Starting phenix.real_space_refine on Wed Feb 14 02:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k48_22661/02_2024/7k48_22661.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k48_22661/02_2024/7k48_22661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k48_22661/02_2024/7k48_22661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k48_22661/02_2024/7k48_22661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k48_22661/02_2024/7k48_22661.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k48_22661/02_2024/7k48_22661.pdb" } resolution = 3.6 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= 0.069 sd= 0.926 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 S 80 5.16 5 C 5696 2.51 5 N 1316 2.21 5 O 1388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 800": "OD1" <-> "OD2" Residue "A ARG 829": "NH1" <-> "NH2" Residue "A TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 879": "NH1" <-> "NH2" Residue "A PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 800": "OD1" <-> "OD2" Residue "B ARG 829": "NH1" <-> "NH2" Residue "B TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 879": "NH1" <-> "NH2" Residue "B PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 889": "OE1" <-> "OE2" Residue "B PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 800": "OD1" <-> "OD2" Residue "C ARG 829": "NH1" <-> "NH2" Residue "C TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 879": "NH1" <-> "NH2" Residue "C PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 889": "OE1" <-> "OE2" Residue "C PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 731": "OE1" <-> "OE2" Residue "D PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 800": "OD1" <-> "OD2" Residue "D ARG 829": "NH1" <-> "NH2" Residue "D TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 879": "NH1" <-> "NH2" Residue "D PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 889": "OE1" <-> "OE2" Residue "D PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8480 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1858 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1858 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1858 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "D" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1858 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "E" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 262 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "F" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 262 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "G" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 262 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 262 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Time building chain proxies: 4.59, per 1000 atoms: 0.54 Number of scatterers: 8480 At special positions: 0 Unit cell: (123.552, 123.552, 72.864, 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) S 80 16.00 O 1388 8.00 N 1316 7.00 C 5696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 17 " distance=2.02 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 24 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 31 " distance=2.02 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 17 " distance=2.02 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 24 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 31 " distance=2.02 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 17 " distance=2.02 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 31 " distance=2.02 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 17 " distance=2.02 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 24 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 31 " distance=2.02 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: 3.26 Conformation dependent library (CDL) restraints added in 1.8 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 79.1% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 720 through 732 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 758 through 787 removed outlier: 3.625A pdb=" N ASN A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.901A pdb=" N ASP A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 811 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 837 through 876 removed outlier: 4.125A pdb=" N LYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) Proline residue: A 852 - end of helix Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.929A pdb=" N PHE A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.599A pdb=" N VAL A 914 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 948 Proline residue: A 924 - end of helix removed outlier: 4.877A pdb=" N ASP A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 732 Processing helix chain 'B' and resid 