.pdb" } resolution = 3.7 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= 0.003 sd= 0.023 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: 3 Type Number sf(0) Gaussians C 7353 2.51 5 N 1919 2.21 5 O 2356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11628 Number of models: 1 Model: "" Number of chains: 19 Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "U" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "V" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "G" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "H" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "I" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "J" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "P" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "S" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Time building chain proxies: 6.37, per 1000 atoms: 0.55 Number of scatterers: 11628 At special positions: 0 Unit cell: (93.94, 92.232, 153.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2356 8.00 N 1919 7.00 C 7353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 2.1 seconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN D 77 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE U 16 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP U 17 " --> pdb=" O SER U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA U 36 " --> pdb=" O ASP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 56 " --> pdb=" O SER U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN U 77 " --> pdb=" O ALA U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE V 16 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP V 17 " --> pdb=" O SER V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU V 56 " --> pdb=" O SER V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN V 77 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN E 77 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN F 77 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN G 77 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.574A pdb=" N GLN H 77 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN I 77 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP J 17 " --> pdb=" O SER J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN J 77 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP K 17 " --> pdb=" O SER K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN K 77 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP L 17 " --> pdb=" O SER L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN L 77 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP M 17 " --> pdb=" O SER M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN M 77 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN N 77 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN O 77 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN P 77 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 17 " --> pdb=" O SER Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Q 56 " --> pdb=" O SER Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN Q 77 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 56 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN R 77 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA S 36 " --> pdb=" O ASP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU S 56 " --> pdb=" O SER S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN S 77 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP T 17 " --> pdb=" O SER T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU T 56 " --> pdb=" O SER T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN T 77 " --> pdb=" O ALA T 74 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2565 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: 3.34 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2071 1.29 - 1.35: 1767 1.35 - 1.41: 1130 1.41 - 1.48: 1777 1.48 - 1.54: 5092 Bond restraints: 11837 Sorted by residual: bond pdb=" CB GLU M 53 " pdb=" CG GLU M 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CB GLU R 53 " pdb=" CG GLU R 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU J 53 " pdb=" CG GLU J 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 11832 not shown) Histogram of bond angle deviations from ideal: 102.41 - 108.70: 553 108.70 - 115.00: 6786 115.00 - 121.29: 6406 121.29 - 127.58: 2272 127.58 - 133.88: 95 Bond angle restraints: 16112 Sorted by residual: angle pdb=" CA LEU N 56 " pdb=" CB LEU N 56 " pdb=" CG LEU N 56 " ideal model delta sigma weight residual 116.30 108.09 8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" CA LEU L 56 " pdb=" CB LEU L 56 " pdb=" CG LEU L 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" CA LEU K 56 " pdb=" CB LEU K 56 " pdb=" CG LEU K 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.48e+00 angle pdb=" CA PRO H 38 " pdb=" C PRO H 38 " pdb=" O PRO H 38 " ideal model delta sigma weight residual 121.38 119.58 1.80 7.70e-01 1.69e+00 5.47e+00 angle pdb=" CA LEU J 56 " pdb=" CB LEU J 56 " pdb=" CG LEU J 56 " ideal model delta sigma weight residual 116.30 108.12 8.18 3.50e+00 8.16e-02 5.47e+00 ... (remaining 16107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.17: 5624 6.17 - 12.34: 1119 12.34 - 18.51: 324 18.51 - 24.68: 77 24.68 - 30.85: 38 Dihedral angle restraints: 7182 sinusoidal: 2755 harmonic: 4427 Sorted by residual: dihedral pdb=" CA ASP D 70 " pdb=" C ASP D 70 " pdb=" N ILE D 71 " pdb=" CA ILE D 71 " ideal model delta harmonic sigma weight residual 180.00 164.46 15.54 0 5.00e+00 4.00e-02 9.66e+00 dihedral pdb=" CA ASP Q 70 " pdb=" C ASP Q 70 " pdb=" N ILE Q 71 " pdb=" CA ILE Q 71 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.65e+00 dihedral pdb=" CA ASP S 70 " pdb=" C ASP S 70 " pdb=" N ILE S 71 " pdb=" CA ILE S 71 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.64e+00 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 423 0.020 - 0.041: 702 0.041 - 0.061: 378 0.061 - 0.082: 212 0.082 - 0.102: 128 Chirality restraints: 1843 Sorted by residual: chirality pdb=" CA SER N 39 " pdb=" N SER N 39 " pdb=" C SER N 39 " pdb=" CB SER N 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA