Starting phenix.real_space_refine on Mon Mar 11 00:00:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npj_0471/03_2024/6npj_0471.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npj_0471/03_2024/6npj_0471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npj_0471/03_2024/6npj_0471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npj_0471/03_2024/6npj_0471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npj_0471/03_2024/6npj_0471.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npj_0471/03_2024/6npj_0471.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 30 5.16 5 C 3936 2.51 5 N 1102 2.21 5 O 1118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 726": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "C GLU 786": "OE1" <-> "OE2" Residue "C ARG 803": "NH1" <-> "NH2" Residue "C ASP 821": "OD1" <-> "OD2" Residue "C GLU 824": "OE1" <-> "OE2" Residue "C PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 955": "OD1" <-> "OD2" Residue "C ASP 956": "OD1" <-> "OD2" Residue "C TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 979": "NH1" <-> "NH2" Residue "C ARG 988": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 994": "NH1" <-> "NH2" Residue "C ARG 1004": "NH1" <-> "NH2" Residue "C PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1015": "OD1" <-> "OD2" Residue "C GLU 1023": "OE1" <-> "OE2" Residue "C GLU 1027": "OE1" <-> "OE2" Residue "C GLU 1039": "OE1" <-> "OE2" Residue "C GLU 1045": "OE1" <-> "OE2" Residue "C TYR 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1072": "NH1" <-> "NH2" Residue "C ARG 1098": "NH1" <-> "NH2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 726": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "B GLU 786": "OE1" <-> "OE2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B ASP 821": "OD1" <-> "OD2" Residue "B GLU 824": "OE1" <-> "OE2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 955": "OD1" <-> "OD2" Residue "B ASP 956": "OD1" <-> "OD2" Residue "B TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 979": "NH1" <-> "NH2" Residue "B ARG 988": "NH1" <-> "NH2" Residue "B ARG 993": "NH1" <-> "NH2" Residue "B ARG 994": "NH1" <-> "NH2" Residue "B ARG 1004": "NH1" <-> "NH2" Residue "B PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1015": "OD1" <-> "OD2" Residue "B GLU 1023": "OE1" <-> "OE2" Residue "B GLU 1027": "OE1" <-> "OE2" Residue "B GLU 1039": "OE1" <-> "OE2" Residue "B GLU 1045": "OE1" <-> "OE2" Residue "B TYR 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1072": "NH1" <-> "NH2" Residue "B ARG 1098": "NH1" <-> "NH2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6186 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3093 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 371} Chain breaks: 1 Chain: "B" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3093 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 371} Chain breaks: 1 Time building chain proxies: 3.84, per 1000 atoms: 0.62 Number of scatterers: 6186 At special positions: 0 Unit cell: (116.05, 88.62, 87.565, 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 30 16.00 O 1118 8.00 N 1102 7.00 C 3936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 43.4% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.753A pdb=" N HIS C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 699 " --> pdb=" O ALA C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 710 removed outlier: 4.018A pdb=" N LYS C 710 " --> pdb=" O ASP C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 733 removed outlier: 3.870A pdb=" N VAL C 733 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 761 removed outlier: 3.685A pdb=" N LEU C 760 " --> pdb=" O ASN C 756 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 756 through 761' Processing helix chain 'C' and resid 761 through 774 removed outlier: 3.612A pdb=" N ARG C 766 " --> pdb=" O SER C 762 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR C 767 " --> pdb=" O ASP C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 798 removed outlier: 3.898A pdb=" N TYR C 794 " --> pdb=" O GLN C 790 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET C 795 " --> pdb=" O GLY C 791 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 797 " --> pdb=" O GLN C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 824 Processing helix chain 'C' and resid 825 through 836 Processing helix chain 'C' and resid 929 through 937 removed outlier: 3.690A pdb=" N