732 through 751 Processing helix chain 'B' and resid 758 through 787 removed outlier: 3.624A pdb=" N ASN B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 removed outlier: 3.901A pdb=" N ASP B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 811 Processing helix chain 'B' and resid 818 through 829 Processing helix chain 'B' and resid 830 through 835 Processing helix chain 'B' and resid 837 through 876 removed outlier: 4.126A pdb=" N LYS B 842 " --> pdb=" O PRO B 838 " (cutoff:3.500A) Proline residue: B 852 - end of helix Processing helix chain 'B' and resid 880 through 885 removed outlier: 3.928A pdb=" N PHE B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 899 Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.599A pdb=" N VAL B 914 " --> pdb=" O PRO B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 948 Proline residue: B 924 - end of helix removed outlier: 4.877A pdb=" N ASP B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA B 944 " --> pdb=" O ILE B 940 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET B 945 " --> pdb=" O ILE B 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 Processing helix chain 'C' and resid 732 through 751 Processing helix chain 'C' and resid 758 through 787 removed outlier: 3.624A pdb=" N ASN C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 removed outlier: 3.901A pdb=" N ASP C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 811 Processing helix chain 'C' and resid 818 through 829 Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'C' and resid 837 through 876 removed outlier: 4.125A pdb=" N LYS C 842 " --> pdb=" O PRO C 838 " (cutoff:3.500A) Proline residue: C 852 - end of helix Processing helix chain 'C' and resid 880 through 885 removed outlier: 3.928A pdb=" N PHE C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 899 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.599A pdb=" N VAL C 914 " --> pdb=" O PRO C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 948 Proline residue: C 924 - end of helix removed outlier: 4.877A pdb=" N ASP C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA C 944 " --> pdb=" O ILE C 940 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 732 Processing helix chain 'D' and resid 732 through 751 Processing helix chain 'D' and resid 758 through 787 removed outlier: 3.624A pdb=" N ASN D 763 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 764 " --> pdb=" O GLU D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 removed outlier: 3.902A pdb=" N ASP D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 811 Processing helix chain 'D' and resid 818 through 829 Processing helix chain 'D' and resid 830 through 835 Processing helix chain 'D' and resid 837 through 876 removed outlier: 4.125A pdb=" N LYS D 842 " --> pdb=" O PRO D 838 " (cutoff:3.500A) Proline residue: D 852 - end of helix Processing helix chain 'D' and resid 880 through 885 removed outlier: 3.929A pdb=" N PHE D 884 " --> pdb=" O PHE D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 899 Processing helix chain 'D' and resid 907 through 915 removed outlier: 3.598A pdb=" N VAL D 914 " --> pdb=" O PRO D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 948 Proline residue: D 924 - end of helix removed outlier: 4.877A pdb=" N ASP D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA D 944 " --> pdb=" O ILE D 940 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET D 945 " --> pdb=" O ILE D 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 20 Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'G' and resid 17 through 20 Processing helix chain 'H' and resid 17 through 20 Processing sheet with id=AA1, first strand: chain 'E' and resid 22 through 24 removed outlier: 3.612A pdb=" N VAL E 23 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 22 through 24 removed outlier: 3.612A pdb=" N VAL F 23 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.612A pdb=" N VAL G 23 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 24 removed outlier: 3.613A pdb=" N VAL H 23 " --> pdb=" O LYS H 32 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2475 1.35 - 1.47: 2411 1.47 - 1.60: 3690 1.60 - 1.72: 0 1.72 - 1.85: 132 Bond restraints: 8708 Sorted by residual: bond pdb=" C ILE D 851 " pdb=" N PRO D 852 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.11e+01 bond pdb=" C ILE A 851 " pdb=" N PRO A 852 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.08e+01 bond pdb=" C ILE C 851 " pdb=" N PRO C 852 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.05e+01 bond pdb=" C ILE B 851 " pdb=" N PRO B 852 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.04e+01 bond pdb=" C HIS D 755 " pdb=" N PRO D 756 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.68e+00 ... (remaining 8703 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.07: 