Starting phenix.real_space_refine on Fri Jan 19 13:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/01_2024/8e41_27876_neut_trim_updated.pdb" } resolution = 2.13 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= -0.022 sd= 0.881 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 34602 2.51 5 N 13683 2.21 5 O 22581 1.98 5 H 41833 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 66": "OD1" <-> "OD2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K GLU 194": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N ASP 176": "OD1" <-> "OD2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O GLU 90": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "P GLU 2": "OE1" <-> "OE2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P ASP 62": "OD1" <-> "OD2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "P ASP 94": "OD1" <-> "OD2" Residue "P ASP 109": "OD1" <-> "OD2" Residue "Q ASP 31": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 115744 Number of models: 1 Model: "" Number of chains: 12 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: 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: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 73 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'MHV:plan-2': 1, 'DBB:plan-1': 1, '004:plan-2': 1, 'MEA:plan-2': 1, 'MHW:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'MUL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 39.73, per 1000 atoms: 0.34 Number of scatterers: 115744 At special positions: 0 Unit cell: (229.656, 222.221, 190.829, 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 22581 8.00 N 13683 7.00 C 34602 6.00 H 41833 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 80.83 Conformation dependent library (CDL) restraints added in 2.8 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB DBB B 3 " Number of C-beta restraints generated: 2126 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 14 sheets defined 29.6% alpha, 16.9% beta 935 base pairs and 1579 stacking pairs defined. Time for finding SS restraints: 58.40 Creating SS restraints... Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.541A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 4.885A 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: 3.827A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.637A 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 Proline residue: K 136 - end of helix 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: 3.543A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 6.957A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.298A 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 'L' and resid 37 through 42 removed outlier: 3.535A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.720A 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: 6.886A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.121A 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: 3.811A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.336A 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: 3.587A 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: 3.669A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (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: 4.507A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.597A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.788A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.560A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.440A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.206A 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: 3.531A 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: 4.113A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.547A 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 122 removed outlier: 3.890A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.505A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 removed outlier: 3.503A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.762A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.553A pdb=" N LEU P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 70' Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.850A 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: 4.203A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.493A 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: 3.626A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.673A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.048A 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: 4.244A 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 5 removed outlier: 4.432A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 42 through 47 removed outlier: 7.620A pdb=" N GLY M 42 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASP M 91 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 5.037A 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: 3.564A pdb=" N LYS M 185 " --> pdb=" O ASP M 145 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 11 through 16 removed outlier: 4.060A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER N 199 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.014A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 179 through 182 Processing sheet with id= 11, first strand: chain 'N' and resid 24 through 28 Processing sheet with id= 12, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.781A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.791A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'P' and resid 2 through 8 262 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2343 hydrogen bonds 3664 hydrogen bond angles 0 basepair planarities 935 basepair parallelities 1579 stacking parallelities Total time for adding SS restraints: 150.84 Time building geometry restraints manager: 84.78 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: 41819 1.04 - 1.23: 1580 1.23 - 1.43: 44402 1.43 - 1.63: 35785 1.63 - 1.83: 56 Bond restraints: 123642 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 3.80e+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 