Starting phenix.real_space_refine on Sat Dec 9 14:11:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e35_27857/12_2023/8e35_27857_neut_trim_updated.pdb" } resolution = 2.27 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= -0.002 sd= 0.717 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: 7 Type Number sf(0) Gaussians P 3019 5.49 5 S 28 5.16 5 C 34634 2.51 5 N 13701 2.21 5 O 22604 1.98 5 F 1 1.80 5 H 41853 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M ASP 154": "OD1" <-> "OD2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 191": "OD1" <-> "OD2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 108": "OD1" <-> "OD2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O GLU 31": "OE1" <-> "OE2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "P ASP 62": "OD1" <-> "OD2" Residue "P ASP 94": "OD1" <-> "OD2" 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: 115840 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93396 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 279, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1386, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 436, 'rna3p': 2461} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1385, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2460} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 100657 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3170 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "P" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1775 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 898 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 794 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'UCR': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P A C I2601 " occ=0.58 ... (60 atoms not shown) pdb=" H6 B C I2601 " occ=0.42 residue: pdb=" P A A I2602 " occ=0.58 ... (64 atoms not shown) pdb=" H2 B A I2602 " occ=0.42 residue: pdb=" P A G I2603 " occ=0.58 ... (66 atoms not shown) pdb=" H22B G I2603 " occ=0.42 Time building chain proxies: 64.61, per 1000 atoms: 0.56 Number of scatterers: 115840 At special positions: 0 Unit cell: (233.415, 224.77, 193.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 28 16.00 P 3019 15.00 F 1 9.00 O 22604 8.00 N 13701 7.00 C 34634 6.00 H 41853 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 66.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 34 helices and 12 sheets defined 29.5% alpha, 15.2% beta 579 base pairs and 1617 stacking pairs defined. Time for finding SS restraints: 49.19 Creating SS restraints... Processing helix chain 'K' and resid 10 through 17 removed outlier: 3.802A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 17' Processing helix chain 'K' and resid 30 through 35 removed outlier: 4.091A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' Processing helix chain 'K' and resid 131 through 136 removed outlier: 3.615A pdb=" N ILE K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Proline residue: K 136 - end of helix No H-bonds generated for 'chain 'K' and resid 131 through 136' Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.959A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.240A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 260 through 265 removed outlier: 6.939A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 265' Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.640A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 7.079A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.999A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.551A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.738A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 removed outlier: 3.537A pdb=" N ASP M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.538A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 3.764A pdb=" N ARG M 162 " --> pdb=" O PHE M 158 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.635A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.595A pdb=" N GLU M 197 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 72 removed outlier: 3.714A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'O' and resid 24 through 38 removed outlier: 4.042A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.364A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU O 109 " --> pdb=" O VAL O 105 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 122 removed outlier: 3.763A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.673A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 removed outlier: 3.632A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR P 39 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASN P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.958A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.998A pdb=" N HIS Q 19 " --> pdb=" O MET Q 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 16 Processing helix chain 'R' and resid 17 through 24 removed outlier: 4.264A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.862A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 162 through 165 removed outlier: 3.541A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 91 through 97 removed outlier: 4.167A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 44 through 47 removed outlier: 7.069A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 117 through 120 removed outlier: 4.093A pdb=" N LYS M 185 " --> pdb=" O ASP M 145 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR M 150 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.367A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.845A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR N 16 " --> pdb=" O VAL N 20 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.201A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.995A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'O' and resid 74 through 78 removed outlier: 3.572A pdb=" N THR O 78 " --> pdb=" O GLY O 83 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'P' and resid 2 through 8 removed outlier: 7.058A pdb=" N VAL P 106 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'P' and resid 73 through 79 removed outlier: 3.660A pdb=" N LYS P 73 " --> pdb=" O VAL P 106 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR P 100 " --> pdb=" O GLY P 79 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1357 hydrogen bonds 2014 hydrogen bond angles 0 basepair planarities 579 basepair parallelities 1619 stacking parallelities Total time for adding SS restraints: 113.27 Time building geometry restraints manager: 70.