202 106.07 - 113.06: 4617 113.06 - 120.04: 3420 120.04 - 127.02: 3470 127.02 - 134.00: 107 Bond angle restraints: 11816 Sorted by residual: angle pdb=" CA ARG H 29 " pdb=" CB ARG H 29 " pdb=" CG ARG H 29 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG F 29 " pdb=" CB ARG F 29 " pdb=" CG ARG F 29 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG E 29 " pdb=" CB ARG E 29 " pdb=" CG ARG E 29 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" CA ARG G 29 " pdb=" CB ARG G 29 " pdb=" CG ARG G 29 " ideal model delta sigma weight residual 114.10 124.26 -10.16 2.00e+00 2.50e-01 2.58e+01 angle pdb=" C VAL A 928 " pdb=" N VAL A 929 " pdb=" CA VAL A 929 " ideal model delta sigma weight residual 121.02 115.09 5.93 1.51e+00 4.39e-01 1.54e+01 ... (remaining 11811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4372 17.90 - 35.81: 552 35.81 - 53.71: 125 53.71 - 71.62: 35 71.62 - 89.52: 20 Dihedral angle restraints: 5104 sinusoidal: 2016 harmonic: 3088 Sorted by residual: dihedral pdb=" CA VAL B 821 " pdb=" C VAL B 821 " pdb=" N LEU B 822 " pdb=" CA LEU B 822 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA VAL D 821 " pdb=" C VAL D 821 " pdb=" N LEU D 822 " pdb=" CA LEU D 822 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA VAL A 821 " pdb=" C VAL A 821 " pdb=" N LEU A 822 " pdb=" CA LEU A 822 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 5101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 857 0.051 - 0.101: 376 0.101 - 0.152: 131 0.152 - 0.203: 18 0.203 - 0.253: 10 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CG LEU B 819 " pdb=" CB LEU B 819 " pdb=" CD1 LEU B 819 " pdb=" CD2 LEU B 819 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CG LEU A 819 " pdb=" CB LEU A 819 " pdb=" CD1 LEU A 819 " pdb=" CD2 LEU A 819 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CG LEU C 819 " pdb=" CB LEU C 819 " pdb=" CD1 LEU C 819 " pdb=" CD2 LEU C 819 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1389 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 901 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU B 901 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU B 901 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU B 901 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 901 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU D 901 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU D 901 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU D 901 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 901 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU A 901 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU A 901 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU A 901 " 0.020 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1792 2.77 - 3.30: 8773 3.30 - 3.83: 14308 3.83 - 4.37: 16301 4.37 - 4.90: 26092 Nonbonded interactions: 67266 Sorted by model distance: nonbonded pdb=" O TYR B 723 " pdb=" OG1 THR B 727 " model vdw 2.233 2.440 nonbonded pdb=" O TYR C 723 " pdb=" OG1 THR C 727 " model vdw 2.234 2.440 nonbonded pdb=" O TYR A 723 " pdb=" OG1 THR A 727 " model vdw 2.234 2.440 nonbonded pdb=" O TYR D 723 " pdb=" OG1 THR D 727 " model vdw 2.234 2.440 nonbonded pdb=" O ILE C 729 " pdb=" OG SER C 732 " model vdw 2.251 2.440 ... (remaining 67261 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' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.010 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: 4.100 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.070 Find NCS groups from input model: 0.530 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 8708 Z= 0.614 Angle : 1.227 10.492 11816 Z= 0.674 Chirality : 0.064 0.253 1392 Planarity : 0.009 0.079 1416 Dihedral : 17.881 89.520 3044 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.40 % Allowed : 14.47 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.21), residues: 1032 helix: -2.11 (0.15), residues: 712 sheet: None (None), residues: 0 loop : -2.43 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP G 30 HIS 0.002 0.001 HIS A 754 PHE 0.026 0.003 PHE C 772 TYR 0.022 0.004 TYR B 915 ARG 0.005 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 325 time to evaluate : 0.921 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: A 866 TYR cc_start: 0.9143 (t80) cc_final: 0.8889 (t80) REVERT: A 867 ILE cc_start: 0.9186 (pt) cc_final: 0.8892 (mp) REVERT: A 874 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 898 MET cc_start: 0.8570 (tmm) cc_final: 0.7940 (tmm) REVERT: B 866 TYR cc_start: 0.8958 (t80) cc_final: 0.8671 (t80) REVERT: B 874 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 898 MET cc_start: 0.8657 (tmm) cc_final: 0.8040 (tmm) REVERT: C 829 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8446 (mtp180) REVERT: