Starting phenix.real_space_refine on Sat Dec 9 13:57:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e42_27877/12_2023/8e42_27877_neut_trim_updated.pdb" } resolution = 2.29 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= -0.028 sd= 0.674 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: 6 Type Number sf(0) Gaussians P 3016 5.49 5 S 29 5.16 5 C 34597 2.51 5 N 13678 2.21 5 O 22583 1.98 5 H 41815 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 98": "OD1" <-> "OD2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "N ASP 18": "OD1" <-> "OD2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 99": "OE1" <-> "OE2" Residue "N ASP 181": "OD1" <-> "OD2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O ASP 49": "OD1" <-> "OD2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 90": "OE1" <-> "OE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "O ASP 141": "OD1" <-> "OD2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "Q GLU 36": "OE1" <-> "OE2" 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: 115718 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1385, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 438, 'rna3p': 2459} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3805 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 46} Link IDs: {'rna2p': 16, 'rna3p': 101} 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'MUL': 1, 'ZIT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 39.47, per 1000 atoms: 0.34 Number of scatterers: 115718 At special positions: 0 Unit cell: (229.91, 222.44, 190.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 3016 15.00 O 22583 8.00 N 13678 7.00 C 34597 6.00 H 41815 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: 83.27 Conformation dependent library (CDL) restraints added in 3.5 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: 35 helices and 16 sheets defined 30.0% alpha, 17.8% beta 923 base pairs and 1592 stacking pairs defined. Time for finding SS restraints: 54.03 Creating SS restraints... Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.560A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 16' Processing helix chain 'K' and resid 30 through 35 removed outlier: 5.525A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 136 removed outlier: 3.515A 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: 3.824A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (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: 4.989A 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 268 removed outlier: 7.501A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 268' Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.531A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.712A 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: 6.849A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.522A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 41 removed outlier: 3.621A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.538A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.527A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.465A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.887A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.688A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 98 through 103' 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: 3.676A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.188A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 123 removed outlier: 3.872A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.504A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.664A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.826A 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 25 removed outlier: 4.126A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.594A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE K 74 " --> pdb=" O SER K 118 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER K 118 " --> pdb=" O ILE K 74 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.141A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 91 through 96 removed outlier: 3.857A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 1 through 6 removed outlier: 3.610A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 44 through 47 removed outlier: 6.878A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.641A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= 9, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.604A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.115A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.660A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.809A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 74 through 78 removed outlier: 7.030A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.926A pdb=" N VAL P 106 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'P' and resid 80 through 88 removed outlier: 3.711A pdb=" N THR P 100 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG P 92 " --> pdb=" O ARG P 88 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.501A pdb=" N SER Q 29 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS Q 37 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP Q 31 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2303 hydrogen bonds 3622 hydrogen bond angles 0 basepair planarities 923 basepair parallelities 1592 stacking parallelities Total time for adding SS restraints: 137.40 Time building geometry restraints manager: 87.