Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 16:44:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/10_2023/6pwf_20507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/10_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_20507/10_2023/6pwf_20507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/10_2023/6pwf_20507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/10_2023/6pwf_20507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/10_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-1.21rc1-5097/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: 8.38, per 1000 atoms: 0.55 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: 7.92 Conformation dependent library (CDL) restraints added in 1.5 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: 6.34 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: 6.51 Time building geometry restraints manager: 8.19 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: 7233 35.28 - 70.56: 1340 70.56 - 105.83: 49 105.83 - 141.11: 2 141.11 - 176.39: 8 Dihedral angle restraints: 8632 sinusoidal: 5122 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 8629 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.840 Check model and map are aligned: 0.250 Set scattering table: 0.120 Process input model: 48.480 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.090 ------------------------------------------------------------------------------- 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 : 26.908 176.386 6364 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 *********************** 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 : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.3732 time to fit residues: 137.5166 Evaluate side-chains 154 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6328 ------------------------------------------------------------------------------- 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: 9.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN H 64 ASN ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7342 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16066 Z= 0.261 Angle : 0.687 6.044 22996 Z= 0.401 Chirality : 0.042 0.222 2640 Planarity : 0.005 0.061 1909 Dihedral : 31.798 176.437 4257 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -4.88 (0.20), residues: 1188 helix: -3.63 (0.14), residues: 656 sheet: -1.70 (0.77), residues: 48 loop : -2.58 (0.27), residues: 484 *********************** 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 222 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2885 time to fit residues: 91.8894 Evaluate side-chains 152 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6617 ------------------------------------------------------------------------------- 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: 0.5980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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** K 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16066 Z= 0.217 Angle : 0.618 5.882 22996 Z= 0.360 Chirality : 0.039 0.200 2640 Planarity : 0.004 0.048 1909 Dihedral : 31.422 179.072 4257 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -4.26 (0.21), residues: 1188 helix: -3.06 (0.16), residues: 652 sheet: -1.32 (0.81), residues: 48 loop : -2.43 (0.27), residues: 488 *********************** 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 202 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.207 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2818 time to fit residues: 82.9023 Evaluate side-chains 149 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5638 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 0.0980 chunk 68 optimal weight: 0.0470 chunk 124 optimal weight: 0.5980 chunk 37 optimal weight: 0.0020 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** F 25 ASN ** 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: 0.7156 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16066 Z= 0.166 Angle : 0.563 7.368 22996 Z= 0.329 Chirality : 0.037 0.150 2640 Planarity : 0.004 0.048 1909 Dihedral : 30.964 179.763 4257 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -3.54 (0.22), residues: 1188 helix: -2.47 (0.18), residues: 660 sheet: -1.03 (0.77), residues: 53 loop : -2.09 (0.28), residues: 475 *********************** 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 209 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2837 time to fit residues: 86.6691 Evaluate side-chains 160 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5916 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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** D 81 ASN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16066 Z= 0.162 Angle : 0.549 6.711 22996 Z= 0.319 Chirality : 0.037 0.172 2640 Planarity : 0.004 0.044 1909 Dihedral : 30.799 179.719 4257 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.23), residues: 1188 helix: -2.03 (0.19), residues: 657 sheet: -1.22 (0.65), residues: 75 loop : -1.81 (0.29), residues: 456 *********************** 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 197 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.204 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2636 time to fit residues: 76.9866 Evaluate side-chains 151 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4636 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16066 Z= 0.240 Angle : 0.596 6.017 22996 Z= 0.341 Chirality : 0.039 0.128 2640 Planarity : 0.004 0.051 1909 Dihedral : 30.895 179.371 4257 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % 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: -2.90 (0.23), residues: 1188 helix: -1.87 (0.19), residues: 653 sheet: -1.27 (0.67), residues: 73 loop : -1.88 (0.28), residues: 462 *********************** 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 183 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.342 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2580 time to fit residues: 71.0523 Evaluate side-chains 145 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6871 ------------------------------------------------------------------------------- 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: 7.9990 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 HIS K 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4540 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= 0.495 Angle : 0.862 10.760 22996 Z= 0.474 Chirality : 0.050 0.218 2640 Planarity : 0.007 0.076 1909 Dihedral : 31.491 179.056 4257 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % 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: -3.55 (0.22), residues: 1188 helix: -2.45 (0.18), residues: 621 sheet: -1.56 (0.65), residues: 72 loop : -2.15 (0.27), residues: 495 *********************** 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 179 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.303 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2815 time to fit residues: 74.9697 Evaluate side-chains 131 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7002 ------------------------------------------------------------------------------- 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: 0.7980 chunk 82 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 75 HIS E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16066 Z= 0.202 Angle : 0.612 6.854 22996 Z= 0.351 Chirality : 0.039 0.140 2640 Planarity : 0.004 0.058 1909 Dihedral : 31.124 178.803 4257 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.11 % Allowed : 0.77 % Favored : 99.12 % 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: -3.09 (0.23), residues: 1188 helix: -2.07 (0.18), residues: 649 sheet: -1.54 (0.63), residues: 72 loop : -1.86 (0.29), residues: 467 *********************** 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 181 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2743 time to fit residues: 72.9241 Evaluate side-chains 142 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6466 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 25 ASN K 600 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5041 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= 0.199 Angle : 0.601 8.852 22996 Z= 0.344 Chirality : 0.038 0.148 2640 Planarity : 0.004 0.058 1909 Dihedral : 30.999 179.302 4257 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.11 % Allowed : 0.44 % Favored : 99.45 % 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: -2.64 (0.24), residues: 1188 helix: -1.67 (0.19), residues: 633 sheet: -1.37 (0.65), residues: 72 loop : -1.70 (0.29), residues: 483 *********************** 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 : 1.311 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2774 time to fit residues: 72.9255 Evaluate side-chains 137 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6367 ------------------------------------------------------------------------------- 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: 5.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 0.0270 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16066 Z= 0.228 Angle : 0.626 8.848 22996 Z= 0.354 Chirality : 0.039 0.154 2640 Planarity : 0.004 0.058 1909 Dihedral : 30.934 179.580 4257 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.11 % Allowed : 0.44 % Favored : 99.45 % 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: -2.51 (0.24), residues: 1188 helix: -1.62 (0.19), residues: 637 sheet: -1.34 (0.64), residues: 72 loop : -1.56 (0.29), residues: 479 ********************** 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 175 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.336 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2611 time to fit residues: 68.3649 Evaluate side-chains 138 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5692 ------------------------------------------------------------------------------- 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: 10.0000 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.161787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144920 restraints weight = 28381.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144624 restraints weight = 39861.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144838 restraints weight = 35074.844| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16066 Z= 0.180 Angle : 0.582 8.923 22996 Z= 0.332 Chirality : 0.037 0.134 2640 Planarity : 0.004 0.057 1909 Dihedral : 30.756 179.560 4257 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -2.28 (0.24), residues: 1188 helix: -1.42 (0.20), residues: 627 sheet: -1.37 (0.64), residues: 72 loop : -1.45 (0.29), residues: 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.71 seconds wall clock time: 46 minutes 49.59 seconds (2809.59 seconds total)