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 41851 1.03 - 1.23: 628 1.23 - 1.42: 42402 1.42 - 1.61: 38814 1.61 - 1.81: 54 Bond restraints: 123749 Sorted by residual: bond pdb=" C6 UCR I3001 " pdb=" N12 UCR I3001 " ideal model delta sigma weight residual 0.090 1.483 -1.393 2.00e-02 2.50e+03 4.85e+03 bond pdb=" C8 UCR I3001 " pdb=" C9 UCR I3001 " ideal model delta sigma weight residual 0.258 1.548 -1.290 2.00e-02 2.50e+03 4.16e+03 bond pdb=" C35 UCR I3001 " pdb=" C36 UCR I3001 " ideal model delta sigma weight residual 1.965 1.351 0.614 2.00e-02 2.50e+03 9.42e+02 bond pdb=" C37 UCR I3001 " pdb=" N9 UCR I3001 " ideal model delta sigma weight residual 1.809 1.343 0.466 2.00e-02 2.50e+03 5.42e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 ... (remaining 123744 not shown) Histogram of bond angle deviations from ideal: 68.83 - 82.05: 15 82.05 - 95.27: 0 95.27 - 108.49: 38748 108.49 - 121.71: 158472 121.71 - 134.93: 24365 Bond angle restraints: 221600 Sorted by residual: angle pdb=" O3' A I2062 " pdb=" C3' A I2062 " pdb=" H3' A I2062 " ideal model delta sigma weight residual 109.00 68.83 40.17 3.00e+00 1.11e-01 1.79e+02 angle pdb=" O3' A I 752 " pdb=" C3' A I 752 " pdb=" H3' A I 752 " ideal model delta sigma weight residual 109.00 68.90 40.10 3.00e+00 1.11e-01 1.79e+02 angle pdb=" C36 UCR I3001 " pdb=" C35 UCR I3001 " pdb=" C37 UCR I3001 " ideal model delta sigma weight residual 86.28 125.97 -39.69 3.00e+00 1.11e-01 1.75e+02 angle pdb=" O3' G I2508 " pdb=" C3' G I2508 " pdb=" H3' G I2508 " ideal model delta sigma weight residual 109.00 74.48 34.52 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C5' A I 751 " pdb=" C4' A I 751 " pdb=" H4' A I 751 " ideal model delta sigma weight residual 109.00 75.18 33.82 3.00e+00 1.11e-01 1.27e+02 ... (remaining 221595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 53287 35.85 - 71.70: 4932 71.70 - 107.55: 767 107.55 - 143.39: 6 143.39 - 179.24: 13 Dihedral angle restraints: 59005 sinusoidal: 55355 harmonic: 3650 Sorted by residual: dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.24 -179.24 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4'B C I2601 " pdb=" C1'B C I2601 " pdb=" N1 B C I2601 " pdb=" C2 B C I2601 " ideal model delta sinusoidal sigma weight residual 232.00 58.78 173.22 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 41.73 -169.73 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 59002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.405: 16437 0.405 - 0.809: 4 0.809 - 1.214: 1 1.214 - 1.619: 0 1.619 - 2.024: 1 Chirality restraints: 16443 Sorted by residual: chirality pdb=" C8 UCR I3001 " pdb=" C7 UCR I3001 " pdb=" C9 UCR I3001 " pdb=" O4 UCR I3001 " both_signs ideal model delta sigma weight residual False 0.53 2.56 -2.02 2.00e-01 2.50e+01 1.02e+02 chirality pdb=" C1'B A I2602 " pdb=" O4'B A I2602 " pdb=" C2'B A I2602 " pdb=" N9 B A I2602 " both_signs ideal model delta sigma weight residual False 2.44 1.59 0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" C3' G I2508 " pdb=" C4' G I2508 " pdb=" O3' G I2508 " pdb=" C2' G I2508 " both_signs ideal model delta sigma weight residual False -2.48 -1.68 -0.79 2.00e-01 2.50e+01 1.58e+01 ... (remaining 16440 not shown) Planarity restraints: 8176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.031 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' OMC I2498 " 0.454 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.753 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.592 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.579 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.225 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.894 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.204 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.041 2.00e-02 2.50e+03 5.69e-01 7.27e+03 pdb=" C4' 2MG I2445 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.605 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.573 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.918 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.233 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.858 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.041 2.00e-02 2.50e+03 5.68e-01 7.25e+03 pdb=" C4' OMG I2251 " 0.427 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.603 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.571 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.203 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.919 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.234 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.855 2.00e-02 2.50e+03 ... (remaining 8173 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 6019 2.21 - 2.81: 154621 2.81 - 3.40: 258331 3.40 - 4.00: 411463 4.00 - 4.60: 583866 Nonbonded interactions: 1414300 Sorted by model distance: nonbonded pdb=" H41 C I1838 " pdb=" OP2 A I1899 " model vdw 1.611 1.850 nonbonded pdb="HO2' G I 141 " pdb=" O4' A I 142 " model vdw 1.647 1.850 nonbonded pdb=" OP2 G I1288 " pdb=" H22 G I1288 " model vdw 1.655 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.656 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.659 1.850 ... (remaining 1414295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.520 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: 0.840 Extract box with map and model: 28.590 Check model and map are aligned: 1.110 Set scattering table: 0.690 Process input model: 382.160 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.280 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:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 429.