1.77e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.350 -0.195 2.00e-02 2.50e+03 9.46e+01 ... (remaining 123637 not shown) Histogram of bond angle deviations from ideal: 74.38 - 86.50: 3 86.50 - 98.62: 0 98.62 - 110.75: 111771 110.75 - 122.87: 88800 122.87 - 134.99: 20848 Bond angle restraints: 221422 Sorted by residual: angle pdb=" N LYS L 29 " pdb=" CA LYS L 29 " pdb=" HA LYS L 29 " ideal model delta sigma weight residual 110.00 74.38 35.62 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C1' G7M I2069 " pdb=" N9 G7M I2069 " pdb=" C8 G7M I2069 " ideal model delta sigma weight residual 94.96 128.65 -33.69 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C LYS L 29 " pdb=" CA LYS L 29 " pdb=" HA LYS L 29 " ideal model delta sigma weight residual 109.00 75.43 33.57 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CB LYS L 29 " pdb=" CA LYS L 29 " pdb=" HA LYS L 29 " ideal model delta sigma weight residual 109.00 76.58 32.42 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C MHW B 1 " pdb=" CA MHW B 1 " pdb=" CB MHW B 1 " ideal model delta sigma weight residual 110.50 121.47 -10.97 1.50e+00 4.44e-01 5.35e+01 ... (remaining 221417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 52676 35.79 - 71.59: 5573 71.59 - 107.38: 798 107.38 - 143.18: 9 143.18 - 178.97: 5 Dihedral angle restraints: 59061 sinusoidal: 55393 harmonic: 3668 Sorted by residual: dihedral pdb=" C MHW B 1 " pdb=" N MHW B 1 " pdb=" CA MHW B 1 " pdb=" CB MHW B 1 " ideal model delta harmonic sigma weight residual -122.60 -178.57 55.97 0 2.50e+00 1.60e-01 5.01e+02 dihedral pdb=" N MHW B 1 " pdb=" C MHW B 1 " pdb=" CA MHW B 1 " pdb=" CB MHW B 1 " ideal model delta harmonic sigma weight residual 122.80 178.56 -55.76 0 2.50e+00 1.60e-01 4.98e+02 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 53.03 178.97 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 59058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 16274 0.082 - 0.163: 150 0.163 - 0.245: 4 0.245 - 0.327: 1 0.327 - 0.408: 1 Chirality restraints: 16430 Sorted by residual: chirality pdb=" CA LYS L 29 " pdb=" N LYS L 29 " pdb=" C LYS L 29 " pdb=" CB LYS L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C5 MUL I3001 " pdb=" C15 MUL I3001 " pdb=" C4 MUL I3001 " pdb=" C6 MUL I3001 " both_signs ideal model delta sigma weight residual False 2.88 3.15 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA THR B 2 " pdb=" N THR B 2 " pdb=" C THR B 2 " pdb=" CB THR B 2 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 16427 not shown) Planarity restraints: 8166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.026 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' OMC I2498 " 0.463 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.771 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.570 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.235 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.876 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.198 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.943 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.042 2.00e-02 2.50e+03 5.78e-01 7.51e+03 pdb=" C4' 2MG I2445 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.637 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.584 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.204 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.918 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.880 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.042 2.00e-02 2.50e+03 5.69e-01 7.28e+03 pdb=" C4' OMG I2251 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.605 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.576 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.202 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.919 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.235 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.856 2.00e-02 2.50e+03 ... (remaining 8163 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 3294 2.12 - 2.74: 139119 2.74 - 3.36: 290347 3.36 - 3.98: 453342 3.98 - 4.60: 639976 Nonbonded interactions: 1526078 Sorted by model distance: nonbonded pdb=" H ILE L 77 " pdb=" O LYS L 109 " model vdw 1.502 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.517 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.563 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.565 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.570 1.850 ... (remaining 1526073 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: 8.870 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: 0.920 Extract box with map and model: 29.230 Check model and map are aligned: 1.420 Set scattering table: 0.810 Process input model: 431.680 Find NCS groups from input model: 1.180 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 486.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 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 81809 Z= 0.309 Angle : 0.377 33.692 125602 Z= 0.192 Chirality : 0.024 0.408 16430 Planarity : 0.022 0.599 4637 Dihedral : 22.463 178.972 48220 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.85 % Allowed : 16.63 % Favored : 82.52 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.82 (0.25), residues: 1163 helix: 1.85 (0.35), residues: 248 sheet: 0.77 (0.39), residues: 187 loop : 0.08 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.002 0.001 HIS O 76 PHE 0.004 0.000 PHE M 183 TYR 0.006 0.001 TYR L 58 ARG 0.004 0.000 ARG N 128 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 3.223 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 201 average time/residue: 2.9843 time to fit residues: 761.7884 Evaluate side-chains 195 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain R residue 15 SER 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: 5.