Starting phenix.real_space_refine on Tue Mar 12 17:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3o_27869/03_2024/8e3o_27869_neut_trim_updated.pdb" } resolution = 1.99 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= 0.005 sd= 0.665 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 3015 5.49 5 S 28 5.16 5 C 34592 2.51 5 N 13679 2.21 5 O 22578 1.98 5 F 1 1.80 5 H 41809 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 221": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 264": "OD1" <-> "OD2" Residue "K ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 198": "OE1" <-> "OE2" Residue "N ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "P ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 109": "OD1" <-> "OD2" Residue "P ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 46": "OD1" <-> "OD2" Residue "Q TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 115702 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 93265 Classifications: {'RNA': 2897} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 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: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'EM1': 1, 'VIR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 EM1 I3001 " occ=0.00 ... (58 atoms not shown) pdb=" O9 EM1 I3001 " occ=0.00 residue: pdb=" C1 VIR I3002 " occ=0.00 ... (36 atoms not shown) pdb=" O7 VIR I3002 " occ=0.00 Time building chain proxies: 37.29, per 1000 atoms: 0.32 Number of scatterers: 115702 At special positions: 0 Unit cell: (228.096, 221.616, 189.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 28 16.00 P 3015 15.00 F 1 9.00 O 22578 8.00 N 13679 7.00 C 34592 6.00 H 41809 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: 75.48 Conformation dependent library (CDL) restraints added in 2.6 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 35 helices and 13 sheets defined 29.6% alpha, 16.5% beta 953 base pairs and 1624 stacking pairs defined. Time for finding SS restraints: 55.74 Creating SS restraints... Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.807A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.516A 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: 3.915A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 6.822A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.209A 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: 3.509A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 7.021A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.725A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.757A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.629A 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 41 removed outlier: 3.541A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 6.679A pdb=" N THR M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.503A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 3.624A pdb=" N PHE M 158 " --> pdb=" O ASP M 154 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 6.341A 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: 5.798A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.706A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.270A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.105A 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 'O' and resid 24 through 38 removed outlier: 4.187A 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: 4.122A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 123 removed outlier: 3.819A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 4.303A pdb=" N LYS O 72 " --> pdb=" O ASN O 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 67 through 72' Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.631A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 removed outlier: 3.632A pdb=" N TYR P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR P 39 " --> pdb=" O ILE P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.880A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.541A pdb=" N LEU P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 5.208A 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: 4.960A 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: 4.373A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.553A 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: 3.605A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 5.096A 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: 6.729A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 3.949A 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: 4.012A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 1 through 6 removed outlier: 4.147A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 Processing sheet with id= 7, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.208A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.696A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 36 through 40 removed outlier: 4.123A pdb=" N LEU N 40 " --> pdb=" O TYR N 45 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR N 45 " --> pdb=" O LEU N 40 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 46 through 51 removed outlier: 6.383A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'N' and resid 105 through 108 removed outlier: 6.063A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.877A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 13, 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: 2411 hydrogen bonds 3844 hydrogen bond angles 0 basepair planarities 953 basepair parallelities 1624 stacking parallelities Total time for adding SS restraints: 143.50 Time building geometry restraints manager: 79.