LEU C 934 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 935 " --> pdb=" O GLN C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 removed outlier: 4.052A pdb=" N LEU C 962 " --> pdb=" O GLY C 958 " (cutoff:3.500A) Proline residue: C 964 - end of helix Processing helix chain 'C' and resid 989 through 1003 removed outlier: 3.916A pdb=" N LEU C 999 " --> pdb=" O ALA C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1032 removed outlier: 3.763A pdb=" N GLU C1030 " --> pdb=" O THR C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1036 removed outlier: 3.704A pdb=" N LYS C1036 " --> pdb=" O GLU C1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1033 through 1036' Processing helix chain 'C' and resid 1041 through 1048 Processing helix chain 'C' and resid 1049 through 1051 No H-bonds generated for 'chain 'C' and resid 1049 through 1051' Processing helix chain 'C' and resid 1066 through 1084 removed outlier: 3.939A pdb=" N GLN C1073 " --> pdb=" O LYS C1069 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C1074 " --> pdb=" O GLY C1070 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C1078 " --> pdb=" O ILE C1074 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C1079 " --> pdb=" O ARG C1075 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS C1083 " --> pdb=" O LEU C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1114 removed outlier: 3.531A pdb=" N ALA C1109 " --> pdb=" O ALA C1105 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C1111 " --> pdb=" O TYR C1107 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C1112 " --> pdb=" O MET C1108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C1113 " --> pdb=" O ALA C1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.753A pdb=" N HIS B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 733 removed outlier: 3.870A pdb=" N VAL B 733 " --> pdb=" O ILE B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.685A pdb=" N LEU B 760 " --> pdb=" O ASN B 756 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 761 " --> pdb=" O PHE B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 761' Processing helix chain 'B' and resid 761 through 774 removed outlier: 3.612A pdb=" N ARG B 766 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR B 767 " --> pdb=" O ASP B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 798 removed outlier: 3.899A pdb=" N TYR B 794 " --> pdb=" O GLN B 790 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET B 795 " --> pdb=" O GLY B 791 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 824 Processing helix chain 'B' and resid 825 through 836 Processing helix chain 'B' and resid 929 through 937 removed outlier: 3.689A pdb=" N LEU B 934 " --> pdb=" O ASP B 930 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 969 removed outlier: 4.052A pdb=" N LEU B 962 " --> pdb=" O GLY B 958 " (cutoff:3.500A) Proline residue: B 964 - end of helix Processing helix chain 'B' and resid 989 through 1003 removed outlier: 3.915A pdb=" N LEU B 999 " --> pdb=" O ALA B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 3.764A pdb=" N GLU B1030 " --> pdb=" O THR B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1036 removed outlier: 3.703A pdb=" N LYS B1036 " --> pdb=" O GLU B1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1033 through 1036' Processing helix chain 'B' and resid 1041 through 1048 Processing helix chain 'B' and resid 1049 through 1051 No H-bonds generated for 'chain 'B' and resid 1049 through 1051' Processing helix chain 'B' and resid 1066 through 1084 removed outlier: 3.939A pdb=" N GLN B1073 " --> pdb=" O LYS B1069 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B1074 " --> pdb=" O GLY B1070 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B1078 " --> pdb=" O ILE B1074 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B1079 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B1083 " --> pdb=" O LEU B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1114 removed outlier: 3.532A pdb=" N ALA B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B1111 " --> pdb=" O TYR B1107 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B1112 " --> pdb=" O MET B1108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 778 through 785 removed outlier: 6.134A pdb=" N LEU C 717 " --> pdb=" O VAL C 810 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY C 812 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET C 719 " --> pdb=" O