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 1.393 81896 Z= 0.698 Angle : 0.455 39.695 125737 Z= 0.210 Chirality : 0.031 2.024 16443 Planarity : 0.022 0.599 4645 Dihedral : 21.841 179.242 48231 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1163 helix: 1.45 (0.36), residues: 240 sheet: 1.03 (0.40), residues: 171 loop : -0.32 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP M 60 HIS 0.002 0.001 HIS L 35 PHE 0.005 0.001 PHE K 240 TYR 0.005 0.001 TYR L 58 ARG 0.003 0.000 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 255 average time/residue: 3.1427 time to fit residues: 1004.7556 Evaluate side-chains 168 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 3.123 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 107 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 376 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 156 ASN N 58 ASN N 126 ASN N 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 81896 Z= 0.343 Angle : 0.729 17.563 125737 Z= 0.387 Chirality : 0.042 1.131 16443 Planarity : 0.007 0.135 4645 Dihedral : 21.875 178.042 45991 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.38 % Allowed : 11.89 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1163 helix: 1.05 (0.34), residues: 255 sheet: 0.69 (0.40), residues: 157 loop : -0.90 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.009 0.002 HIS K 230 PHE 0.011 0.002 PHE N 127 TYR 0.012 0.002 TYR K 103 ARG 0.005 0.001 ARG K 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 3.035 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 172 average time/residue: 3.2791 time to fit residues: 705.6638 Evaluate side-chains 166 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 1.3016 time to fit residues: 8.6120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 302 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 136 GLN N 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 81896 Z= 0.231 Angle : 0.597 17.401 125737 Z= 0.329 Chirality : 0.037 0.976 16443 Planarity : 0.006 0.132 4645 Dihedral : 21.840 179.260 45991 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.49 % Allowed : 12.21 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1163 helix: 1.19 (0.34), residues: 255 sheet: 0.58 (0.38), residues: 164 loop : -1.04 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.012 0.001 PHE K 240 TYR 0.009 0.001 TYR O 75 ARG 0.004 0.000 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 3.033 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 170 average time/residue: 3.3114 time to fit residues: 703.9987 Evaluate side-chains 169 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 165 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.5024 time to fit residues: 6.9294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 378 optimal weight: 7.9990 chunk 401 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN N 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 81896 Z= 0.357 Angle : 0.691 17.395 125737 Z= 0.373 Chirality : 0.042 1.000 16443 Planarity : 0.007 0.141 4645 Dihedral : 21.892 179.102 45991 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 1.38 % Allowed : 12.85 % Favored : 85.77 % 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: -0.58 (0.23), residues: 1163 helix: 1.14 (0.34), residues: 256 sheet: 0.53 (0.41), residues: 137 loop : -1.16 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.008 0.002 HIS K 230 PHE 0.013 0.001 PHE K 240 TYR 0.011 0.001 TYR K 103 ARG 0.005 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 3.021 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 178 average time/residue: 3.3428 time to fit residues: 742.8227 Evaluate side-chains 162 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.8937 time to fit residues: 4.0547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 342 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN N 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 81896 Z= 0.293 Angle : 0.645 17.324 125737 Z= 0.356 Chirality : 0.040 0.994 16443 Planarity : 0.007 0.136 4645 Dihedral : 21.905 178.807 45991 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 0.96 % Allowed : 14.12 % Favored : 84.93 % 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: -0.70 (0.23), residues: 1163 helix: 1.14 (0.34), residues: 256 sheet: 0.33 (0.40), residues: 144 loop : -1.27 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.007 0.002 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.009 0.001 TYR K 103 ARG 0.003 0.000 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 2.751 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 165 average time/residue: 3.3754 time to fit residues: 696.7575 Evaluate side-chains 161 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.8975 time to fit residues: 4.0506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 6.9990 chunk 361 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 8.9990 chunk 333 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 210 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN N 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 81896 Z= 0.319 