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 41807 1.03 - 1.22: 634 1.22 - 1.42: 37564 1.42 - 1.61: 43535 1.61 - 1.80: 56 Bond restraints: 123596 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.364 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.347 -0.192 2.00e-02 2.50e+03 9.25e+01 ... (remaining 123591 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.98: 18009 106.98 - 113.94: 123672 113.94 - 120.90: 50479 120.90 - 127.86: 23993 127.86 - 134.82: 5179 Bond angle restraints: 221332 Sorted by residual: angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 126.11 -19.79 3.00e+00 1.11e-01 4.35e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C4 OMG I2251 " ideal model delta sigma weight residual 108.29 126.81 -18.52 3.00e+00 1.11e-01 3.81e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C8 OMG I2251 " ideal model delta sigma weight residual 142.82 125.85 16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C1' 2MG I2445 " pdb=" N9 2MG I2445 " pdb=" C8 2MG I2445 " ideal model delta sigma weight residual 110.07 126.26 -16.19 3.00e+00 1.11e-01 2.91e+01 angle pdb=" C1' 2MG I1835 " pdb=" N9 2MG I1835 " pdb=" C8 2MG I1835 " ideal model delta sigma weight residual 110.07 125.50 -15.43 3.00e+00 1.11e-01 2.65e+01 ... (remaining 221327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 53720 35.99 - 71.98: 7555 71.98 - 107.97: 802 107.97 - 143.95: 33 143.95 - 179.94: 113 Dihedral angle restraints: 62223 sinusoidal: 58573 harmonic: 3650 Sorted by residual: dihedral pdb=" CA THR N 151 " pdb=" C THR N 151 " pdb=" N PRO N 152 " pdb=" CA PRO N 152 " ideal model delta harmonic sigma weight residual -180.00 -138.49 -41.51 0 5.00e+00 4.00e-02 6.89e+01 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.85 -179.85 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 47.61 -175.61 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 62220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.117: 16425 1.117 - 2.233: 0 2.233 - 3.350: 0 3.350 - 4.466: 0 4.466 - 5.583: 1 Chirality restraints: 16426 Sorted by residual: chirality pdb=" C28 EM1 I3001 " pdb=" C24 EM1 I3001 " pdb=" C33 EM1 I3001 " pdb=" C34 EM1 I3001 " both_signs ideal model delta sigma weight residual False -2.80 2.78 -5.58 2.00e-01 2.50e+01 7.79e+02 chirality pdb=" C19 EM1 I3001 " pdb=" C13 EM1 I3001 " pdb=" C23 EM1 I3001 " pdb=" C24 EM1 I3001 " both_signs ideal model delta sigma weight residual False 2.80 2.26 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C2 EM1 I3001 " pdb=" C3 EM1 I3001 " pdb=" C4 EM1 I3001 " pdb=" O5 EM1 I3001 " both_signs ideal model delta sigma weight residual False -2.52 -2.99 0.47 2.00e-01 2.50e+01 5.58e+00 ... (remaining 16423 not shown) Planarity restraints: 8165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.029 2.00e-02 2.50e+03 5.84e-01 7.66e+03 pdb=" C4' 2MG I2445 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.572 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.217 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.894 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.216 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.904 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.039 2.00e-02 2.50e+03 5.83e-01 7.65e+03 pdb=" C4' OMG I2251 " 0.439 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.657 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.587 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.205 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.921 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.223 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.890 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.013 2.00e-02 2.50e+03 5.79e-01 7.55e+03 pdb=" C4' OMC I2498 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.724 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.541 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.232 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.864 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.216 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.902 2.00e-02 2.50e+03 ... (remaining 8162 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 3929 2.13 - 2.75: 145321 2.75 - 3.37: 292669 3.37 - 3.98: 461243 3.98 - 4.60: 645700 Nonbonded interactions: 1548862 Sorted by model distance: nonbonded pdb=" H THR K 246 " pdb=" O VAL K 250 " model vdw 1.517 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.527 1.850 nonbonded pdb=" O ALA K 170 " pdb=" H ALA K 186 " model vdw 1.533 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.536 1.850 nonbonded pdb=" OP2 G I1799 " pdb="HH21 ARG K 270 " model vdw 1.538 1.850 ... (remaining 1548857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.760 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: 0.940 Extract box with map and model: 27.990 Check model and map are aligned: 1.260 Set scattering table: 0.750 Process input model: 410.470 Find NCS groups from input model: 1.140 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: 0.010 Load rotamer database and sin/cos tables:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 456.