C 898 MET cc_start: 0.8662 (tmm) cc_final: 0.7998 (tmm) REVERT: D 748 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8908 (mm) REVERT: D 759 GLU cc_start: 0.8308 (tp30) cc_final: 0.7604 (pm20) REVERT: D 829 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8426 (mtp180) REVERT: D 898 MET cc_start: 0.8679 (tmm) cc_final: 0.8066 (tmm) outliers start: 32 outliers final: 11 residues processed: 337 average time/residue: 0.2176 time to fit residues: 96.6964 Evaluate side-chains 275 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 263 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 936 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 720 ASN C 720 ASN C 746 ASN D 720 ASN D 746 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8708 Z= 0.197 Angle : 0.673 10.414 11816 Z= 0.342 Chirality : 0.039 0.133 1392 Planarity : 0.006 0.063 1416 Dihedral : 7.930 54.452 1130 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.00 % Allowed : 20.85 % Favored : 74.15 % 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: -1.49 (0.24), residues: 1032 helix: -0.62 (0.18), residues: 712 sheet: None (None), residues: 0 loop : -1.55 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 903 HIS 0.002 0.001 HIS C 754 PHE 0.027 0.002 PHE B 831 TYR 0.019 0.002 TYR C 866 ARG 0.005 0.001 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 276 time to evaluate : 0.892 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: A 748 LEU cc_start: 0.8983 (mm) cc_final: 0.8700 (mm) REVERT: A 829 ARG cc_start: 0.8752 (mtp180) cc_final: 0.8332 (mtp85) REVERT: A 840 MET cc_start: 0.6723 (mmm) cc_final: 0.6292 (mmp) REVERT: A 866 TYR cc_start: 0.9054 (t80) cc_final: 0.8746 (t80) REVERT: A 871 MET cc_start: 0.9110 (mtp) cc_final: 0.8835 (mtp) REVERT: A 880 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8287 (p90) REVERT: A 898 MET cc_start: 0.8691 (tmm) cc_final: 0.8156 (tmm) REVERT: B 748 LEU cc_start: 0.8984 (mm) cc_final: 0.8648 (mm) REVERT: B 829 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8227 (mmm-85) REVERT: B 866 TYR cc_start: 0.8873 (t80) cc_final: 0.8620 (t80) REVERT: B 874 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 880 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8245 (p90) REVERT: B 898 MET cc_start: 0.8645 (tmm) cc_final: 0.8036 (tmm) REVERT: C 748 LEU cc_start: 0.9170 (mm) cc_final: 0.8889 (mm) REVERT: C 750 MET cc_start: 0.8697 (tpt) cc_final: 0.8422 (tpt) REVERT: C 829 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8040 (mmm-85) REVERT: C 880 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7725 (p90) REVERT: C 898 MET cc_start: 0.8677 (tmm) cc_final: 0.8136 (tmm) REVERT: D 748 LEU cc_start: 0.9168 (mm) cc_final: 0.8922 (mm) REVERT: D 750 MET cc_start: 0.8817 (tpt) cc_final: 0.8498 (tpt) REVERT: D 829 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8213 (mtp85) REVERT: D 866 TYR cc_start: 0.8923 (t80) cc_final: 0.8666 (t80) REVERT: D 880 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8201 (p90) REVERT: D 898 MET cc_start: 0.8680 (tmm) cc_final: 0.8155 (tmm) outliers start: 47 outliers final: 25 residues processed: 306 average time/residue: 0.1881 time to fit residues: 79.0049 Evaluate side-chains 300 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 271 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 880 PHE Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 929 VAL Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN D 746 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8708 Z= 0.333 Angle : 0.711 7.740 11816 Z= 0.370 Chirality : 0.042 0.195 1392 Planarity : 0.005 0.046 1416 Dihedral : 7.631 59.596 1128 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 6.91 % Allowed : 23.72 % Favored : 69.36 % 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: -0.87 (0.25), residues: 1032 helix: -0.04 (0.18), residues: 708 sheet: -1.78 (0.80), residues: 36 loop : -1.51 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 903 HIS 0.001 0.001 HIS D 755 PHE 0.028 0.002 PHE B 831 TYR 0.016 0.003 TYR C 915 ARG 0.005 0.001 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 285 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 829 ARG cc_start: 0.8804 (mtp180) cc_final: 0.8216 (mmm-85) REVERT: A 840 MET cc_start: 0.6924 (mmm) cc_final: 0.6669 (mmp) REVERT: A 866 TYR cc_start: 0.9092 (t80) cc_final: 0.8866 (t80) REVERT: A 880 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (p90) REVERT: A 898 MET cc_start: 0.8805 (tmm) cc_final: 0.8191 (tmm) REVERT: B 748 LEU cc_start: 0.9043 (mm) cc_final: 0.8788 (mm) REVERT: B 874 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8445 (tm-30) REVERT: B 880 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8544 (p90) REVERT: C 745 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9261 (mm) REVERT: C 748 LEU cc_start: 0.9243 (mm) cc_final: 0.9034 (mm) REVERT: C 750 MET cc_start: 0.8690 (tpt) cc_final: 0.8364 (tpt) REVERT: C 829 ARG cc_start: 0.8877 (mtp180) cc_final: 0.8624 (mtp180) REVERT: C 878 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8170 (pp20) REVERT: C 880 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8308 (p90) REVERT: C 898 MET cc_start: 0.8806 (tmm) cc_final: 0.8269 (tmm) REVERT: C 902 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9089 (p) REVERT: D 745 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9285 (mm) REVERT: D 750 MET cc_start: 0.8843 (tpt) cc_final: 0.8567 (tpt) REVERT: D 826 ARG cc_start: 0.8871 (mmm-85) cc_final: 0.8620 (mmm-85) REVERT: D 840 MET cc_start: 0.6844 (mmm) cc_final: 0.6484 (mmp) REVERT: D 878 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8071 (pp20) REVERT: D 880 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8403 (p90) REVERT: D 898 MET cc_start: 0.8731 (tmm) cc_final: 0.8203 (tmm) outliers start: 65 outliers final: 27 residues processed: 320 average time/residue: 0.1927 time to fit residues: 84.5750 Evaluate side-chains 285 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 249 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 880 PHE Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 902 SER Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 ASN A 746 ASN C 746 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8708 Z= 0.209 Angle : 0.662 7.566 11816 Z= 0.340 Chirality : 0.040 0.183 1392 Planarity : 0.004 0.036 1416 Dihedral : 7.342 56.901 1128 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.96 % Allowed : 25.85 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1032 helix: 0.45 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 30 HIS 0.001 0.001 HIS C 787 PHE 0.024 0.001 PHE C 802 TYR 0.011 0.002 TYR D 785 ARG 0.004 0.000 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 271 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 829 ARG cc_start: 0.8838 (mtp180) cc_final: 0.7942 (mmm-85) REVERT: A 874 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 898 MET cc_start: 0.8731 (tmm) cc_final: 0.8127 (tmm) REVERT: A 902 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8937 (p) REVERT: B 748 LEU cc_start: 0.9025 (mm) cc_final: 0.8792 (mm) REVERT: B 829 ARG cc_start: 0.8813 (mtp180) cc_final: 0.8232 (mmm-85) REVERT: B 874 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 880 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8540 (p90) REVERT: B 898 MET cc_start: 0.8668 (tmm) cc_final: 0.8173 (tmm) REVERT: C 745 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9264 (mm) REVERT: C 748 LEU cc_start: 0.9207 (mm) cc_final: 0.8989 (mm) REVERT: C 750 MET cc_start: 0.8565 (tpt) cc_final: 0.8278 (tpt) REVERT: C 829 ARG cc_start: 0.8829 (mtp180) cc_final: 0.8489 (mtp180) REVERT: C 840 MET cc_start: 0.6863 (mmm) cc_final: 0.6548 (mmp) REVERT: C 878 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: C 880 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8343 (p90) REVERT: C 898 MET cc_start: 0.8705 (tmm) cc_final: 0.8168 (tmm) REVERT: D 745 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9233 (mm) REVERT: D 750 MET cc_start: 0.8793 (tpt) cc_final: 0.8428 (tpt) REVERT: D 829 ARG cc_start: 0.8714 (mtp180) cc_final: 0.8456 (mtp180) REVERT: D 840 MET cc_start: 0.6886 (mmm) cc_final: 0.6528 (mmp) REVERT: D 880 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8516 (p90) REVERT: D 898 MET cc_start: 0.8731 (tmm) cc_final: 0.8201 (tmm) outliers start: 56 outliers final: 36 residues processed: 297 average time/residue: 0.1919 time to fit residues: 78.0126 Evaluate side-chains 289 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 246 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 880 PHE Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 941 ILE Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 929 VAL Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain D residue 941 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN B 746 ASN C 746 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8708 Z= 0.299 Angle : 0.712 10.017 11816 Z= 0.366 Chirality : 0.043 0.297 1392 Planarity : 0.005 0.033 1416 Dihedral : 7.024 54.433 1128 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 7.23 % Allowed : 26.60 % Favored : 66.17 % 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 (0.26), residues: 1032 helix: 0.43 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.23 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 30 HIS 0.001 0.000 HIS C 755 PHE 0.031 0.002 PHE B 831 TYR 0.015 0.002 TYR C 785 ARG 0.004 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 256 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7916 (mm) REVERT: A 829 