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 41813 1.04 - 1.24: 2485 1.24 - 1.43: 43606 1.43 - 1.63: 35654 1.63 - 1.83: 56 Bond restraints: 123614 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.81e+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 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.369 0.266 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.349 -0.194 2.00e-02 2.50e+03 9.43e+01 ... (remaining 123609 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.58: 17955 106.58 - 113.65: 121483 113.65 - 120.71: 50281 120.71 - 127.78: 26566 127.78 - 134.84: 5092 Bond angle restraints: 221377 Sorted by residual: angle pdb=" C1' G7M I2069 " pdb=" N9 G7M I2069 " pdb=" C8 G7M I2069 " ideal model delta sigma weight residual 94.96 129.24 -34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 126.02 -19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C4 OMG I2251 " ideal model delta sigma weight residual 108.29 126.51 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C1' G7M I2069 " pdb=" N9 G7M I2069 " pdb=" C4 G7M I2069 " ideal model delta sigma weight residual 142.80 125.56 17.24 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C8 OMG I2251 " ideal model delta sigma weight residual 142.82 126.07 16.75 3.00e+00 1.11e-01 3.12e+01 ... (remaining 221372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 51702 36.00 - 72.00: 5640 72.00 - 108.00: 866 108.00 - 144.00: 63 144.00 - 180.00: 726 Dihedral angle restraints: 58997 sinusoidal: 55347 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 232.00 54.13 177.87 1 1.70e+01 3.46e-03 6.64e+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 43.58 -171.58 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U I1313 " pdb=" C1' U I1313 " pdb=" N1 U I1313 " pdb=" C2 U I1313 " ideal model delta sinusoidal sigma weight residual 200.00 94.35 105.65 1 1.50e+01 4.44e-03 5.42e+01 ... (remaining 58994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.093: 16438 1.093 - 2.187: 0 2.187 - 3.280: 0 3.280 - 4.373: 0 4.373 - 5.466: 3 Chirality restraints: 16441 Sorted by residual: chirality pdb=" C3B ZIT I3002 " pdb=" C2B ZIT I3002 " pdb=" C4B ZIT I3002 " pdb=" C7B ZIT I3002 " both_signs ideal model delta sigma weight residual False 2.67 -2.79 5.47 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" C6 ZIT I3002 " pdb=" C19 ZIT I3002 " pdb=" C5 ZIT I3002 " pdb=" C7 ZIT I3002 " both_signs ideal model delta sigma weight residual False -2.74 2.72 -5.46 2.00e-01 2.50e+01 7.45e+02 chirality pdb=" C1B ZIT I3002 " pdb=" C2B ZIT I3002 " pdb=" O1B ZIT I3002 " pdb=" O5B ZIT I3002 " both_signs ideal model delta sigma weight residual False -2.37 2.23 -4.60 2.00e-01 2.50e+01 5.30e+02 ... (remaining 16438 not shown) Planarity restraints: 8153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.028 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' OMC I2498 " 0.464 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.768 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.577 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.232 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.883 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.199 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.024 2.00e-02 2.50e+03 5.90e-01 7.82e+03 pdb=" C4' 2MG I2445 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.730 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.565 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.227 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.884 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.209 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.039 2.00e-02 2.50e+03 5.72e-01 7.35e+03 pdb=" C4' OMG I2251 " 0.433 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.620 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.575 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.205 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.916 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.232 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.865 2.00e-02 2.50e+03 ... (remaining 8150 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 3318 2.14 - 2.75: 143234 2.75 - 3.37: 291597 3.37 - 3.98: 455681 3.98 - 4.60: 636504 Nonbonded interactions: 1530334 Sorted by model distance: nonbonded pdb=" OE1 GLU M 16 " pdb=" H GLU M 16 " model vdw 1.519 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.529 1.850 nonbonded pdb=" OP2 G I2581 " pdb=" H22 G I2581 " model vdw 1.534 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.571 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.576 1.850 ... (remaining 1530329 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=1.00 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: 4.410 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: 0.960 Extract box with map and model: 28.490 Check model and map are aligned: 1.290 Set scattering table: 0.770 Process input model: 413.790 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 460.