GLY C 812 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C1090 " --> pdb=" O LEU C1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C1124 " --> pdb=" O ILE C1090 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET C1092 " --> pdb=" O VAL C1124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C1089 " --> pdb=" O THR C 947 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 949 " --> pdb=" O LEU C1089 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C1093 " --> pdb=" O TRP C 951 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 977 " --> pdb=" O GLY C 946 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 778 through 785 removed outlier: 6.134A pdb=" N LEU C 717 " --> pdb=" O VAL C 810 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY C 812 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET C 719 " --> pdb=" O GLY C 812 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C1090 " --> pdb=" O LEU C1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C1124 " --> pdb=" O ILE C1090 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET C1092 " --> pdb=" O VAL C1124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C1089 " --> pdb=" O THR C 947 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 949 " --> pdb=" O LEU C1089 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C1093 " --> pdb=" O TRP C 951 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY C 983 " --> pdb=" O TRP C 952 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 980 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU C1013 " --> pdb=" O VAL C 980 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE C 982 " --> pdb=" O LEU C1013 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 778 through 785 removed outlier: 6.135A pdb=" N LEU B 717 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY B 812 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET B 719 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B1090 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B1124 " --> pdb=" O ILE B1090 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET B1092 " --> pdb=" O VAL B1124 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B1089 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 949 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B1093 " --> pdb=" O TRP B 951 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 977 " --> pdb=" O GLY B 946 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 778 through 785 removed outlier: 6.135A pdb=" N LEU B 717 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY B 812 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET B 719 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B1090 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B1124 " --> pdb=" O ILE B1090 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET B1092 " --> pdb=" O VAL B1124 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B1089 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 949 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B1093 " --> pdb=" O TRP B 951 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 983 " --> pdb=" O TRP B 952 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 980 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B1013 " --> pdb=" O VAL B 980 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B 982 " --> pdb=" O LEU B1013 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 714 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: 1.92 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1881 1.34 - 1.45: 1057 1.45 - 1.57: 3320 1.57 - 1.69: 2 1.69 - 1.81: 50 Bond restraints: 6310 Sorted by residual: bond pdb=" N LEU C 933 " pdb=" CA LEU C 933 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.97e+00 bond pdb=" N ILE C 709 " pdb=" CA ILE C 709 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.83e+00 bond pdb=" CB THR C 792 " pdb=" CG2 THR C 792 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.52e+00 bond pdb=" CB THR B 792 " pdb=" CG2 THR B 792 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.40e+00 bond pdb=" N LYS C 710 " pdb=" CA LYS C 710 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.87e+00 ... (remaining 6305 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.50: 162 106.50 - 113.46: 3430 113.46 - 120.42: 2581 120.42 - 127.38: 2268 127.38 - 134.34: 83 Bond angle restraints: 8524 Sorted by residual: angle pdb=" CA