Angle : 0.656 17.332 125737 Z= 0.359 Chirality : 0.041 0.988 16443 Planarity : 0.007 0.137 4645 Dihedral : 21.934 178.659 45991 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 1.17 % Allowed : 13.06 % Favored : 85.77 % 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: -0.80 (0.23), residues: 1163 helix: 1.06 (0.34), residues: 261 sheet: 0.20 (0.39), residues: 154 loop : -1.36 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.007 0.002 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR K 103 ARG 0.004 0.000 ARG K 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 3.090 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 168 average time/residue: 3.1602 time to fit residues: 664.9238 Evaluate side-chains 159 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 3.123 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.3233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 0.0980 chunk 45 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 81896 Z= 0.210 Angle : 0.620 17.385 125737 Z= 0.345 Chirality : 0.038 1.014 16443 Planarity : 0.007 0.135 4645 Dihedral : 21.933 178.631 45991 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 0.64 % Allowed : 14.01 % Favored : 85.35 % 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: -0.78 (0.23), residues: 1163 helix: 1.12 (0.34), residues: 261 sheet: 0.17 (0.39), residues: 155 loop : -1.35 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.013 0.001 PHE K 240 TYR 0.009 0.001 TYR K 103 ARG 0.002 0.000 ARG K 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 3.020 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 160 average time/residue: 3.1890 time to fit residues: 639.2714 Evaluate side-chains 159 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.2973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 314 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN N 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 81896 Z= 0.293 Angle : 0.641 17.413 125737 Z= 0.354 Chirality : 0.040 1.012 16443 Planarity : 0.007 0.136 4645 Dihedral : 21.935 178.690 45991 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 1.06 % Allowed : 13.48 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1163 helix: 1.07 (0.34), residues: 261 sheet: 0.30 (0.39), residues: 152 loop : -1.34 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.006 0.002 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.010 0.001 TYR K 103 ARG 0.004 0.000 ARG M 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 170 average time/residue: 3.0821 time to fit residues: 659.9798 Evaluate side-chains 171 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 3.039 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.4971 time to fit residues: 6.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 352 optimal weight: 8.9990 chunk 371 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN ** O 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 81896 Z= 0.271 Angle : 0.635 17.413 125737 Z= 0.352 Chirality : 0.039 1.000 16443 Planarity : 0.007 0.136 4645 Dihedral : 21.933 178.689 45991 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.06 % Allowed : 13.59 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1163 helix: 1.11 (0.35), residues: 261 sheet: 0.35 (0.39), residues: 151 loop : -1.35 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.006 0.002 HIS K 230 PHE 0.015 0.001 PHE K 240 TYR 0.010 0.001 TYR K 103 ARG 0.004 0.000 ARG M 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 3.043 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 169 average time/residue: 3.1973 time to fit residues: 682.3468 Evaluate side-chains 169 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 2.0982 time to fit residues: 5.2503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 4.9990 chunk 394 optimal weight: 0.3980 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 380 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 81896 Z= 0.243 Angle : 0.623 17.478 125737 Z= 0.348 Chirality : 0.039 0.996 16443 Planarity : 0.007 0.135 4645 Dihedral : 21.934 178.691 45991 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.50 % Rotamer: Outliers : 0.96 % Allowed : 13.69 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1163 helix: 1.12 (0.35), residues: 261 sheet: 0.35 (0.39), residues: 151 loop : -1.35 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.015 0.001 PHE K 240 TYR 0.009 0.001 TYR K 103 ARG 0.005 0.000 ARG M 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 169 average time/residue: 3.1893 time to fit residues: 678.0325 Evaluate side-chains 170 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 3.057 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 2.3315 time to fit residues: 8.5369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 338 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.056601 restraints weight = 248600.335| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 0.57 r_work: 0.2441 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 81896 Z= 0.333 Angle : 0.675 17.332 125737 Z= 0.369 Chirality : 0.041 1.006 16443 Planarity : 0.007 0.140 4645 Dihedral : 21.975 179.085 45991 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.93 % Favored : 93.98 % Rotamer: Outliers : 0.74 % Allowed : 13.91 % Favored : 85.35 % 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: -0.81 (0.23), residues: 1163 helix: 1.02 (0.34), residues: 261 sheet: 0.32 (0.40), residues: 151 loop : -1.37 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.007 0.002 HIS K 230 PHE 0.013 0.001 PHE K 240 TYR 0.011 0.001 TYR K 103 ARG 0.004 0.001 ARG M 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33113.38 seconds wall clock time: 568 minutes 3.19 seconds (34083.19 seconds total)