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 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 : 0.005 0.390 81799 Z= 0.310 Angle : 0.384 34.283 125598 Z= 0.189 Chirality : 0.074 5.466 16441 Planarity : 0.022 0.601 4627 Dihedral : 22.641 177.871 48232 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.53 % Allowed : 17.62 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1163 helix: 1.96 (0.35), residues: 259 sheet: 0.59 (0.34), residues: 228 loop : 0.16 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.003 0.001 HIS O 76 PHE 0.003 0.001 PHE K 240 TYR 0.007 0.001 TYR L 58 ARG 0.010 0.000 ARG M 21 *********************** 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 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 235 time to evaluate : 3.176 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 237 average time/residue: 2.9296 time to fit residues: 891.4078 Evaluate side-chains 233 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 229 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.8763 time to fit residues: 5.6752 ------------------------------------------------------------------------------- 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: 0.3980 chunk 314 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 GLN N 130 GLN O 138 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 81799 Z= 0.314 Angle : 0.611 27.038 125598 Z= 0.323 Chirality : 0.042 1.986 16441 Planarity : 0.007 0.136 4627 Dihedral : 22.545 178.687 45992 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.85 % Allowed : 18.05 % Favored : 81.10 % 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: 0.68 (0.25), residues: 1163 helix: 1.57 (0.33), residues: 266 sheet: 0.36 (0.35), residues: 205 loop : 0.11 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.009 0.001 PHE O 119 TYR 0.010 0.001 TYR P 38 ARG 0.003 0.000 ARG K 156 *********************** 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 233 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 230 average time/residue: 2.9296 time to fit residues: 866.8126 Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 3.274 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.6702 time to fit residues: 7.3403 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 8.9990 chunk 313 optimal weight: 0.0270 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 81799 Z= 0.282 Angle : 0.590 25.595 125598 Z= 0.318 Chirality : 0.041 1.970 16441 Planarity : 0.007 0.135 4627 Dihedral : 22.610 179.464 45992 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.06 % Allowed : 17.20 % Favored : 81.74 % 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: 0.45 (0.25), residues: 1163 helix: 1.33 (0.33), residues: 273 sheet: 0.26 (0.35), residues: 196 loop : -0.04 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS P 60 PHE 0.007 0.001 PHE M 183 TYR 0.008 0.001 TYR Q 49 ARG 0.003 0.000 ARG O 27 *********************** 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 243 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 237 average time/residue: 3.0310 time to fit residues: 916.7270 Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 219 time to evaluate : 3.261 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.9392 time to fit residues: 7.6114 ------------------------------------------------------------------------------- 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: 0.9990 chunk 283 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN O 138 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 81799 Z= 0.359 Angle : 0.623 26.551 125598 Z= 0.333 Chirality : 0.043 1.880 16441 Planarity : 0.007 0.137 4627 Dihedral : 22.658 179.137 45992 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.27 % Allowed : 17.83 % Favored : 80.89 % 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: 0.28 (0.25), residues: 1163 helix: 1.29 (0.33), residues: 274 sheet: -0.07 (0.33), residues: 219 loop : -0.12 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.006 0.001 HIS P 60 PHE 0.010 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.004 0.000 ARG O 27 *********************** 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 242 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 233 average time/residue: 3.0770 time to fit residues: 928.9746 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 3.236 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.5368 time to fit residues: 9.6546 ------------------------------------------------------------------------------- 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: 0.1980 chunk 227 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 0.2980 chunk 277 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 81799 Z= 0.251 Angle : 0.598 26.282 125598 Z= 0.322 Chirality : 0.040 1.922 16441 Planarity : 0.006 0.131 4627 Dihedral : 22.689 178.985 45992 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.64 % Allowed : 19.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1163 helix: 1.31 (0.33), residues: 275 sheet: 0.00 (0.35), residues: 208 loop : -0.15 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS P 60 PHE 0.010 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.002 0.000 ARG O 27 *********************** 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 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 225 average time/residue: 3.0558 time to fit residues: 882.5273 Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.3399 ------------------------------------------------------------------------------- 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: 4.9990 chunk 361 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 81799 Z= 0.427 Angle : 0.648 26.119 125598 Z= 0.344 Chirality : 0.045 1.899 16441 Planarity : 0.007 0.141 4627 Dihedral : 22.682 178.548 45992 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.49 % Allowed : 17.41 % Favored : 81.10 % 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: 0.21 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 266 sheet: -0.17 (0.33), residues: 223 loop : -0.17 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.007 0.001 HIS P 60 PHE 0.010 0.001 PHE M 183 TYR 0.013 0.002 TYR P 38 ARG 0.004 0.000 ARG O 27 *********************** 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 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 216 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 226 average time/residue: 2.9967 time to fit residues: 