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN R 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 81809 Z= 0.409 Angle : 0.622 14.494 125602 Z= 0.335 Chirality : 0.040 0.429 16430 Planarity : 0.007 0.138 4637 Dihedral : 22.366 179.307 45985 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.48 % Allowed : 16.21 % Favored : 82.31 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.40 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 267 sheet: 0.26 (0.37), residues: 194 loop : -0.10 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.008 0.001 PHE M 183 TYR 0.009 0.001 TYR Q 49 ARG 0.004 0.001 ARG R 3 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 3.083 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 197 average time/residue: 3.2502 time to fit residues: 823.2847 Evaluate side-chains 187 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain P residue 2 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 0.5980 chunk 336 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 81809 Z= 0.238 Angle : 0.552 13.514 125602 Z= 0.307 Chirality : 0.034 0.414 16430 Planarity : 0.007 0.133 4637 Dihedral : 22.393 178.986 45979 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.38 % Allowed : 15.57 % Favored : 83.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.39 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 269 sheet: 0.41 (0.37), residues: 185 loop : -0.15 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.003 0.001 HIS K 200 PHE 0.008 0.001 PHE M 183 TYR 0.009 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 3.237 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 194 average time/residue: 3.2183 time to fit residues: 795.4224 Evaluate side-chains 199 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 2.9990 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: 5.9990 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 81809 Z= 0.421 Angle : 0.616 14.138 125602 Z= 0.336 Chirality : 0.040 0.428 16430 Planarity : 0.007 0.142 4637 Dihedral : 22.418 179.271 45977 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 2.22 % Allowed : 14.72 % Favored : 83.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.18 (0.32), residues: 269 sheet: 0.08 (0.35), residues: 203 loop : -0.21 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.008 0.001 PHE O 89 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.000 ARG M 69 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 3.209 Fit side-chains REVERT: K 185 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8186 (mt-10) REVERT: M 1 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7713 (mtt) REVERT: M 195 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8358 (mt0) outliers start: 21 outliers final: 14 residues processed: 202 average time/residue: 3.0919 time to fit residues: 792.6315 Evaluate side-chains 209 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 2 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 0.5980 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: 6.9990 chunk 277 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 360 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 81809 Z= 0.233 Angle : 0.579 13.872 125602 Z= 0.322 Chirality : 0.034 0.416 16430 Planarity : 0.007 0.135 4637 Dihedral : 22.460 179.588 45977 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 1.80 % Allowed : 15.25 % Favored : 82.94 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.30 (0.25), residues: 1163 helix: 1.24 (0.32), residues: 269 sheet: 0.24 (0.36), residues: 195 loop : -0.17 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.009 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 3.225 Fit side-chains revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8167 (mt-10) REVERT: M 1 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7632 (mtt) outliers start: 17 outliers final: 14 residues processed: 203 average time/residue: 2.9889 time to fit residues: 770.3844 Evaluate side-chains 213 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain P residue 2 GLU Chi-restraints excluded: chain P residue 108 SER 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: 3.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 333 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 81809 Z= 0.382 Angle : 0.606 13.978 125602 Z= 0.333 Chirality : 0.039 0.425 16430 Planarity : 0.007 0.142 4637 Dihedral : 22.454 179.746 45977 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 2.22 % Allowed : 14.72 % Favored : 83.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.14 (0.25), residues: 1163 helix: 1.17 (0.32), residues: 269 sheet: 0.14 (0.36), residues: 198 loop : -0.30 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.014 0.001 TYR P 38 ARG 0.004 0.000 ARG M 69 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 3.351 Fit side-chains REVERT: K 185 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8184 (mt-10) REVERT: M 1 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: M 184 ASP cc_start: 0.7865 (m-30) cc_final: 0.7630 (m-30) REVERT: M 195 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: O 136 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8960 (mt0) REVERT: Q 37 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8657 (mtmp) outliers start: 21 outliers final: 15 residues processed: 207 average time/residue: 2.9656 time to fit residues: 780.4336 Evaluate side-chains 224 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 2 GLU Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 37 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 81809 Z= 0.277 Angle : 0.584 13.868 125602 Z= 0.325 Chirality : 0.036 0.416 16430 Planarity : 0.007 0.138 4637 Dihedral : 22.474 179.731 45977 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 2.01 % Allowed : 15.78 % Favored : 82.