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 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 : 0.006 0.392 81787 Z= 0.321 Angle : 0.409 19.790 125569 Z= 0.207 Chirality : 0.051 5.583 16426 Planarity : 0.022 0.584 4638 Dihedral : 23.676 179.853 50561 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.56 % Favored : 95.10 % Rotamer: Outliers : 0.74 % Allowed : 8.39 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.21), residues: 1163 helix: -2.00 (0.25), residues: 248 sheet: -1.32 (0.31), residues: 213 loop : -1.97 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 78 HIS 0.003 0.001 HIS K 230 PHE 0.007 0.001 PHE K 266 TYR 0.006 0.001 TYR Q 49 ARG 0.004 0.000 ARG N 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 323 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 117 GLN cc_start: 0.8706 (tt0) cc_final: 0.8420 (tt0) REVERT: K 187 ASP cc_start: 0.8310 (m-30) cc_final: 0.8101 (m-30) REVERT: K 256 LYS cc_start: 0.8420 (mttm) cc_final: 0.8211 (mttt) REVERT: L 91 ASP cc_start: 0.7478 (p0) cc_final: 0.7263 (p0) REVERT: M 136 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8012 (tp40) REVERT: M 140 ASP cc_start: 0.8478 (m-30) cc_final: 0.8233 (m-30) REVERT: M 171 ASP cc_start: 0.7926 (p0) cc_final: 0.7638 (p0) REVERT: N 157 LYS cc_start: 0.8937 (tttm) cc_final: 0.8624 (ttmm) outliers start: 7 outliers final: 4 residues processed: 329 average time/residue: 3.4245 time to fit residues: 1386.7136 Evaluate side-chains 244 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 240 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 62 ASP Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 376 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 200 HIS L 104 GLN M 41 GLN N 126 ASN N 150 GLN P 15 GLN P 40 ASN Q 6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 81787 Z= 0.401 Angle : 0.669 26.682 125569 Z= 0.352 Chirality : 0.041 1.740 16426 Planarity : 0.007 0.137 4638 Dihedral : 23.667 179.803 48330 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 1.80 % Allowed : 15.61 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1163 helix: -0.03 (0.30), residues: 261 sheet: -0.79 (0.33), residues: 208 loop : -1.40 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 248 HIS 0.005 0.001 HIS O 76 PHE 0.012 0.001 PHE M 183 TYR 0.010 0.002 TYR P 38 ARG 0.005 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 117 GLN cc_start: 0.8749 (tt0) cc_final: 0.8544 (tt0) REVERT: K 175 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8141 (ttp-170) REVERT: M 136 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8010 (tp40) REVERT: M 171 ASP cc_start: 0.8018 (p0) cc_final: 0.7701 (p0) REVERT: P 28 LYS cc_start: 0.8565 (mttm) cc_final: 0.8231 (mtpm) outliers start: 17 outliers final: 13 residues processed: 243 average time/residue: 3.1971 time to fit residues: 978.3389 Evaluate side-chains 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 7 HIS Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 62 ASP Chi-restraints excluded: chain P residue 70 LYS Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 0.2980 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 4.9990 chunk 407 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 chunk 374 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 302 optimal weight: 0.0770 overall best weight: 2.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 81787 Z= 0.179 Angle : 0.563 26.402 125569 Z= 0.305 Chirality : 0.035 2.025 16426 Planarity : 0.006 0.129 4638 Dihedral : 23.667 177.220 48330 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.82 % Favored : 95.01 % Rotamer: Outliers : 2.02 % Allowed : 15.82 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1163 helix: 0.75 (0.33), residues: 263 sheet: -0.42 (0.34), residues: 198 loop : -1.03 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS Q 38 PHE 0.011 0.001 PHE M 183 TYR 0.008 0.001 TYR P 38 ARG 0.004 0.000 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 229 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 117 GLN cc_start: 0.8749 (tt0) cc_final: 0.8538 (tt0) REVERT: L 106 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8014 (mt-10) REVERT: M 136 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8158 (tp40) REVERT: M 171 ASP cc_start: 0.7947 (p0) cc_final: 0.7615 (p0) REVERT: N 157 LYS cc_start: 0.9003 (tttm) cc_final: 0.8655 (ttmm) REVERT: P 28 LYS cc_start: 0.8475 (mttm) cc_final: 0.8158 (mtpm) REVERT: P 59 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6969 (tm-30) outliers start: 19 outliers final: 13 residues processed: 239 average time/residue: 3.3218 time to fit residues: 1001.1897 Evaluate side-chains 241 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain P residue 62 ASP Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 57 LYS 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: 6.9990 chunk 195 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 108 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN N 173 GLN P 31 GLN P 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 81787 Z= 0.398 Angle : 0.629 27.310 125569 Z= 0.338 Chirality : 0.041 1.917 16426 Planarity : 0.007 0.140 4638 Dihedral : 23.713 178.062 48329 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.73 % Favored : 95.01 % Rotamer: Outliers : 2.12 % Allowed : 15.82 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1163 helix: 0.95 (0.33), residues: 264 sheet: -0.47 (0.34), residues: 194 loop : -0.86 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 248 HIS 0.005 0.001 HIS P 7 PHE 0.011 0.001 PHE M 183 TYR 0.009 0.002 TYR P 38 ARG 0.004 0.000 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 3.040 Fit side-chains revert: symmetry clash REVERT: K 117 GLN cc_start: 0.8773 (tt0) cc_final: 0.8568 (tt0) REVERT: M 157 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7897 (tt) REVERT: M 171 ASP cc_start: 0.7955 (p0) cc_final: 0.7620 (p0) REVERT: P 28 LYS cc_start: 0.8450 (mttm) cc_final: 0.8156 (mtpm) outliers start: 20 outliers final: 12 residues processed: 241 average time/residue: 3.1756 time to fit residues: 965.2090 Evaluate side-chains 241 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain P residue 70 LYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN N 173 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 81787 Z= 0.322 Angle : 0.612 27.213 125569 Z= 0.331 Chirality : 0.039 1.941 16426 Planarity : 0.007 0.138 4638 Dihedral : 23.710 178.962 48327 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 3.29 % Allowed : 14.12 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1163 helix: 1.12 (0.33), residues: 264 sheet: -0.34 (0.34), residues: 194 loop : -0.71 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.007 0.001 HIS Q 38 PHE 0.012 0.001 PHE M 183 TYR 0.008 0.001 TYR K 161 ARG 0.005 0.000 ARG O 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 157 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7977 (tt) REVERT: M 171 ASP cc_start: 0.7934 (p0) cc_final: 0.7609 (p0) REVERT: P 28 LYS cc_start: 0.8436 (mttm) cc_final: 0.8157 (mtpm) outliers start: 31 outliers final: 15 residues processed: 244 average time/residue: 3.0812 time to fit residues: 950.8070 Evaluate side-chains 244 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 5.9990 chunk 361 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 333 optimal weight: 0.3980 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 210 optimal weight: 50.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN N 173 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 81787 Z= 0.269 Angle : 0.600 27.254 125569 Z= 0.327 Chirality : 0.038 1.952 16426 Planarity : 0.007 0.136 4638 Dihedral : 23.725 179.029 48327 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.73 % Favored : 95.01 % Rotamer: Outliers : 1.70 % Allowed : 15.61 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1163 helix: 1.15 (0.33), residues: 264 sheet: -0.21 (0.35), residues: 189 loop : -0.70 (0.23), residues: 710 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 0.011 0.001 PHE M 183 TYR 0.008 0.001 TYR K 161 ARG 0.006 0.000 ARG O 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 157 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7973 (tt) REVERT: M 171 ASP cc_start: 0.7934 (p0) cc_final: 0.7609 (p0) REVERT: P 28 LYS cc_start: 0.8428 (mttm) cc_final: 0.8151 (mtpm) outliers start: 16 outliers final: 14 residues processed: 234 average time/residue: 3.1398 time to fit residues: 929.2618 Evaluate side-chains 243 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 228 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 57 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: 5.9990 chunk 228 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN N 173 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 81787 Z= 0.349 Angle : 0.622 27.175 125569 Z= 0.336 Chirality : 0.040 1.937 16426 Planarity : 0.007 0.140 4638 Dihedral : 23.764 179.644 48327 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 2.76 % Allowed : 14.97 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1163 helix: 1.20 (0.33), residues: 270 sheet: -0.10 (0.36), residues: 187 loop : -0.56 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.005 0.001 HIS P 60 PHE 0.012 0.001 PHE M 183 TYR 0.011 0.002 TYR K 161 ARG 0.006 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 157 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8062 (tt) REVERT: M 171 ASP cc_start: 0.7864 (p0) cc_final: 0.7526 (p0) REVERT: P 28 LYS cc_start: 0.8400 (mttm) cc_final: 0.8147 (mtpm) outliers start: 26 outliers final: 16 residues processed: 238 average time/residue: 3.0979 time to fit residues: 929.7439 Evaluate side-chains 244 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 227 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN L 104 GLN N 173 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 81787 Z= 0.385 Angle : 0.635 27.310 125569 Z= 0.342 Chirality : 0.041 1.918 16426 Planarity : 0.007 0.141 4638 Dihedral : 23.791 179.212 48327 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 2.12 % Allowed : 16.14 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1163 helix: 1.21 (0.33), residues: 270 sheet: -0.06 (0.36), residues: 187 loop : -0.53 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.013 0.001 PHE K 240 TYR 0.013 0.002 TYR K 161 ARG 0.008 0.000 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 3.092 Fit side-chains REVERT: M 157 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8117 (tp) REVERT: M 171 ASP cc_start: 0.7813 (p0) cc_final: 0.7481 (p0) REVERT: P 28 LYS cc_start: 0.8400 (mttm) cc_final: 0.8156 (mtpm) outliers start: 20 outliers final: 16 residues processed: 240 average time/residue: 3.1456 time to fit residues: 974.9065 Evaluate side-chains 246 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.9980 chunk 383 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 chunk 352 optimal weight: 6.9990 chunk 371 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 GLN P 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 81787 Z= 0.301 Angle : 0.619 27.367 125569 Z= 0.337 Chirality : 0.039 1.943 16426 Planarity : 0.007 0.139 4638 Dihedral : 23.808 179.074 48327 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 2.02 % Allowed : 16.35 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1163 helix: 1.25 (0.33), residues: 270 sheet: -0.07 (0.36), residues: 187 loop : -0.51 (0.23), residues: 706 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 0.012 0.001 PHE M 183 TYR 0.012 0.001 TYR K 161 ARG 0.009 0.000 ARG O 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 3.047 Fit side-chains revert: symmetry clash REVERT: M 157 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8112 (tp) REVERT: M 171 ASP cc_start: 0.7813 (p0) cc_final: 0.7481 (p0) REVERT: M 197 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: P 28 LYS cc_start: 0.8396 (mttm) cc_final: 0.8154 (mtpm) outliers start: 19 outliers final: 16 residues processed: 237 average time/residue: 3.1355 time to fit residues: 959.0165 Evaluate side-chains 248 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 4.9990 chunk 394 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 413 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 329 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN N 173 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 81787 Z= 0.320 Angle : 0.620 27.212 125569 Z= 0.336 Chirality : 0.040 1.937 16426 Planarity : 0.007 0.139 4638 Dihedral : 23.806 179.565 48327 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 1.91 % Allowed : 16.67 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1163 helix: 1.26 (0.33), residues: 270 sheet: -0.06 (0.36), residues: 187 loop : -0.50 (0.23), residues: 706 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 0.012 0.001 PHE M 183 TYR 0.011 0.001 TYR K 161 ARG 0.007 0.000 ARG O 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 3.380 Fit side-chains REVERT: M 157 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8117 (tp) REVERT: M 171 ASP cc_start: 0.7807 (p0) cc_final: 0.7475 (p0) REVERT: M 197 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: P 28 LYS cc_start: 0.8394 (mttm) cc_final: 0.8151 (mtpm) REVERT: Q 54 VAL cc_start: 0.8783 (p) cc_final: 0.8548 (m) outliers start: 18 outliers final: 15 residues processed: 236 average time/residue: 3.0906 time to fit residues: 937.6865 Evaluate side-chains 246 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 5.9990 chunk 350 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 338 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN N 173 GLN P 31 GLN P 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.070185 restraints weight = 189706.269| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 0.53 r_work: 0.2672 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 81787 Z= 0.346 Angle : 0.622 27.322 125569 Z= 0.336 Chirality : 0.040 1.932 16426 Planarity : 0.007 0.140 4638 Dihedral : 23.784 179.683 48327 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 2.23 % Allowed : 16.67 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1163 helix: 1.32 (0.33), residues: 270 sheet: -0.02 (0.36), residues: 187 loop : -0.45 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.004 0.001 HIS P 60 PHE 0.013 0.001 PHE K 240 TYR 0.012 0.002 TYR K 161 ARG 0.006 0.000 ARG O 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37243.95 seconds wall clock time: 639 minutes 45.88 seconds (38385.88 seconds total)