Starting phenix.real_space_refine on Sun Feb 18 18:32:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swe_10324/02_2024/6swe_10324_updated.pdb" } resolution = 3.1 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= -0.000 sd= 0.001 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 Zn 1 6.06 5 P 486 5.49 5 Mg 8 5.21 5 S 49 5.16 5 C 12428 2.51 5 N 4238 2.21 5 O 5527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "K GLU 21": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K ARG 135": "NH1" <-> "NH2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 86": "OE1" <-> "OE2" Residue "O GLU 104": "OE1" <-> "OE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S GLU 62": "OE1" <-> "OE2" Residue "T GLU 22": "OE1" <-> "OE2" Residue "U GLU 14": "OE1" <-> "OE2" Residue "U GLU 22": "OE1" <-> "OE2" Residue "U GLU 141": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X GLU 66": "OE1" <-> "OE2" Residue "Y GLU 47": "OE1" <-> "OE2" Residue "Z GLU 19": "OE1" <-> "OE2" Residue "Z GLU 64": "OE1" <-> "OE2" Residue "Z GLU 84": "OE1" <-> "OE2" Residue "3 GLU 10": "OE1" <-> "OE2" Residue "3 GLU 14": "OE1" <-> "OE2" Residue "3 GLU 17": "OE1" <-> "OE2" Residue "3 GLU 24": "OE1" <-> "OE2" Residue "3 GLU 61": "OE1" <-> "OE2" Residue "3 GLU 71": "OE1" <-> "OE2" Residue "3 GLU 85": "OE1" <-> "OE2" Residue "3 GLU 93": "OE1" <-> "OE2" Residue "3 GLU 103": "OE1" <-> "OE2" Residue "3 GLU 112": "OE1" <-> "OE2" Residue "3 GLU 120": "OE1" <-> "OE2" Residue "6 GLU 103": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22737 Number of models: 1 Model: "" Number of chains: 21 Chain: "2" Number of atoms: 10068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 10068 Classifications: {'RNA': 468} Modifications used: {'rna2p_pur': 41, 'rna2p_pyr': 37, 'rna3p': 10, 'rna3p_pur': 217, 'rna3p_pyr': 163} Link IDs: {'rna2p': 78, 'rna3p': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1720 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "K" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 817 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "O" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1151 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "P" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "S" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "T" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1057 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1223 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 11, 'TRANS': 137} Chain: "X" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "Y" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 408 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1550 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "3" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 114} Chain: "4" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 384 Classifications: {'RNA': 18} Modifications used: {'rna3p': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "6" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "2" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14985 SG CYS P 21 92.396 72.031 80.842 1.00 28.23 S ATOM 15010 SG CYS P 24 90.937 70.637 84.552 1.00 33.25 S ATOM 15125 SG CYS P 39 90.941 69.183 80.674 1.00 27.52 S ATOM 15152 SG CYS P 42 89.326 71.758 83.719 1.00 29.16 S Time building chain proxies: 12.05, per 1000 atoms: 0.53 Number of scatterers: 22737 At special positions: 0 Unit cell: (175.49, 130.8, 127.53, 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) Zn 1 29.99 S 49 16.00 P 486 15.00 Mg 8 11.99 O 5527 8.00 N 4238 7.00 C 12428 6.00 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=0, symmetry=0 Time building additional restraints: 11.21 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 39 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 24 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 42 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 21 " Number of angles added : 6 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 16 sheets defined 31.9% alpha, 10.2% beta 117 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 10.65 Creating SS restraints... Processing helix chain 'H' and resid 5 through 8 No H-bonds generated for 'chain 'H' and resid 5 through 8' Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.828A pdb=" N ILE