870.4133 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 3.264 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.9626 time to fit residues: 5.9163 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 0.2980 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 81799 Z= 0.194 Angle : 0.600 25.888 125598 Z= 0.323 Chirality : 0.040 1.923 16441 Planarity : 0.006 0.129 4627 Dihedral : 22.761 179.131 45992 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.64 % Allowed : 18.79 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: 0.25 (0.25), residues: 1163 helix: 1.29 (0.33), residues: 276 sheet: -0.03 (0.35), residues: 208 loop : -0.17 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS P 60 PHE 0.009 0.001 PHE M 183 TYR 0.011 0.001 TYR P 38 ARG 0.002 0.000 ARG O 27 *********************** 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 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 228 average time/residue: 2.9298 time to fit residues: 857.0399 Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.0278 time to fit residues: 4.2025 ------------------------------------------------------------------------------- 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: 4.9990 chunk 159 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 81799 Z= 0.447 Angle : 0.651 26.197 125598 Z= 0.346 Chirality : 0.046 1.899 16441 Planarity : 0.007 0.142 4627 Dihedral : 22.695 178.499 45992 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.53 % Allowed : 19.00 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1163 helix: 1.36 (0.33), residues: 266 sheet: -0.13 (0.34), residues: 211 loop : -0.26 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.007 0.001 HIS P 60 PHE 0.011 0.001 PHE M 183 TYR 0.012 0.002 TYR P 38 ARG 0.004 0.000 ARG O 27 *********************** 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 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 221 average time/residue: 3.0565 time to fit residues: 872.4546 Evaluate side-chains 217 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.9486 time to fit residues: 4.1354 ------------------------------------------------------------------------------- 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: 0.9980 chunk 383 optimal weight: 4.9990 chunk 349 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 352 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 81799 Z= 0.273 Angle : 0.615 26.192 125598 Z= 0.331 Chirality : 0.041 1.916 16441 Planarity : 0.007 0.135 4627 Dihedral : 22.742 178.675 45992 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.53 % Allowed : 19.43 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1163 helix: 1.28 (0.33), residues: 274 sheet: -0.08 (0.34), residues: 205 loop : -0.26 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS L 35 PHE 0.010 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.002 0.000 ARG O 27 *********************** 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 220 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 215 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 219 average time/residue: 3.0798 time to fit residues: 868.8161 Evaluate side-chains 218 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 3.179 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.0791 time to fit residues: 4.2940 ------------------------------------------------------------------------------- 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: 3.9990 chunk 394 optimal weight: 0.0570 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 413 optimal weight: 0.2980 chunk 380 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 81799 Z= 0.219 Angle : 0.601 26.192 125598 Z= 0.325 Chirality : 0.039 1.928 16441 Planarity : 0.007 0.133 4627 Dihedral : 22.746 179.139 45992 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.53 % Allowed : 19.43 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: 0.18 (0.25), residues: 1163 helix: 1.29 (0.33), residues: 276 sheet: 0.02 (0.35), residues: 202 loop : -0.28 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.011 0.001 PHE M 183 TYR 0.011 0.001 TYR P 38 ARG 0.002 0.000 ARG O 96 ********************** 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 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 220 average time/residue: 3.0992 time to fit residues: 880.6537 Evaluate side-chains 219 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 3.168 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.9304 time to fit residues: 4.1393 ------------------------------------------------------------------------------- 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: 4.9990 chunk 350 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 303 optimal weight: 0.0980 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 138 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.062677 restraints weight = 230459.927| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 0.45 r_work: 0.2547 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 81799 Z= 0.286 Angle : 0.593 26.309 125598 Z= 0.318 Chirality : 0.041 1.925 16441 Planarity : 0.006 0.132 4627 Dihedral : 22.703 179.810 45992 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.32 % Allowed : 19.53 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1163 helix: 1.40 (0.33), residues: 270 sheet: -0.09 (0.34), residues: 213 loop : -0.25 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS P 60 PHE 0.009 0.001 PHE M 183 TYR 0.011 0.001 TYR P 38 ARG 0.002 0.000 ARG O 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33633.08 seconds wall clock time: 577 minutes 52.31 seconds (34672.31 seconds total)