Starting phenix.real_space_refine on Tue Mar 12 17:21:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_2024/8e41_27876_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_2024/8e41_27876.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_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_27876/03_2024/8e41_27876_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_2024/8e41_27876_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_2024/8e41_27876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_2024/8e41_27876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_2024/8e41_27876_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e41_27876/03_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-dev-5265/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: 39.74, 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: 81.48 Conformation dependent library (CDL) restraints added in 3.4 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: 56.35 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: 144.21 Time building geometry restraints manager: 85.77 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=" 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=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 126.29 -19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C4 OMG I2251 " ideal model delta sigma weight residual 108.29 126.74 -18.45 3.00e+00 1.11e-01 3.78e+01 ... (remaining 221417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 54235 35.79 - 71.59: 7238 71.59 - 107.38: 798 107.38 - 143.18: 9 143.18 - 178.97: 5 Dihedral angle restraints: 62285 sinusoidal: 58617 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 62282 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: 4.480 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: 0.900 Extract box with map and model: 28.220 Check model and map are aligned: 1.270 Set scattering table: 0.770 Process input model: 417.510 Find NCS groups from input model: 1.170 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:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 464.880 ------------------------------------------------------------------------------- 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 : 0.365 19.969 125602 Z= 0.187 Chirality : 0.024 0.408 16430 Planarity : 0.022 0.599 4637 Dihedral : 23.366 178.972 50604 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 : 3.092 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 201 average time/residue: 2.9417 time to fit residues: 749.7200 Evaluate side-chains 195 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 3.120 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.8978 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 81809 Z= 0.362 Angle : 0.600 14.655 125602 Z= 0.324 Chirality : 0.038 0.426 16430 Planarity : 0.007 0.138 4637 Dihedral : 23.243 179.824 48369 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.59 % Allowed : 16.21 % 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: 0.49 (0.25), residues: 1163 helix: 1.44 (0.33), residues: 267 sheet: 0.31 (0.37), residues: 200 loop : -0.04 (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 0.007 0.001 PHE M 183 TYR 0.008 0.001 TYR Q 49 ARG 0.006 0.001 ARG Q 13 *********************** 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 206 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 2.767 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 198 average time/residue: 3.0849 time to fit residues: 778.4447 Evaluate side-chains 188 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 3.131 ------------------------------------------------------------------------------- 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 15 SER 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: 1.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 2.9990 chunk 336 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8963 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 81809 Z= 0.269 Angle : 0.573 14.467 125602 Z= 0.314 Chirality : 0.035 0.415 16430 Planarity : 0.007 0.135 4637 Dihedral : 23.270 179.407 48363 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.38 % Allowed : 15.78 % Favored : 82.84 % 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: 0.41 (0.25), residues: 1163 helix: 1.31 (0.32), residues: 267 sheet: 0.35 (0.37), residues: 195 loop : -0.10 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.008 0.001 PHE M 183 TYR 0.009 0.001 TYR P 38 ARG 0.004 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 195 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 3.135 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 189 average time/residue: 3.1549 time to fit residues: 752.9252 Evaluate side-chains 191 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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 15 SER 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 P residue 2 GLU 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: 3.9990 chunk 401 optimal weight: 0.0570 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- 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: 0.8977 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 81809 Z= 0.319 Angle : 0.585 13.798 125602 Z= 0.323 Chirality : 0.037 0.418 16430 Planarity : 0.007 0.138 4637 Dihedral : 23.271 179.494 48363 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 1.91 % Allowed : 14.51 % Favored : 83.58 % 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: 0.34 (0.25), residues: 1163 helix: 1.25 (0.32), residues: 269 sheet: 0.30 (0.36), residues: 195 loop : -0.14 (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 0.008 0.001 PHE M 183 TYR 0.011 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 209 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 3.078 Fit side-chains revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8174 (mt-10) outliers start: 18 outliers final: 11 residues processed: 200 average time/residue: 3.0904 time to fit residues: 790.7052 Evaluate side-chains 213 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain L residue 120 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.8978 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 : 0.006 0.046 81809 Z= 0.332 Angle : 0.585 13.868 125602 Z= 0.322 Chirality : 0.037 0.419 16430 Planarity : 0.007 0.137 4637 Dihedral : 23.314 179.833 48360 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 2.12 % Allowed : 14.51 % Favored : 83.37 % 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: 0.29 (0.25), residues: 1163 helix: 1.28 (0.32), residues: 269 sheet: 0.31 (0.37), residues: 185 loop : -0.21 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.010 0.001 PHE K 240 TYR 0.012 0.001 TYR P 38 ARG 0.006 0.000 ARG M 21 *********************** 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 222 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 3.169 Fit side-chains revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8180 (mt-10) REVERT: M 195 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: O 136 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8946 (mt0) REVERT: Q 37 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8655 (mtmp) outliers start: 20 outliers final: 14 residues processed: 208 average time/residue: 2.8255 time to fit residues: 751.9746 Evaluate side-chains 222 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 2.817 ------------------------------------------------------------------------------- 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 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 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=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: 7.9990 chunk 33 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 210 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8987 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 81809 Z= 0.368 Angle : 0.599 13.878 125602 Z= 0.330 Chirality : 0.038 0.423 16430 Planarity : 0.007 0.140 4637 Dihedral : 23.329 179.919 48360 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 2.22 % Allowed : 15.15 % Favored : 82.63 % 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: 