Starting phenix.real_space_refine on Sun Dec 10 17:41:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/12_2023/6pwf_20507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/12_2023/6pwf_20507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/12_2023/6pwf_20507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/12_2023/6pwf_20507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/12_2023/6pwf_20507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/12_2023/6pwf_20507.pdb" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 27 5.16 5 C 8674 2.51 5 N 2812 2.21 5 O 3392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 19": "NH1" <-> "NH2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "K ARG 228": "NH1" <-> "NH2" Residue "K ARG 251": "NH1" <-> "NH2" Residue "K ARG 272": "NH1" <-> "NH2" Residue "K ARG 279": "NH1" <-> "NH2" Residue "K ARG 297": "NH1" <-> "NH2" Residue "K ARG 317": "NH1" <-> "NH2" Residue "K ARG 330": "NH1" <-> "NH2" Residue "K PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 460": "NH1" <-> "NH2" Residue "K TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 500": "NH1" <-> "NH2" Residue "K ARG 516": "NH1" <-> "NH2" Residue "K ARG 528": "NH1" <-> "NH2" Residue "K TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 553": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15197 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 671 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 723 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 807 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3263 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 15, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 463 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 306 Time building chain proxies: 8.07, per 1000 atoms: 0.53 Number of scatterers: 15197 At special positions: 0 Unit cell: (111.72, 149.52, 115.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 292 15.00 O 3392 8.00 N 2812 7.00 C 8674 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: 7.39 Conformation dependent library (CDL) restraints added in 2.0 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 53.5% alpha, 3.6% beta 79 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 5.85 Creating SS restraints... Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.900A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.589A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.701A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.105A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.853A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 removed outlier: 4.014A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.647A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.080A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 removed outlier: 3.813A pdb=" N ARG C 34 " --> pdb=" O HIS C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 67 removed outlier: 3.565A pdb=" N ALA C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 78 through 87 removed outlier: 3.947A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.757A pdb=" N LEU C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.650A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 61 removed outlier: 3.620A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 81 removed outlier: 4.794A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 97 removed outlier: 3.780A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 4.127A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.900A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 88 through 112 removed outlier: 3.590A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 120 through 133 removed outlier: 3.701A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.881A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.744A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.353A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.737A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.894A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 36 removed outlier: 4.300A pdb=" N ARG G 34 " --> pdb=" O HIS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 removed outlier: 3.857A pdb=" N ALA G 52 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 78 through 89 removed outlier: 3.885A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.782A pdb=" N LYS G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 46 removed outlier: 3.698A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 82 removed outlier: 3.898A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 112 removed outlier: 3.561A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 120 removed outlier: 4.705A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 191 Processing helix chain 'K' and resid 193 through 203 removed outlier: 3.787A pdb=" N SER K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU K 199 " --> pdb=" O TRP K 195 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN K 202 " --> pdb=" O SER K 198 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY K 203 " --> pdb=" O LEU K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 225 removed outlier: 3.894A pdb=" N SER K 222 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 230 removed outlier: 4.228A pdb=" N HIS K 229 " --> pdb=" O GLY K 225 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE K 230 " --> pdb=" O TYR K 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 225 through 230' Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 245 through 257 removed outlier: 3.816A pdb=" N TRP K 249 " --> pdb=" O THR K 245 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS K 250 " --> pdb=" O