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8224 (mmm-85) REVERT: A 840 MET cc_start: 0.6327 (mmp) cc_final: 0.6061 (mmp) REVERT: A 874 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 898 MET cc_start: 0.8749 (tmm) cc_final: 0.8153 (tmm) REVERT: B 748 LEU cc_start: 0.9040 (mm) cc_final: 0.8799 (mm) REVERT: B 808 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7933 (mm) REVERT: B 829 ARG cc_start: 0.8750 (mtp180) cc_final: 0.8136 (mmm-85) REVERT: B 874 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 724 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7838 (tp) REVERT: C 745 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9126 (mm) REVERT: C 750 MET cc_start: 0.8554 (tpt) cc_final: 0.8306 (tpt) REVERT: C 780 ILE cc_start: 0.9108 (mm) cc_final: 0.8779 (mm) REVERT: C 808 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7962 (mm) REVERT: C 829 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8118 (mmm-85) REVERT: C 840 MET cc_start: 0.6876 (mmm) cc_final: 0.6449 (mmp) REVERT: C 874 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 878 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: C 880 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8429 (p90) REVERT: C 898 MET cc_start: 0.8806 (tmm) cc_final: 0.8271 (tmm) REVERT: D 745 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9160 (mm) REVERT: D 750 MET cc_start: 0.8773 (tpt) cc_final: 0.8489 (tpt) REVERT: D 878 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8109 (pp20) REVERT: D 880 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8600 (p90) REVERT: D 898 MET cc_start: 0.8767 (tmm) cc_final: 0.8273 (tmm) REVERT: D 902 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.8967 (p) outliers start: 68 outliers final: 32 residues processed: 298 average time/residue: 0.1907 time to fit residues: 78.2922 Evaluate side-chains 292 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 249 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 93 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN B 728 ASN B 746 ASN C 746 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8708 Z= 0.248 Angle : 0.709 10.543 11816 Z= 0.362 Chirality : 0.042 0.277 1392 Planarity : 0.004 0.036 1416 Dihedral : 6.585 59.982 1124 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.70 % Allowed : 28.30 % Favored : 65.00 % 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: -0.08 (0.26), residues: 1032 helix: 0.47 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 30 HIS 0.001 0.000 HIS D 787 PHE 0.023 0.001 PHE B 831 TYR 0.012 0.002 TYR C 785 ARG 0.005 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 266 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7992 (mm) REVERT: A 829 ARG cc_start: 0.8813 (mtp180) cc_final: 0.8232 (mmm-85) REVERT: A 898 MET cc_start: 0.8734 (tmm) cc_final: 0.8154 (tmm) REVERT: B 745 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9099 (mm) REVERT: B 748 LEU cc_start: 0.9070 (mm) cc_final: 0.8852 (mm) REVERT: B 808 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7983 (mm) REVERT: B 829 ARG cc_start: 0.8761 (mtp180) cc_final: 0.7920 (mmm-85) REVERT: B 840 MET cc_start: 0.6501 (mmm) cc_final: 0.6170 (mmp) REVERT: B 874 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8365 (tm-30) REVERT: B 898 MET cc_start: 0.8805 (tmm) cc_final: 0.8317 (tmm) REVERT: C 724 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7809 (tp) REVERT: C 750 MET cc_start: 0.8576 (tpt) cc_final: 0.8318 (tpt) REVERT: C 808 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8012 (mm) REVERT: C 829 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8109 (mmm-85) REVERT: C 878 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8072 (pp20) REVERT: C 880 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8517 (p90) REVERT: C 898 MET cc_start: 0.8790 (tmm) cc_final: 0.8260 (tmm) REVERT: C 903 TRP cc_start: 0.8742 (p-90) cc_final: 0.7806 (p-90) REVERT: D 724 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7836 (tp) REVERT: D 750 MET cc_start: 0.8737 (tpt) cc_final: 0.8500 (tpt) REVERT: D 779 GLU cc_start: 0.9287 (pt0) cc_final: 0.8929 (pt0) REVERT: D 808 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7937 (mm) REVERT: D 878 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8155 (pp20) REVERT: D 898 MET cc_start: 0.8784 (tmm) cc_final: 0.8267 (tmm) outliers start: 63 outliers final: 37 residues processed: 300 average time/residue: 0.1942 time to fit residues: 79.4361 Evaluate side-chains 295 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 248 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain D residue 902 SER Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 0.0370 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8708 Z= 0.225 Angle : 0.730 11.490 11816 Z= 0.365 Chirality : 0.043 