H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 114 removed outlier: 3.701A pdb=" N LYS H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 129 removed outlier: 3.989A pdb=" N GLU H 128 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN H 129 " --> pdb=" O TRP H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 169 Processing helix chain 'H' and resid 180 through 193 removed outlier: 3.536A pdb=" N ALA H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN H 193 " --> pdb=" O ILE H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 214 removed outlier: 3.720A pdb=" N ILE H 210 " --> pdb=" O GLU H 206 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 42 No H-bonds generated for 'chain 'K' and resid 39 through 42' Processing helix chain 'K' and resid 44 through 50 removed outlier: 3.934A pdb=" N GLU K 47 " --> pdb=" O THR K 44 " (cutoff:3.500A) Proline residue: K 48 - end of helix No H-bonds generated for 'chain 'K' and resid 44 through 50' Processing helix chain 'K' and resid 57 through 59 No H-bonds generated for 'chain 'K' and resid 57 through 59' Processing helix chain 'K' and resid 75 through 89 removed outlier: 3.820A pdb=" N GLU K 88 " --> pdb=" O ARG K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 101 removed outlier: 3.886A pdb=" N LYS K 98 " --> pdb=" O ASN K 94 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.733A pdb=" N VAL K 108 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 29 removed outlier: 3.895A pdb=" N GLU L 18 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 82 No H-bonds generated for 'chain 'L' and resid 79 through 82' Processing helix chain 'O' and resid 21 through 24 No H-bonds generated for 'chain 'O' and resid 21 through 24' Processing helix chain 'O' and resid 33 through 43 removed outlier: 3.827A pdb=" N MET O 38 " --> pdb=" O ASN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 53 No H-bonds generated for 'chain 'O' and resid 51 through 53' Processing helix chain 'O' and resid 56 through 65 Processing helix chain 'O' and resid 70 through 72 No H-bonds generated for 'chain 'O' and resid 70 through 72' Processing helix chain 'O' and resid 95 through 111 removed outlier: 4.119A pdb=" N ASP O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA O 101 " --> pdb=" O LYS O 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 122 removed outlier: 3.529A pdb=" N ARG O 119 " --> pdb=" O TYR O 115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 18 No H-bonds generated for 'chain 'P' and resid 16 through 18' Processing helix chain 'P' and resid 40 through 50 removed outlier: 3.959A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU P 45 " --> pdb=" O HIS P 41 " (cutoff:3.500A) Proline residue: P 48 - end of helix Processing helix chain 'S' and resid 7 through 15 removed outlier: 3.720A pdb=" N GLU S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.647A pdb=" N LYS S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU S 38 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 58 removed outlier: 3.615A pdb=" N ARG S 49 " --> pdb=" O LYS S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 16 No H-bonds generated for 'chain 'T' and resid 13 through 16' Processing helix chain 'T' and resid 30 through 37 Processing helix chain 'T' and resid 42 through 56 removed outlier: 3.964A pdb=" N LEU T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 106 No H-bonds generated for 'chain 'T' and resid 104 through 106' Processing helix chain 'U' and resid 9 through 22 removed outlier: 3.702A pdb=" N GLN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG U 19 " --> pdb=" O ARG U 15 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 34 No H-bonds generated for 'chain 'U' and resid 32 through 34' Processing helix chain 'U' and resid 50 through 63 removed outlier: 3.582A pdb=" N ARG U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG U 61 " --> pdb=" O SER U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 76 removed outlier: 4.391A pdb=" N THR U 75 " --> pdb=" O GLU U 71 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR U 76 " --> pdb=" O ARG U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 108 Processing helix chain 'U' and resid 123 through 139 removed outlier: 3.969A pdb=" N GLU U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 7 No H-bonds generated for 'chain 'Z' and resid 