LEU K 246 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU K 254 " --> pdb=" O LYS K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 273 removed outlier: 4.197A pdb=" N HIS K 273 " --> pdb=" O LYS K 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 278 removed outlier: 3.676A pdb=" N ASP K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 297 removed outlier: 4.032A pdb=" N LEU K 296 " --> pdb=" O TYR K 292 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG K 297 " --> pdb=" O GLU K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 320 removed outlier: 3.795A pdb=" N LYS K 319 " --> pdb=" O HIS K 316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN K 320 " --> pdb=" O ARG K 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 316 through 320' Processing helix chain 'K' and resid 325 through 330 Processing helix chain 'K' and resid 349 through 360 removed outlier: 3.743A pdb=" N TRP K 353 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU K 355 " --> pdb=" O GLU K 351 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 360 " --> pdb=" O LEU K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 368 removed outlier: 4.109A pdb=" N ASP K 368 " --> pdb=" O PHE K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 374 removed outlier: 3.738A pdb=" N PHE K 374 " --> pdb=" O ASP K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 393 Processing helix chain 'K' and resid 400 through 404 Processing helix chain 'K' and resid 430 through 436 Processing helix chain 'K' and resid 453 through 460 removed outlier: 3.852A pdb=" N ARG K 460 " --> pdb=" O VAL K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 490 through 501 removed outlier: 3.584A pdb=" N LEU K 494 " --> pdb=" O LYS K 490 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS K 496 " --> pdb=" O ILE K 492 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS K 499 " --> pdb=" O ASP K 495 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG K 500 " --> pdb=" O LYS K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 526 removed outlier: 3.729A pdb=" N LEU K 518 " --> pdb=" O MET K 514 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE K 520 " --> pdb=" O ARG K 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP K 523 " --> pdb=" O ASP K 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS K 525 " --> pdb=" O LEU K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 552 removed outlier: 3.547A pdb=" N ILE K 545 " --> pdb=" O HIS K 541 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA K 547 " --> pdb=" O ASP K 543 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU K 550 " --> pdb=" O ALA K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 595 Processing helix chain 'K' and resid 596 through 599 Processing helix chain 'K' and resid 619 through 630 Processing helix chain 'K' and resid 634 through 640 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.330A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.788A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.875A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.965A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.654A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 207 through 209 removed outlier: 5.972A pdb=" N GLU K 308 " --> pdb=" O ASN K 336 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU K 338 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE K 310 " --> pdb=" O LEU K 338 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE K 340 " --> pdb=" O ILE K 310 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE K 312 " --> pdb=" O ILE K 340 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU K 238 " --> pdb=" O ILE K 311 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP K 313 " --> pdb=" O LEU K 238 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA K 240 " --> pdb=" O ASP K 313 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N HIS K 237 " --> pdb=" O CYS K 288 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR K 290 " --> pdb=" O HIS K 237 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL K 239 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 532 through 534 removed outlier: 6.902A pdb=" N VAL K 508 " --> pdb=" O PHE K 561 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 184 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 79 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2513 1.33 - 1.45: 5206 1.45 - 1.57: 7718 1.57 - 1.69: 582 1.69 - 1.81: 47 Bond restraints: 16066 Sorted by residual: bond pdb=" C1' DA I -73 " pdb=" N9 DA I -73 " ideal model delta sigma weight residual 1.460 1.405 0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C3' DG J 25 " pdb=" O3' DG J 25 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.53e+00 bond pdb=" C3' DG J -34 " pdb=" O3' DG J -34 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.94e+00 bond pdb=" C3' DA I -3 " pdb=" O3' DA I -3 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.87e+00 bond pdb=" C3' DG I -8 " pdb=" O3' DG I -8 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.29e+00 ... (remaining 16061 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.46: 1181 104.46 - 111.86: 8258 111.86 - 119.26: 5510 119.26 - 126.67: 7145 126.67 - 134.07: 902 Bond angle restraints: 22996 Sorted by residual: angle pdb=" C ARG B 19 " pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 120.79 129.01 -8.22 1.39e+00 5.18e-01 3.50e+01 angle pdb=" N VAL D 95 " pdb=" CA VAL D 95 " pdb=" C VAL D 95 " ideal model delta sigma weight residual 113.42 107.02 6.40 1.17e+00 7.31e-01 2.99e+01 angle pdb=" N VAL H 95 " pdb=" CA VAL H 95 " pdb=" C VAL H 95 " ideal model delta sigma weight residual 