GLN B 941 " pdb=" CB GLN B 941 " pdb=" CG GLN B 941 " ideal model delta sigma weight residual 114.10 127.34 -13.24 2.00e+00 2.50e-01 4.38e+01 angle pdb=" CA GLN C 941 " pdb=" CB GLN C 941 " pdb=" CG GLN C 941 " ideal model delta sigma weight residual 114.10 127.29 -13.19 2.00e+00 2.50e-01 4.35e+01 angle pdb=" N LEU C 933 " pdb=" CA LEU C 933 " pdb=" C LEU C 933 " ideal model delta sigma weight residual 111.14 117.95 -6.81 1.08e+00 8.57e-01 3.97e+01 angle pdb=" CA LEU B 933 " pdb=" CB LEU B 933 " pdb=" CG LEU B 933 " ideal model delta sigma weight residual 116.30 134.34 -18.04 3.50e+00 8.16e-02 2.66e+01 angle pdb=" CA LEU C 933 " pdb=" C LEU C 933 " pdb=" O LEU C 933 " ideal model delta sigma weight residual 120.70 115.84 4.86 1.03e+00 9.43e-01 2.22e+01 ... (remaining 8519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3291 17.54 - 35.08: 378 35.08 - 52.62: 96 52.62 - 70.16: 33 70.16 - 87.70: 12 Dihedral angle restraints: 3810 sinusoidal: 1580 harmonic: 2230 Sorted by residual: dihedral pdb=" CA GLN B 941 " pdb=" C GLN B 941 " pdb=" N LYS B 942 " pdb=" CA LYS B 942 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN C 941 " pdb=" C GLN C 941 " pdb=" N LYS C 942 " pdb=" CA LYS C 942 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ALA B 735 " pdb=" C ALA B 735 " pdb=" N PHE B 736 " pdb=" CA PHE B 736 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 730 0.074 - 0.148: 193 0.148 - 0.222: 22 0.222 - 0.296: 3 0.296 - 0.369: 2 Chirality restraints: 950 Sorted by residual: chirality pdb=" CG LEU C1050 " pdb=" CB LEU C1050 " pdb=" CD1 LEU C1050 " pdb=" CD2 LEU C1050 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CG LEU B1050 " pdb=" CB LEU B1050 " pdb=" CD1 LEU B1050 " pdb=" CD2 LEU B1050 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASP C 707 " pdb=" N ASP C 707 " pdb=" C ASP C 707 " pdb=" CB ASP C 707 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 947 not shown) Planarity restraints: 1086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 690 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU C 690 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU C 690 " 0.024 2.00e-02 2.50e+03 pdb=" N THR C 691 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 690 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU B 690 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU B 690 " 0.024 2.00e-02 2.50e+03 pdb=" N THR B 691 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C1119 " 0.060 5.00e-02 4.00e+02 9.17e-02 1.34e+01 pdb=" N PRO C1120 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO C1120 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C1120 " 0.051 5.00e-02 4.00e+02 ... (remaining 1083 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1328 2.78 - 3.31: 5451 3.31 - 3.84: 9638 3.84 - 4.37: 11199 4.37 - 4.90: 19271 Nonbonded interactions: 46887 Sorted by model distance: nonbonded pdb=" CB GLU B1030 " pdb=" OE2 GLU B1033 " model vdw 2.246 3.440 nonbonded pdb=" CB GLU C1030 " pdb=" OE2 GLU C1033 " model vdw 2.250 3.440 nonbonded pdb=" O VAL C 705 " pdb=" NH2 ARG B 769 " model vdw 2.301 2.520 nonbonded pdb=" OG SER B1052 " pdb=" O GLU B1054 " model vdw 2.314 2.440 nonbonded pdb=" OG SER C1052 " pdb=" O GLU C1054 " model vdw 2.314 2.440 ... (remaining 46882 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 'B' selection = chain 'C' } 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: 1.270 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: 0.000 Extract box with map and model: 2.750 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 6310 Z= 0.526 Angle : 1.244 18.035 8524 Z= 0.673 Chirality : 0.067 0.369 950 Planarity : 0.009 0.092 1086 Dihedral : 17.118 87.704 2366 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.25 % Allowed : 12.95 % Favored : 80.80 % 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: -5.64 (0.22), residues: 760 helix: -3.93 (0.17), residues: 328 sheet: -2.35 (0.45), residues: 134 loop : -4.01 (0.24), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 973 HIS 0.009 0.002 HIS B 708 PHE 0.023 0.003 PHE C 736 TYR 0.018 0.003 TYR C 828 ARG 0.016 0.001 ARG C 753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 710 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5813 (mtpt) REVERT: C 1041 ASP cc_start: 0.5783 (m-30) cc_final: 0.4904 (m-30) REVERT: C 1074 ILE cc_start: 0.7971 (mt) cc_final: 0.7675 (mt) REVERT: B 729 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 