0.334 1392 Planarity : 0.004 0.035 1416 Dihedral : 6.496 59.961 1122 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 6.38 % Allowed : 30.96 % Favored : 62.66 % 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: -0.06 (0.26), residues: 1032 helix: 0.51 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.20 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 903 HIS 0.002 0.001 HIS D 755 PHE 0.032 0.001 PHE B 831 TYR 0.012 0.002 TYR C 785 ARG 0.006 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 266 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 829 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8241 (mmm-85) REVERT: A 903 TRP cc_start: 0.8810 (p-90) cc_final: 0.7927 (p-90) REVERT: B 745 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9116 (mm) REVERT: B 748 LEU cc_start: 0.9084 (mm) cc_final: 0.8863 (mm) REVERT: B 808 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8094 (mm) REVERT: B 829 ARG cc_start: 0.8791 (mtp180) cc_final: 0.7947 (mmm-85) REVERT: B 874 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8308 (tm-30) REVERT: C 750 MET cc_start: 0.8606 (tpt) cc_final: 0.8401 (tpt) REVERT: C 808 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7988 (mm) REVERT: C 829 ARG cc_start: 0.8811 (mtp180) cc_final: 0.8093 (mmm-85) REVERT: C 878 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: C 898 MET cc_start: 0.8721 (tmm) cc_final: 0.8187 (tmm) REVERT: D 749 PHE cc_start: 0.8541 (t80) cc_final: 0.8180 (t80) REVERT: D 779 GLU cc_start: 0.9306 (pt0) cc_final: 0.9067 (pt0) REVERT: D 808 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7931 (mm) REVERT: D 878 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8129 (pp20) REVERT: D 898 MET cc_start: 0.8750 (tmm) cc_final: 0.8217 (tmm) outliers start: 60 outliers final: 38 residues processed: 298 average time/residue: 0.1865 time to fit residues: 76.3746 Evaluate side-chains 293 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 249 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 728 ASN D 728 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8708 Z= 0.259 Angle : 0.767 11.611 11816 Z= 0.383 Chirality : 0.043 0.301 1392 Planarity : 0.004 0.034 1416 Dihedral : 6.419 57.314 1122 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 7.66 % Allowed : 30.53 % Favored : 61.81 % 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: -0.13 (0.26), residues: 1032 helix: 0.49 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 903 HIS 0.003 0.001 HIS D 787 PHE 0.041 0.001 PHE B 802 TYR 0.013 0.002 TYR D 785 ARG 0.006 0.000 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 261 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 MET cc_start: 0.8529 (ptp) cc_final: 0.7213 (mmt) REVERT: A 829 ARG cc_start: 0.8829 (mtp180) cc_final: 0.8266 (mmm-85) REVERT: A 902 SER cc_start: 0.9297 (OUTLIER) cc_final: 0.8927 (p) REVERT: A 903 TRP cc_start: 0.8788 (p-90) cc_final: 0.8000 (p-90) REVERT: B 745 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9137 (mm) REVERT: B 748 LEU cc_start: 0.9084 (mm) cc_final: 0.8720 (mm) REVERT: B 752 MET cc_start: 0.8567 (ptp) cc_final: 0.7237 (mmt) REVERT: B 808 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 829 ARG cc_start: 0.8790 (mtp180) cc_final: 0.7962 (mmm-85) REVERT: B 874 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8284 (tm-30) REVERT: C 749 PHE cc_start: 0.8550 (t80) cc_final: 0.8273 (t80) REVERT: C 750 MET cc_start: 0.8582 (tpt) cc_final: 0.8382 (tpt) REVERT: C 808 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8006 (mm) REVERT: C 829 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8110 (mmm-85) REVERT: C 880 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8303 (p90) REVERT: C 898 MET cc_start: 0.8711 (tmm) cc_final: 0.8183 (tmm) REVERT: C 902 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8954 (p) REVERT: D 749 PHE cc_start: 0.8565 (t80) cc_final: 0.8127 (t80) REVERT: D 779 GLU cc_start: 0.9341 (pt0) cc_final: 0.9051 (pt0) REVERT: D 808 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7902 (mm) REVERT: D 901 GLU cc_start: 0.8769 (pp20) cc_final: 0.8563 (pp20) outliers start: 72 outliers final: 44 residues processed: 302 average time/residue: 0.1947 time to fit residues: 81.0823 Evaluate side-chains 305 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 254 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 902 SER Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 787 HIS Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 728 ASN D 728 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8708 Z= 0.245 Angle : 0.784 12.404 11816 Z= 0.387 Chirality : 0.044 0.326 1392 Planarity : 0.004 0.037 1416 Dihedral : 6.374 55.368 1122 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.32 % Allowed : 32.45 