112.96 107.50 5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ILE C 78 " pdb=" C ILE C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 117.57 122.21 -4.64 1.01e+00 9.80e-01 2.11e+01 angle pdb=" C LEU K 345 " pdb=" N GLN K 346 " pdb=" CA GLN K 346 " ideal model delta sigma weight residual 120.90 126.75 -5.85 1.41e+00 5.03e-01 1.72e+01 ... (remaining 22991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 7439 35.28 - 70.56: 1390 70.56 - 105.83: 49 105.83 - 141.11: 2 141.11 - 176.39: 8 Dihedral angle restraints: 8888 sinusoidal: 5378 harmonic: 3510 Sorted by residual: dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta harmonic sigma weight residual 180.00 146.87 33.13 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA HIS K 465 " pdb=" C HIS K 465 " pdb=" N PRO K 466 " pdb=" CA PRO K 466 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ALA K 369 " pdb=" C ALA K 369 " pdb=" N PHE K 370 " pdb=" CA PHE K 370 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 8885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2012 0.063 - 0.126: 545 0.126 - 0.189: 76 0.189 - 0.253: 6 0.253 - 0.316: 1 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CB ILE K 310 " pdb=" CA ILE K 310 " pdb=" CG1 ILE K 310 " pdb=" CG2 ILE K 310 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CG LEU H 99 " pdb=" CB LEU H 99 " pdb=" CD1 LEU H 99 " pdb=" CD2 LEU H 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C3' DA I -3 " pdb=" C4' DA I -3 " pdb=" O3' DA I -3 " pdb=" C2' DA I -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2637 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 476 " -0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO K 477 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO K 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 477 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 360 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO K 361 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO K 361 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO K 361 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 393 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO K 394 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO K 394 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 394 " -0.038 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 268 2.63 - 3.20: 12437 3.20 - 3.77: 25605 3.77 - 4.33: 33907 4.33 - 4.90: 49504 Nonbonded interactions: 121721 Sorted by model distance: nonbonded pdb=" OP1 DA J 23 " pdb=" ND2 ASN K 588 " model vdw 2.066 2.520 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.265 2.440 nonbonded pdb=" O TYR C 38 " pdb=" OG SER D 75 " model vdw 2.288 2.440 nonbonded pdb=" OD1 ASP K 536 " pdb=" OG1 THR K 539 " model vdw 2.289 2.440 nonbonded pdb=" N2 DG I -21 " pdb=" O2 DC J 22 " model vdw 2.295 2.520 ... (remaining 121716 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 'E' } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 121) } 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=0.00 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.710 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 47.520 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.009 0.085 16066 Z= 0.535 Angle : 1.013 12.731 22996 Z= 0.570 Chirality : 0.056 0.316 2640 Planarity : 0.008 0.085 1909 Dihedral : 26.976 176.386 6620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.10 (0.16), residues: 1188 helix: -4.62 (0.09), residues: 644 sheet: -2.34 (0.67), residues: 48 loop : -3.19 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP K 427 HIS 0.011 0.003 HIS K 389 PHE 0.035 0.005 PHE K 613 TYR 0.040 0.004 TYR K 583 ARG 0.017 0.002 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.3673 time to fit residues: 135.2522 Evaluate side-chains 154 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 37 ASN D 81 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN K 389 HIS K 487 ASN K 513 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16066 Z= 0.262 Angle : 0.689 6.808 22996 Z= 0.401 Chirality : 0.042 0.231 2640 Planarity : 0.006 0.063 1909 Dihedral : 31.499 176.804 4513 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -5.01 (0.20), residues: 1188 helix: -3.67 (0.14), residues: 662 sheet: -1.71 (0.78), residues: 48 loop : -2.71 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 256 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.002 PHE K 332 TYR 0.019 0.002 TYR K 467 ARG 0.005 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2914 time to fit residues: 93.7512 Evaluate side-chains 151 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 GLN ** K 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16066 Z= 0.304 Angle : 0.704 7.242 22996 Z= 0.401 Chirality : 0.043 0.206 2640 Planarity : 0.005 0.048 1909 Dihedral : 31.239 179.974 4513 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 0.11 % Allowed : 4.30 % Favored : 95.59 % 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: -4.39 (0.21), residues: 1188 helix: -3.14 (0.16), residues: 645 sheet: -1.85 (0.65), residues: 63 loop : -2.48 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 587 HIS 0.005 0.001 HIS K 316 PHE 0.019 0.002 PHE K 332 TYR 0.051 0.003 TYR D 80 ARG 0.009 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.219 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2869 time to fit residues: 80.5044 Evaluate side-chains 146 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 37 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16066 Z= 0.188 Angle : 0.588 6.032 22996 Z= 0.343 Chirality : 0.038 0.171 2640 Planarity : 0.004 0.048 1909 Dihedral : 30.851 179.117 4513 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -3.75 (0.22), residues: 1188 helix: -2.63 (0.17), residues: 658 sheet: -1.37 (0.68), residues: 63 loop : -2.17 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 307 HIS 0.003 0.001 HIS D 106 PHE 0.016 0.001 PHE G 24 TYR 0.016 0.001 TYR C 56 ARG 0.007 0.001 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2903 time to fit residues: 85.5506 Evaluate side-chains 150 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS K 237 HIS K 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 16066 Z= 0.475 Angle : 0.823 8.888 22996 Z= 0.455 Chirality : 0.049 0.221 2640 Planarity : 0.006 0.046 1909 Dihedral : 31.301 179.271 4513 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -3.98 (0.22), residues: 1188 helix: -2.79 (0.17), residues: 638 sheet: -1.68 (0.67), residues: 63 loop : -2.35 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 307 HIS 0.007 0.002 HIS K 389 PHE 0.029 0.004 PHE K 511 TYR 0.032 0.003 TYR K 467 ARG 0.007 0.001 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2800 time to fit residues: 74.2391 Evaluate side-chains 133 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16066 Z= 0.176 Angle : 0.588 5.730 22996 Z= 0.342 Chirality : 0.038 0.169 2640 Planarity : 0.004 0.048 1909 Dihedral : 30.715 179.047 4513 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.11 % Allowed : 1.21 % Favored : 98.68 % 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: -3.34 (0.23), residues: 1188 helix: -2.24 (0.18), residues: 651 sheet: -1.69 (0.67), residues: 61 loop : -2.02 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 307 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.001 PHE K 511 TYR 0.019 0.002 TYR K 486 ARG 0.007 0.001 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2834 time to fit residues: 76.9898 Evaluate side-chains 142 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 541 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 16066 Z= 0.474 Angle : 0.794 8.789 22996 Z= 0.438 Chirality : 0.047 0.239 2640 Planarity : 0.006 0.044 1909 Dihedral : 31.088 179.800 4513 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -3.53 (0.22), residues: 1188 helix: -2.42 (0.18), residues: 626 sheet: -1.79 (0.64), residues: 63 loop : -2.12 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 307 HIS 0.007 0.002 HIS D 106 PHE 0.021 0.003 PHE K 332 TYR 0.031 0.003 TYR D 80 ARG 0.010 0.001 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2693 time to fit residues: 68.7773 Evaluate side-chains 134 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.0070 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16066 Z= 0.193 Angle : 0.610 7.366 22996 Z= 0.347 Chirality : 0.039 0.191 2640 Planarity : 0.004 0.054 1909 Dihedral : 30.765 178.614 4513 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.23), residues: 1188 helix: -2.17 (0.18), residues: 654 sheet: -1.72 (0.62), residues: 66 loop : -1.90 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 587 HIS 0.004 0.001 HIS K 600 PHE 0.014 0.001 PHE K 561 TYR 0.023 0.002 TYR H 37 ARG 0.006 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2672 time to fit residues: 74.3303 Evaluate side-chains 142 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS F 25 ASN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16066 Z= 0.192 Angle : 0.592 8.268 22996 Z= 0.340 Chirality : 0.038 0.180 2640 Planarity : 0.004 0.046 1909 Dihedral : 30.634 179.179 4513 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.24), residues: 1188 helix: -1.81 (0.19), residues: 645 sheet: -1.59 (0.63), residues: 66 loop : -1.73 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 307 HIS 0.012 0.001 HIS K 600 PHE 0.021 0.001 PHE K 561 TYR 0.017 0.001 TYR C 56 ARG 0.008 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2843 time to fit residues: 73.3206 Evaluate side-chains 137 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 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 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 44 GLN K 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16066 Z= 0.331 Angle : 0.709 12.014 22996 Z= 0.395 Chirality : 0.044 0.322 2640 Planarity : 0.005 0.045 1909 Dihedral : 30.819 179.724 4513 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.11 % Allowed : 0.66 % Favored : 99.23 % 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: -3.00 (0.23), residues: 1188 helix: -2.03 (0.19), residues: 631 sheet: -1.54 (0.65), residues: 63 loop : -1.78 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K 307 HIS 0.010 0.001 HIS K 600 PHE 0.020 0.002 PHE K 561 TYR 0.021 0.002 TYR D 34 ARG 0.009 0.001 ARG G 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2613 time to fit residues: 65.4076 Evaluate side-chains 124 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143905 restraints weight = 28617.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143436 restraints weight = 37916.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143682 restraints weight = 35259.430| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16066 Z= 0.176 Angle : 0.590 10.647 22996 Z= 0.336 Chirality : 0.038 0.217 2640 Planarity : 0.004 0.047 1909 Dihedral : 30.530 179.775 4513 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.78 % 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: -2.58 (0.24), residues: 1188 helix: -1.65 (0.20), residues: 642 sheet: -1.52 (0.63), residues: 66 loop : -1.61 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 307 HIS 0.011 0.001 HIS K 600 PHE 0.021 0.001 PHE K 561 TYR 0.014 0.001 TYR C 56 ARG 0.009 0.000 ARG G 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.30 seconds wall clock time: 47 minutes 58.36 seconds (2878.36 seconds total)