1.22 (0.32), residues: 269 sheet: 0.18 (0.36), residues: 198 loop : -0.27 (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 0.009 0.001 PHE K 240 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.000 ARG M 69 *********************** REFINEMENT MACRO_CYCLE 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 230 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8180 (mt-10) REVERT: M 171 ASP cc_start: 0.8269 (p0) cc_final: 0.7952 (p0) REVERT: M 184 ASP cc_start: 0.7812 (m-30) cc_final: 0.7608 (m-30) REVERT: M 195 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: O 136 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8946 (mt0) REVERT: Q 37 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8652 (mtmp) outliers start: 21 outliers final: 14 residues processed: 217 average time/residue: 3.0388 time to fit residues: 836.9560 Evaluate side-chains 223 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 3.066 ------------------------------------------------------------------------------- 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 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 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: 2.9990 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: 1.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8975 moved from start: 0.1530 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= 0.246 Angle : 0.577 13.884 125602 Z= 0.323 Chirality : 0.034 0.419 16430 Planarity : 0.007 0.137 4637 Dihedral : 23.355 179.975 48360 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 1.80 % Allowed : 16.63 % Favored : 81.57 % 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: 1.25 (0.32), residues: 269 sheet: 0.18 (0.36), residues: 198 loop : -0.27 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.010 0.001 PHE K 240 TYR 0.013 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 *********************** 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 224 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 207 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8173 (mt-10) REVERT: M 51 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8336 (mt-10) REVERT: M 171 ASP cc_start: 0.8260 (p0) cc_final: 0.7945 (p0) REVERT: O 136 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8946 (mt0) REVERT: Q 37 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8664 (mtmp) outliers start: 17 outliers final: 15 residues processed: 213 average time/residue: 2.9616 time to fit residues: 799.8477 Evaluate side-chains 223 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 2.848 ------------------------------------------------------------------------------- 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 69 ARG Chi-restraints excluded: chain M residue 150 THR 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 P residue 2 GLU Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 36 GLU 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: 5.9990 chunk 197 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 81809 Z= 0.402 Angle : 0.614 13.980 125602 Z= 0.336 Chirality : 0.039 0.424 16430 Planarity : 0.007 0.142 4637 Dihedral : 23.354 179.751 48360 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.22 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: 0.11 (0.24), residues: 1163 helix: 1.25 (0.33), residues: 263 sheet: 0.11 (0.35), residues: 204 loop : -0.35 (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 0.009 0.001 PHE K 240 TYR 0.014 0.001 TYR P 38 ARG 0.005 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 225 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 207 time to evaluate : 3.088 Fit side-chains revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8184 (mt-10) REVERT: M 171 ASP cc_start: 0.8268 (p0) cc_final: 0.7955 (p0) REVERT: M 195 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: O 136 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8949 (mt0) REVERT: Q 37 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8645 (mtmp) outliers start: 18 outliers final: 14 residues processed: 213 average time/residue: 3.1109 time to fit residues: 863.4237 Evaluate side-chains 222 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 3.170 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 349 optimal weight: 2.9990 chunk 372 optimal weight: 2.9990 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: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8985 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 81809 Z= 0.309 Angle : 0.595 13.920 125602 Z= 0.330 Chirality : 0.036 0.421 16430 Planarity : 0.007 0.140 4637 Dihedral : 23.370 179.773 48360 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.27 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: 0.13 (0.24), residues: 1163 helix: 1.27 (0.33), residues: 263 sheet: 0.11 (0.35), residues: 204 loop : -0.34 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 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 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 223 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8178 (mt-10) REVERT: M 171 ASP cc_start: 0.8264 (p0) cc_final: 0.7950 (p0) REVERT: M 195 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: Q 37 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8643 (mtmp) outliers start: 18 outliers final: 14 residues processed: 212 average time/residue: 3.1298 time to fit residues: 853.1493 Evaluate side-chains 222 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 3.129 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 413 optimal weight: 1.9990 chunk 380 optimal weight: 4.9990 chunk 329 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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: 0.8968 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 81809 Z= 0.205 Angle : 0.573 13.850 125602 Z= 0.320 Chirality : 0.033 0.416 16430 Planarity : 0.007 0.134 4637 Dihedral : 23.406 179.958 48360 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 1.48 % Allowed : 16.84 % 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: 0.22 (0.24), residues: 1163 helix: 1.33 (0.33), residues: 263 sheet: 0.09 (0.36), residues: 190 loop : -0.24 (0.23), residues: 710 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 M 183 TYR 0.012 0.001 TYR P 38 ARG 0.003 0.000 ARG L 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 214 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 185 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8163 (mt-10) REVERT: M 171 ASP cc_start: 0.8270 (p0) cc_final: 0.7960 (p0) REVERT: M 195 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: Q 37 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8637 (mtmp) outliers start: 14 outliers final: 12 residues processed: 205 average time/residue: 3.1632 time to fit residues: 828.1245 Evaluate side-chains 223 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 3.088 ------------------------------------------------------------------------------- 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 10 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 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: 3.9990 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: 1.9990 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: 3.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.062176 restraints weight = 215180.221| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 0.49 r_work: 0.2569 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 81809 Z= 0.316 Angle : 0.585 13.789 125602 Z= 0.323 Chirality : 0.036 0.421 16430 Planarity : 0.007 0.137 4637 Dihedral : 23.352 179.724 48360 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 1.59 % Allowed : 16.84 % Favored : 81.57 % 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: 0.23 (0.25), residues: 1163 helix: 1.34 (0.33), residues: 263 sheet: 0.18 (0.36), residues: 201 loop : -0.27 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.010 0.001 PHE K 240 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.000 ARG M 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35081.82 seconds wall clock time: 602 minutes 54.22 seconds (36174.22 seconds total)