1044 GLN cc_start: 0.7583 (pt0) cc_final: 0.6771 (tp40) outliers start: 42 outliers final: 10 residues processed: 194 average time/residue: 0.2733 time to fit residues: 63.9015 Evaluate side-chains 119 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 1008 SER Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1008 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 774 ASN C 815 ASN C 833 HIS C1083 HIS B 731 HIS B 739 ASN B 774 ASN B 793 GLN B 833 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6310 Z= 0.171 Angle : 0.637 12.469 8524 Z= 0.324 Chirality : 0.044 0.134 950 Planarity : 0.005 0.073 1086 Dihedral : 6.628 39.580 854 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.83 % Allowed : 18.15 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.23), residues: 760 helix: -2.69 (0.21), residues: 318 sheet: -2.02 (0.43), residues: 148 loop : -4.00 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 770 HIS 0.003 0.001 HIS B1128 PHE 0.016 0.002 PHE B 736 TYR 0.016 0.002 TYR B1135 ARG 0.004 0.000 ARG C 803 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 954 PHE cc_start: 0.5731 (t80) cc_final: 0.5286 (t80) REVERT: C 1041 ASP cc_start: 0.5528 (m-30) cc_final: 0.4944 (m-30) REVERT: B 730 LEU cc_start: 0.8576 (mp) cc_final: 0.8276 (tt) REVERT: B 734 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7337 (t-90) REVERT: B 769 ARG cc_start: 0.7706 (tpp80) cc_final: 0.7406 (tpp80) REVERT: B 1035 TYR cc_start: 0.8696 (m-80) cc_final: 0.8443 (m-80) REVERT: B 1051 LYS cc_start: 0.6712 (mtpp) cc_final: 0.6500 (mttm) REVERT: B 1075 ARG cc_start: 0.6560 (tpp-160) cc_final: 0.6218 (tpt170) outliers start: 19 outliers final: 14 residues processed: 137 average time/residue: 0.2058 time to fit residues: 35.9802 Evaluate side-chains 113 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 1065 LEU Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1086 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 68 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 724 ASN C1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6310 Z= 0.151 Angle : 0.610 10.128 8524 Z= 0.302 Chirality : 0.044 0.244 950 Planarity : 0.004 0.064 1086 Dihedral : 5.751 34.921 845 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.57 % Allowed : 20.98 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.26), residues: 760 helix: -1.87 (0.25), residues: 330 sheet: -1.67 (0.44), residues: 144 loop : -3.73 (0.26), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 770 HIS 0.004 0.001 HIS B1128 PHE 0.012 0.001 PHE B 736 TYR 0.015 0.001 TYR B1135 ARG 0.003 0.000 ARG C 803 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 954 PHE cc_start: 0.5885 (t80) cc_final: 0.5679 (t80) REVERT: C 1041 ASP cc_start: 0.5526 (m-30) cc_final: 0.4893 (m-30) REVERT: B 734 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: B 743 MET cc_start: 0.8635 (ttt) cc_final: 0.8263 (ttt) REVERT: B 1075 ARG cc_start: 0.6579 (tpp-160) cc_final: 0.6334 (tpt170) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 0.1914 time to fit residues: 32.9347 Evaluate side-chains 118 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 0.0370 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 734 HIS C 739 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6310 Z= 0.183 Angle : 0.604 8.437 8524 Z= 0.303 Chirality : 0.044 0.174 950 Planarity : 0.004 0.062 1086 Dihedral : 5.733 36.107 845 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.36 % Allowed : 19.79 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.27), residues: 760 helix: -1.42 (0.26), residues: 328 sheet: -1.40 (0.45), residues: 144 loop : -3.58 (0.28), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 770 HIS 0.007 0.001 HIS C 734 PHE 0.014 0.002 PHE C 736 TYR 0.012 0.001 TYR B1135 ARG 0.002 0.000 ARG C 803 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 764 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7097 (tmm) REVERT: B 700 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8539 (mm) REVERT: B 729 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8630 (tt) REVERT: B 1042 MET cc_start: 0.6699 (tpp) cc_final: 0.6317 (ttp) REVERT: B 1075 ARG cc_start: 0.6696 (tpp-160) cc_final: 0.6415 (tpt170) outliers start: 36 outliers final: 23 residues processed: 135 average time/residue: 0.2209 time to fit residues: 37.7816 Evaluate side-chains 124 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 986 