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.17 (0.25), residues: 1163 helix: 1.18 (0.32), residues: 269 sheet: 0.17 (0.36), residues: 204 loop : -0.29 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.009 0.001 PHE K 240 TYR 0.013 0.001 TYR P 38 ARG 0.003 0.000 ARG M 21 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 3.200 Fit side-chains REVERT: K 185 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8180 (mt-10) REVERT: M 1 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: M 171 ASP cc_start: 0.8262 (p0) cc_final: 0.7961 (p0) REVERT: M 195 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: O 136 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8935 (mt0) REVERT: Q 37 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8648 (mtmp) outliers start: 19 outliers final: 15 residues processed: 215 average time/residue: 3.0254 time to fit residues: 824.2119 Evaluate side-chains 208 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 2 GLU Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 37 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 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: 5.9990 chunk 314 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 165 HIS R 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 81809 Z= 0.354 Angle : 0.596 13.879 125602 Z= 0.328 Chirality : 0.038 0.421 16430 Planarity : 0.007 0.139 4637 Dihedral : 22.469 179.901 45977 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 2.12 % Allowed : 16.10 % Favored : 81.78 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.13 (0.25), residues: 1163 helix: 1.24 (0.33), residues: 263 sheet: 0.11 (0.35), residues: 204 loop : -0.33 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.009 0.001 PHE K 240 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.000 ARG M 69 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 3.387 Fit side-chains revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8186 (mt-10) REVERT: M 1 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7620 (mtt) REVERT: M 171 ASP cc_start: 0.8266 (p0) cc_final: 0.7955 (p0) REVERT: M 195 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: O 136 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8937 (mt0) outliers start: 20 outliers final: 16 residues processed: 199 average time/residue: 3.0624 time to fit residues: 771.1823 Evaluate side-chains 217 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 2 GLU Chi-restraints excluded: chain P residue 108 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 3.9990 chunk 383 optimal weight: 6.9990 chunk 349 optimal weight: 0.6980 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: 4.9990 chunk 371 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 81809 Z= 0.330 Angle : 0.592 13.874 125602 Z= 0.327 Chirality : 0.037 0.419 16430 Planarity : 0.007 0.138 4637 Dihedral : 22.472 179.898 45977 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 2.01 % Allowed : 16.31 % Favored : 81.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.13 (0.25), residues: 1163 helix: 1.25 (0.33), residues: 263 sheet: 0.11 (0.35), residues: 204 loop : -0.33 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.009 0.001 PHE K 240 TYR 0.012 0.001 TYR P 38 ARG 0.004 0.000 ARG M 69 *********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 3.209 Fit side-chains revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8185 (mt-10) REVERT: M 1 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7621 (mtt) REVERT: M 171 ASP cc_start: 0.8277 (p0) cc_final: 0.7964 (p0) REVERT: M 195 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: O 136 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8934 (mt0) REVERT: Q 37 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8653 (mtmp) outliers start: 19 outliers final: 16 residues processed: 207 average time/residue: 2.8368 time to fit residues: 748.3543 Evaluate side-chains 216 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 2 GLU Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 37 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 2.9990 chunk 394 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 413 optimal weight: 1.9990 chunk 380 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 81809 Z= 0.242 Angle : 0.575 13.850 125602 Z= 0.322 Chirality : 0.034 0.417 16430 Planarity : 0.007 0.136 4637 Dihedral : 22.491 179.887 45977 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 1.91 % Allowed : 16.63 % Favored : 81.46 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 263 sheet: 0.12 (0.35), residues: 204 loop : -0.32 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.008 0.001 PHE K 240 TYR 0.012 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 ********************** 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 **************************** Residue THR 2 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 3.152 Fit side-chains REVERT: K 185 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8174 (mt-10) REVERT: M 1 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7660 (mtt) REVERT: M 171 ASP cc_start: 0.8268 (p0) cc_final: 0.7968 (p0) REVERT: M 195 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: O 136 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8932 (mt0) REVERT: Q 37 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8666 (mtmp) outliers start: 18 outliers final: 15 residues processed: 205 average time/residue: 2.9743 time to fit residues: 772.6854 Evaluate side-chains 208 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 62 VAL Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 2 GLU Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 37 LYS 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: 0.8980 chunk 100 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.062554 restraints weight = 214106.120| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 0.46 r_work: 0.2572 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 81809 Z= 0.281 Angle : 0.579 13.790 125602 Z= 0.322 Chirality : 0.035 0.418 16430 Planarity : 0.007 0.136 4637 Dihedral : 22.486 179.974 45977 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 1.91 % Allowed : 16.31 % Favored : 81.78 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.28 (0.33), residues: 263 sheet: 0.16 (0.36), residues: 201 loop : -0.26 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.008 0.001 PHE K 240 TYR 0.012 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35497.31 seconds wall clock time: 609 minutes 49.16 seconds (36589.16 seconds total)