SER U 39 " pdb=" N SER U 39 " pdb=" C SER U 39 " pdb=" CB SER U 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA PRO U 38 " pdb=" N PRO U 38 " pdb=" C PRO U 38 " pdb=" CB PRO U 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 ... (remaining 1840 not shown) Planarity restraints: 2109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 76 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ILE P 76 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE P 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN P 77 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 76 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE R 76 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE R 76 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN R 77 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 76 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ILE O 76 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE O 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN O 77 " 0.009 2.00e-02 2.50e+03 ... (remaining 2106 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 106 2.66 - 3.22: 11323 3.22 - 3.78: 17158 3.78 - 4.34: 24963 4.34 - 4.90: 40716 Nonbonded interactions: 94266 Sorted by model distance: nonbonded pdb=" OD1 ASP D 10 " pdb=" OG SER H 49 " model vdw 2.097 2.440 nonbonded pdb=" NZ LYS G 66 " pdb=" OD2 ASP G 70 " model vdw 2.098 2.520 nonbonded pdb=" NZ LYS F 66 " pdb=" OD2 ASP F 70 " model vdw 2.098 2.520 nonbonded pdb=" NZ LYS P 66 " pdb=" OD2 ASP P 70 " model vdw 2.098 2.520 nonbonded pdb=" NZ LYS L 66 " pdb=" OD2 ASP L 70 " model vdw 2.098 2.520 ... (remaining 94261 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 '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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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 group one per residue 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.730 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.008 0.035 11837 Z= 0.495 Angle : 0.752 8.205 16112 Z= 0.416 Chirality : 0.045 0.102 1843 Planarity : 0.005 0.028 2109 Dihedral : 7.705 30.854 4294 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -6.76 (0.10), residues: 1444 helix: -4.06 (0.06), residues: 1254 sheet: None (None), residues: 0 loop : -4.86 (0.27), residues: 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.2406 time to fit residues: 214.7393 Evaluate side-chains 509 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN U 26 GLN F 61 GLN F 77 GLN F 78 ASN G 61 GLN G 78 ASN I 63 ASN I 78 ASN J 24 GLN J 26 GLN L 63 ASN L 78 ASN M 61 GLN M 78 ASN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 ASN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN R 61 GLN R 63 ASN S 48 GLN ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11837 Z= 0.200 Angle : 0.557 7.852 16112 Z= 0.302 Chirality : 0.037 0.141 1843 Planarity : 0.004 0.026 2109 Dihedral : 4.165 22.861 1596 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.11 % Allowed : 14.83 % Favored : 82.06 % 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 (0.18), residues: 1444 helix: -0.88 (0.12), residues: 1292 sheet: None (None), residues: 0 loop : -5.22 (0.25), residues: 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 565 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 575 average time/residue: 0.2360 time to fit residues: 191.0265 Evaluate side-chains 541 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 516 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1061 time to fit residues: 6.8189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN F 61 GLN F 78 ASN H 61 GLN J 24 GLN K 24 GLN K 63 ASN K 78 ASN M 26 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 ASN R 61 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11837 Z= 0.225 Angle : 0.533 8.112 16112 Z= 0.278 Chirality : 0.038 0.165 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.826 22.784 1596 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.15 % Allowed : 19.14 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1444 helix: 0.74 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -5.01 (0.25), residues: 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 553 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 563 average time/residue: 0.2250 time to fit residues: 178.8854 Evaluate side-chains 528 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 516 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1175 time to fit residues: 4.5236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN H 77 GLN J 26 GLN J 78 ASN K 24 GLN K 26 GLN L 61 GLN L 78 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN N 48 GLN O 77 GLN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 ASN R 61 GLN S 59 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11837 Z= 0.263 Angle : 0.543 8.109 16112 Z= 0.283 Chirality : 0.040 0.172 1843 Planarity : 0.003 0.017 2109 Dihedral : 3.831 25.537 1596 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.79 % Allowed : 21.37 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1444 helix: 1.21 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.88 (0.27), residues: 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 546 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 553 average time/residue: 0.2403 time to fit residues: 187.3966 Evaluate side-chains 535 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 516 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1060 time to fit residues: 5.6233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN G 55 ASN H 61 GLN K 78 ASN M 26 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 GLN P 63 ASN ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN S 59 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11837 Z= 0.276 Angle : 0.567 10.346 16112 Z= 0.292 Chirality : 0.041 0.199 1843 Planarity : 0.003 0.022 2109 Dihedral : 3.830 26.300 1596 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.95 % Allowed : 21.85 % Favored : 75.20 % 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: 1.28 (0.22), residues: 1444 helix: 1.47 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.60 (0.30), residues: 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 545 time to evaluate : 1.304 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 554 average time/residue: 0.2375 time to fit residues: 184.1833 Evaluate side-chains 553 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 528 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0998 time to fit residues: 6.3950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN K 78 ASN L 78 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN O 77 GLN P 26 GLN P 63 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11837 Z= 0.227 Angle : 0.547 8.337 16112 Z= 0.282 Chirality : 0.039 0.203 1843 Planarity : 0.003 0.024 2109 Dihedral : 3.728 25.088 1596 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.96 % Allowed : 23.84 % Favored : 75.20 % 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: 1.67 (0.22), residues: 1444 helix: 1.71 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.37 (0.33), residues: 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 532 time to evaluate : 1.309 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 536 average time/residue: 0.2305 time to fit residues: 174.2759 Evaluate side-chains 522 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 513 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1427 time to fit residues: 3.9148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN U 59 ASN K 78 ASN L 78 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN O 77 GLN P 26 GLN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11837 Z= 0.256 Angle : 0.570 8.372 16112 Z= 0.292 Chirality : 0.040 0.235 1843 Planarity : 0.003 0.021 2109 Dihedral : 3.766 26.408 1596 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.80 % Allowed : 26.48 % Favored : 72.73 % 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: 1.76 (0.22), residues: 1444 helix: 1.76 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.19 (0.35), residues: 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 529 time to evaluate : 1.389 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 531 average time/residue: 0.2360 time to fit residues: 176.7698 Evaluate side-chains 527 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 519 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1033 time to fit residues: 3.3896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN U 59 ASN K 78 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN M 78 ASN N 78 ASN O 77 GLN P 63 ASN R 59 ASN R 61 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11837 Z= 0.220 Angle : 0.557 8.095 16112 Z= 0.286 Chirality : 0.040 0.240 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.712 25.936 1596 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.12 % Allowed : 26.87 % Favored : 72.01 % 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: 1.95 (0.22), residues: 1444 helix: 1.88 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.11 (0.36), residues: 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 532 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 534 average time/residue: 0.2369 time to fit residues: 177.3950 Evaluate side-chains 528 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 516 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1408 time to fit residues: 4.5940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 0.0670 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN U 59 ASN K 78 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN O 61 GLN P 63 ASN R 61 GLN S 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11837 Z= 0.255 Angle : 0.588 10.790 16112 Z= 0.300 Chirality : 0.041 0.252 1843 Planarity : 0.003 0.022 2109 Dihedral : 3.784 27.256 1596 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.64 % Allowed : 27.75 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.22), residues: 1444 helix: 1.87 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.02 (0.36), residues: 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 527 time to evaluate : 1.327 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 528 average time/residue: 0.2296 time to fit residues: 171.6418 Evaluate side-chains 526 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 518 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1412 time to fit residues: 3.7915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN O 59 ASN O 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11837 Z= 0.290 Angle : 0.613 7.923 16112 Z= 0.314 Chirality : 0.042 0.276 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.876 28.102 1596 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.72 % Allowed : 27.83 % Favored : 71.45 % 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: 1.86 (0.22), residues: 1444 helix: 1.80 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -3.92 (0.37), residues: 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 523 time to evaluate : 1.187 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 524 average time/residue: 0.2379 time to fit residues: 178.4612 Evaluate side-chains 521 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 516 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1300 time to fit residues: 2.9423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 59 ASN P 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100797 restraints weight = 17496.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103996 restraints weight = 9150.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106206 restraints weight = 5941.841| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11837 Z= 0.228 Angle : 0.597 9.891 16112 Z= 0.306 Chirality : 0.041 0.252 1843 Planarity : 0.003 0.024 2109 Dihedral : 3.803 26.290 1596 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.40 % Allowed : 29.27 % Favored : 70.33 % 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: 1.97 (0.22), residues: 1444 helix: 1.86 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -3.75 (0.38), residues: 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.44 seconds wall clock time: 56 minutes 8.48 seconds (3368.48 seconds total)