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1032 helix: 0.56 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 903 HIS 0.004 0.001 HIS C 787 PHE 0.023 0.001 PHE D 802 TYR 0.024 0.002 TYR C 866 ARG 0.006 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 260 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 MET cc_start: 0.8542 (ptp) cc_final: 0.7220 (mmt) REVERT: A 810 GLU cc_start: 0.7985 (tp30) cc_final: 0.7776 (tp30) REVERT: A 829 ARG cc_start: 0.8846 (mtp180) cc_final: 0.8296 (mmm-85) REVERT: A 902 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.8929 (p) REVERT: A 903 TRP cc_start: 0.8799 (p-90) cc_final: 0.7992 (p-90) REVERT: B 745 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9151 (mm) REVERT: B 748 LEU cc_start: 0.9000 (mm) cc_final: 0.8745 (mm) REVERT: B 752 MET cc_start: 0.8573 (ptp) cc_final: 0.7225 (tpt) REVERT: B 808 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8100 (mm) REVERT: B 829 ARG cc_start: 0.8807 (mtp180) cc_final: 0.8077 (mmm-85) REVERT: B 874 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 749 PHE cc_start: 0.8515 (t80) cc_final: 0.8201 (t80) REVERT: C 808 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7995 (mm) REVERT: C 829 ARG cc_start: 0.8815 (mtp180) cc_final: 0.8112 (mmm-85) REVERT: C 880 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8338 (p90) REVERT: C 898 MET cc_start: 0.8687 (tmm) cc_final: 0.8157 (tmm) REVERT: D 749 PHE cc_start: 0.8469 (t80) cc_final: 0.8030 (t80) REVERT: D 808 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7901 (mm) REVERT: D 898 MET cc_start: 0.8796 (tmm) cc_final: 0.8281 (tmm) outliers start: 50 outliers final: 36 residues processed: 286 average time/residue: 0.1998 time to fit residues: 78.4094 Evaluate side-chains 292 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 250 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 99 optimal weight: 0.0980 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 728 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8708 Z= 0.212 Angle : 0.808 13.942 11816 Z= 0.397 Chirality : 0.044 0.344 1392 Planarity : 0.004 0.039 1416 Dihedral : 6.320 53.483 1122 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.68 % Allowed : 33.51 % Favored : 61.81 % 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: -0.14 (0.27), residues: 1032 helix: 0.56 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 903 HIS 0.005 0.001 HIS C 787 PHE 0.024 0.001 PHE B 802 TYR 0.020 0.002 TYR A 866 ARG 0.005 0.000 ARG B 841 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 MET cc_start: 0.8474 (ptp) cc_final: 0.7200 (mmt) REVERT: A 779 GLU cc_start: 0.9353 (tt0) cc_final: 0.8904 (pt0) REVERT: A 829 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8294 (mmm-85) REVERT: A 902 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8852 (p) REVERT: A 903 TRP cc_start: 0.8723 (p-90) cc_final: 0.7838 (p-90) REVERT: B 745 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9132 (mm) REVERT: B 748 LEU cc_start: 0.9016 (mm) cc_final: 0.8738 (mm) REVERT: B 752 MET cc_start: 0.8492 (ptp) cc_final: 0.6912 (tpp) REVERT: B 779 GLU cc_start: 0.9372 (tt0) cc_final: 0.8945 (pt0) REVERT: B 829 ARG cc_start: 0.8800 (mtp180) cc_final: 0.8072 (mmm-85) REVERT: C 749 PHE cc_start: 0.8428 (t80) cc_final: 0.7946 (t80) REVERT: C 829 ARG cc_start: 0.8815 (mtp180) cc_final: 0.8095 (mmm-85) REVERT: C 880 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8303 (p90) REVERT: D 749 PHE cc_start: 0.8493 (t80) cc_final: 0.8102 (t80) REVERT: D 808 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7855 (mm) REVERT: D 898 MET cc_start: 0.8637 (tmm) cc_final: 0.8160 (tmm) outliers start: 44 outliers final: 33 residues processed: 283 average time/residue: 0.1903 time to fit residues: 74.0110 Evaluate side-chains 282 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 787 HIS Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.0000 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.111670 restraints weight = 20689.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.115162 restraints weight = 9128.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.117108 restraints weight = 5679.112| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8708 Z= 0.256 Angle : 0.812 13.146 11816 Z= 0.402 Chirality : 0.044 0.330 1392 Planarity : 0.004 0.042 1416 Dihedral : 6.219 51.268 1122 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.68 % Allowed : 33.72 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1032 helix: 0.52 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 903 HIS 0.004 0.001 HIS C 787 PHE 0.025 0.002 PHE C 925 TYR 0.017 0.002 TYR B 866 ARG 0.008 0.000 ARG B 841 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2039.10 seconds wall clock time: 37 minutes 29.46 seconds (2249.46 seconds total)