4 through 7' Processing helix chain 'Z' and resid 12 through 24 removed outlier: 3.842A pdb=" N LYS Z 23 " --> pdb=" O GLU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 55 Processing helix chain 'Z' and resid 60 through 71 removed outlier: 3.902A pdb=" N GLU Z 64 " --> pdb=" O ARG Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 90 No H-bonds generated for 'chain 'Z' and resid 88 through 90' Processing helix chain 'Z' and resid 92 through 105 removed outlier: 4.449A pdb=" N VAL Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 122 Processing helix chain 'Z' and resid 156 through 160 removed outlier: 3.819A pdb=" N THR Z 160 " --> pdb=" O PRO Z 157 " (cutoff:3.500A) Processing helix chain '3' and resid 14 through 20 Processing helix chain '3' and resid 23 through 27 Processing helix chain '3' and resid 36 through 45 removed outlier: 5.424A pdb=" N LYS 3 41 " --> pdb=" O ASN 3 37 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA 3 42 " --> pdb=" O GLU 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 72 removed outlier: 4.193A pdb=" N GLU 3 71 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU 3 72 " --> pdb=" O PRO 3 68 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 67 through 72' Processing helix chain '3' and resid 84 through 89 Processing helix chain '3' and resid 109 through 121 removed outlier: 4.206A pdb=" N MET 3 116 " --> pdb=" O GLU 3 112 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 58 No H-bonds generated for 'chain '6' and resid 55 through 58' Processing helix chain '6' and resid 93 through 96 No H-bonds generated for 'chain '6' and resid 93 through 96' Processing helix chain '6' and resid 102 through 106 Processing sheet with id= A, first strand: chain 'H' and resid 135 through 137 Processing sheet with id= B, first strand: chain 'K' and resid 4 through 9 Processing sheet with id= C, first strand: chain 'L' and resid 73 through 75 Processing sheet with id= D, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.566A pdb=" N LEU L 40 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS L 70 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 45 through 50 removed outlier: 3.592A pdb=" N THR L 49 " --> pdb=" O ASP L 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'O' and resid 7 through 9 Processing sheet with id= G, first strand: chain 'T' and resid 80 through 84 removed outlier: 3.808A pdb=" N ILE T 81 " --> pdb=" O VAL T 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'U' and resid 79 through 81 removed outlier: 4.092A pdb=" N ARG U 89 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'U' and resid 111 through 114 removed outlier: 3.503A pdb=" N GLY U 118 " --> pdb=" O VAL U 114 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'X' and resid 54 through 57 removed outlier: 6.606A pdb=" N LYS X 28 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE X 14 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLN X 26 " --> pdb=" O ILE X 14 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Z' and resid 33 through 38 Processing sheet with id= L, first strand: chain 'Z' and resid 144 through 147 Processing sheet with id= M, first strand: chain '3' and resid 31 through 33 removed outlier: 4.104A pdb=" N LYS 3 31 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE 3 102 " --> pdb=" O LYS 3 31 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '3' and resid 51 through 54 removed outlier: 3.539A pdb=" N ILE 3 53 " --> pdb=" O ILE 3 78 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 23 through 26 Processing sheet with id= P, first strand: chain '6' and resid 47 through 49 removed outlier: 4.091A pdb=" N ARG 6 47 " --> pdb=" O VAL 6 39 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 9.38 Time building geometry restraints manager: 11.