ILE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1078 GLU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 30 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6310 Z= 0.139 Angle : 0.577 9.725 8524 Z= 0.283 Chirality : 0.042 0.149 950 Planarity : 0.004 0.058 1086 Dihedral : 5.389 35.181 845 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.02 % Allowed : 22.02 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.28), residues: 760 helix: -0.80 (0.28), residues: 314 sheet: -1.03 (0.51), residues: 120 loop : -3.34 (0.27), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 770 HIS 0.004 0.001 HIS B1128 PHE 0.026 0.001 PHE C 954 TYR 0.012 0.001 TYR B1135 ARG 0.003 0.000 ARG B 769 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 700 LEU cc_start: 0.7743 (mm) cc_final: 0.7366 (mp) REVERT: C 764 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7170 (tmm) REVERT: C 1041 ASP cc_start: 0.6032 (m-30) cc_final: 0.5595 (m-30) REVERT: B 700 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8384 (mm) REVERT: B 734 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7457 (t-90) REVERT: B 743 MET cc_start: 0.8670 (ttt) cc_final: 0.8229 (ttp) REVERT: B 840 TYR cc_start: 0.8213 (m-10) cc_final: 0.7994 (m-80) REVERT: B 1075 ARG cc_start: 0.6747 (tpp-160) cc_final: 0.6354 (tpt170) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 0.2061 time to fit residues: 33.6848 Evaluate side-chains 119 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1078 GLU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 991 HIS ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6310 Z= 0.153 Angle : 0.590 12.777 8524 Z= 0.288 Chirality : 0.043 0.126 950 Planarity : 0.004 0.058 1086 Dihedral : 5.339 34.913 845 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.06 % Allowed : 21.73 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.29), residues: 760 helix: -0.43 (0.29), residues: 314 sheet: -1.06 (0.47), residues: 132 loop : -3.24 (0.29), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 770 HIS 0.004 0.001 HIS B1128 PHE 0.012 0.001 PHE C 736 TYR 0.011 0.001 TYR B1135 ARG 0.006 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 700 LEU cc_start: 0.7796 (mm) cc_final: 0.7385 (mp) REVERT: C 764 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7034 (tmm) REVERT: C 933 LEU cc_start: 0.8528 (tp) cc_final: 0.8309 (mp) REVERT: B 700 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8463 (mm) REVERT: B 734 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7512 (t-90) REVERT: B 840 TYR cc_start: 0.8256 (m-10) cc_final: 0.8031 (m-80) REVERT: B 1075 ARG cc_start: 0.6763 (tpp-160) cc_final: 0.6375 (tpt170) outliers start: 34 outliers final: 23 residues processed: 127 average time/residue: 0.1861 time to fit residues: 30.9347 Evaluate side-chains 128 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1078 GLU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6310 Z= 0.150 Angle : 0.581 11.867 8524 Z= 0.285 Chirality : 0.043 0.131 950 Planarity : 0.004 0.057 1086 Dihedral : 5.240 35.002 845 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.87 % Allowed : 22.92 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.29), residues: 760 helix: -0.18 (0.30), residues: 312 sheet: -0.83 (0.49), residues: 120 loop : -3.35 (0.27), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 770 HIS 0.005 0.001 HIS B 991 PHE 0.013 0.001 PHE B 736 TYR 0.010 0.001 TYR B1135 ARG 0.007 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: C 700 LEU cc_start: 0.7814 (mm) cc_final: 0.7392 (mp) REVERT: C 764 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7009 (tmm) REVERT: C 933 LEU cc_start: 0.8534 (tp) cc_final: 0.8331 (mp) REVERT: B 734 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7541 (t-90) REVERT: B 743 MET cc_start: 0.8696 (ttt) cc_final: 0.8344 (ttt) REVERT: B 1075 ARG cc_start: 0.6773 (tpp-160) cc_final: 0.6365 (tpt170) outliers start: 26 outliers final: 22 residues processed: 121 average time/residue: 0.1907 time to fit residues: 30.2532 Evaluate side-chains 122 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1078 GLU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 0.0470 chunk 41 optimal weight: 0.7980 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 739 ASN C 793 GLN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN B 991 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6310 Z= 0.250 Angle : 0.655 11.242 8524 Z= 0.324 Chirality : 0.045 0.137 950 Planarity : 0.004 0.055 1086 Dihedral : 5.727 37.576 845 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.06 % Allowed : 22.32 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.29), residues: 760 helix: -0.19 (0.30), residues: 302 sheet: -1.38 (0.43), residues: 148 loop : -3.19 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 973 HIS 0.007 0.001 HIS B 991 PHE 0.019 0.002 PHE B 736 TYR 0.011 0.002 TYR C 828 ARG 0.006 0.000 ARG C 988 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: C 764 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7191 (tmm) REVERT: C 933 LEU cc_start: 0.8603 (tp) cc_final: 0.8398 (mp) REVERT: B 974 LYS cc_start: 0.7241 (pttt) cc_final: 0.6895 (tptp) outliers start: 34 outliers final: 27 residues processed: 129 average time/residue: 0.1913 time to fit residues: 32.0620 Evaluate side-chains 128 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 986 ILE Chi-restraints excluded: chain C residue 1057 ARG Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 734 HIS ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6310 Z= 0.160 Angle : 0.608 11.680 8524 Z= 0.297 Chirality : 0.044 0.136 950 Planarity : 0.004 0.055 1086 Dihedral : 5.472 37.530 845 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.57 % Allowed : 24.11 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.30), residues: 760 helix: 0.07 (0.30), residues: 302 sheet: -1.16 (0.44), residues: 142 loop : -3.16 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 770 HIS 0.005 0.001 HIS B 991 PHE 0.019 0.001 PHE B 736 TYR 0.010 0.001 TYR B1135 ARG 0.005 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 700 LEU cc_start: 0.7920 (mm) cc_final: 0.7533 (mp) REVERT: C 764 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7230 (tmm) REVERT: C 933 LEU cc_start: 0.8598 (tp) cc_final: 0.8391 (mp) REVERT: B 734 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7668 (t-90) outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 0.1843 time to fit residues: 29.7213 Evaluate side-chains 123 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN B 991 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6310 Z= 0.233 Angle : 0.675 11.808 8524 Z= 0.323 Chirality : 0.045 0.142 950 Planarity : 0.004 0.054 1086 Dihedral : 5.719 38.586 845 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.57 % Allowed : 24.85 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.30), residues: 760 helix: -0.03 (0.30), residues: 302 sheet: -1.27 (0.44), residues: 146 loop : -3.15 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 973 HIS 0.005 0.001 HIS B1128 PHE 0.032 0.002 PHE C 954 TYR 0.010 0.002 TYR C 828 ARG 0.005 0.000 ARG C 994 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 764 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7303 (tmm) REVERT: B 734 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7638 (t-90) REVERT: B 1042 MET cc_start: 0.6956 (tpp) cc_final: 0.6322 (ttp) outliers start: 24 outliers final: 22 residues processed: 119 average time/residue: 0.1913 time to fit residues: 29.9862 Evaluate side-chains 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 810 VAL Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 1096 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 949 ASP Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 991 HIS Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 731 HIS C 797 GLN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131324 restraints weight = 8986.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131903 restraints weight = 7846.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132175 restraints weight = 6902.954| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6310 Z= 0.146 Angle : 0.619 11.829 8524 Z= 0.296 Chirality : 0.043 0.133 950 Planarity : 0.004 0.054 1086 Dihedral : 5.392 37.958 845 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.42 % Allowed : 24.55 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.30), residues: 760 helix: 0.19 (0.30), residues: 302 sheet: -1.09 (0.44), residues: 142 loop : -3.12 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1056 HIS 0.011 0.001 HIS B 991 PHE 0.017 0.001 PHE B 736 TYR 0.011 0.001 TYR B1135 ARG 0.005 0.000 ARG C 994 =============================================================================== Job complete usr+sys time: 1638.92 seconds wall clock time: 30 minutes 25.56 seconds (1825.56 seconds total)