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3377 1.32 - 1.44: 8677 1.44 - 1.57: 11049 1.57 - 1.69: 969 1.69 - 1.81: 84 Bond restraints: 24156 Sorted by residual: bond pdb=" C4 B8H 2 938 " pdb=" C5 B8H 2 938 " ideal model delta sigma weight residual 1.834 1.369 0.465 2.00e-02 2.50e+03 5.40e+02 bond pdb=" N1 B8H 2 938 " pdb=" C6 B8H 2 938 " ideal model delta sigma weight residual 1.682 1.346 0.336 2.00e-02 2.50e+03 2.82e+02 bond pdb=" N3 B8H 2 938 " pdb=" C4 B8H 2 938 " ideal model delta sigma weight residual 1.136 1.396 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C5 B8H 2 938 " pdb=" C6 B8H 2 938 " ideal model delta sigma weight residual 1.135 1.338 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C5 4AC 21193 " pdb=" C6 4AC 21193 " ideal model delta sigma weight residual 1.493 1.294 0.199 2.00e-02 2.50e+03 9.86e+01 ... (remaining 24151 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.01: 2416 105.01 - 112.38: 12927 112.38 - 119.74: 9061 119.74 - 127.11: 9313 127.11 - 134.47: 1237 Bond angle restraints: 34954 Sorted by residual: angle pdb=" N ILE 3 62 " pdb=" CA ILE 3 62 " pdb=" C ILE 3 62 " ideal model delta sigma weight residual 112.29 105.78 6.51 9.40e-01 1.13e+00 4.79e+01 angle pdb=" N VAL 6 83 " pdb=" CA VAL 6 83 " pdb=" C VAL 6 83 " ideal model delta sigma weight residual 113.71 109.37 4.34 9.50e-01 1.11e+00 2.09e+01 angle pdb=" C2' B8H 2 938 " pdb=" C1' B8H 2 938 " pdb=" C5 B8H 2 938 " ideal model delta sigma weight residual 110.19 123.85 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" N4 4AC 21193 " pdb=" C7 4AC 21193 " pdb=" O7 4AC 21193 " ideal model delta sigma weight residual 119.99 131.88 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N GLY Y 41 " pdb=" CA GLY Y 41 " pdb=" C GLY Y 41 " ideal model delta sigma weight residual 113.58 109.48 4.10 1.07e+00 8.73e-01 1.47e+01 ... (remaining 34949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 13942 33.92 - 67.84: 1304 67.84 - 101.76: 177 101.76 - 135.68: 4 135.68 - 169.60: 2 Dihedral angle restraints: 15429 sinusoidal: 11071 harmonic: 4358 Sorted by residual: dihedral pdb=" O4' C 21132 " pdb=" C1' C 21132 " pdb=" N1 C 21132 " pdb=" C2 C 21132 " ideal model delta sinusoidal sigma weight residual 200.00 73.04 126.96 1 1.50e+01 4.44e-03 6.83e+01 dihedral pdb=" O4' U 2 932 " pdb=" C1' U 2 932 " pdb=" N1 U 2 932 " pdb=" C2 U 2 932 " ideal model delta sinusoidal sigma weight residual 232.00 62.40 169.60 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" CA PRO K 119 " pdb=" C PRO K 119 " pdb=" N ASN K 120 " pdb=" CA ASN K 120 " ideal model delta harmonic sigma weight residual 180.00 148.57 31.43 0 5.00e+00 4.00e-02 3.95e+01 ... (remaining 15426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3798 0.089 - 0.178: 403 0.178 - 0.266: 18 0.266 - 0.355: 4 0.355 - 0.444: 1 Chirality restraints: 4224 Sorted by residual: chirality pdb=" C1' B8H 2 938 " pdb=" O4' B8H 2 938 " pdb=" C2' B8H 2 938 " pdb=" C5 B8H 2 938 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1' G 2 987 " pdb=" O4' G 2 987 " pdb=" C2' G 2 987 " pdb=" N9 G 2 987 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1' A 21199 " pdb=" O4' A 21199 " pdb=" C2' A 21199 " pdb=" N9 A 21199 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4221 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 4 33 " -0.025 2.00e-02 2.50e+03 5.45e-01 6.69e+03 pdb=" C4' OMC 4 33 " -0.418 2.00e-02 2.50e+03 pdb=" O4' OMC 4 33 " -0.584 2.00e-02 2.50e+03 pdb=" C3' OMC 4 33 " 0.593 2.00e-02 2.50e+03 pdb=" O3' OMC 4 33 " 0.527 2.00e-02 2.50e+03 pdb=" C2' OMC 4 33 " 0.221 2.00e-02 2.50e+03 pdb=" O2' OMC 4 33 " -0.878 2.00e-02 2.50e+03 pdb=" C1' OMC 4 33 " -0.241 2.00e-02 2.50e+03 pdb=" N1 OMC 4 33 " 0.807 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21202 " -0.004 2.00e-02 2.50e+03 5.32e-01 6.37e+03 pdb=" C4' 5MC 21202 " -0.423 2.00e-02 2.50e+03 pdb=" O4' 5MC 21202 " -0.595 2.00e-02 2.50e+03 pdb=" C3' 5MC 21202 " 0.579 2.00e-02 2.50e+03 pdb=" O3' 5MC 21202 " 0.483 2.00e-02 2.50e+03 pdb=" C2' 5MC 21202 " 0.242 2.00e-02 2.50e+03 pdb=" O2' 5MC 21202 " -0.832 2.00e-02 2.50e+03 pdb=" C1' 5MC 21202 " -0.246 2.00e-02 2.50e+03 pdb=" N1 5MC 21202 " 0.796 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 2 939 " -0.021 2.00e-02 2.50e+03 5.01e-01 5.65e+03 pdb=" C4' 5MC 2 939 " -0.407 2.00e-02 2.50e+03 pdb=" O4' 5MC 2 939 " -0.462 2.00e-02 2.50e+03 pdb=" C3' 5MC 2 939 " 0.577 2.00e-02 2.50e+03 pdb=" O3' 5MC 2 939 " 0.462 2.00e-02 2.50e+03 pdb=" C2' 5MC 2 939 " 0.241 2.00e-02 2.50e+03 pdb=" O2' 5MC 2 939 " -0.848 2.00e-02 2.50e+03 pdb=" C1' 5MC 2 939 " -0.247 2.00e-02 2.50e+03 pdb=" N1 5MC 2 939 " 0.706 2.00e-02 2.50e+03 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 149 2.54 - 3.13: 15601 3.13 - 3.72: 35111 3.72 - 4.31: 54924 4.31 - 4.90: 81536 Nonbonded interactions: 187321 Sorted by model distance: nonbonded pdb=" OP2 G 21172 " pdb="MG MG 21402 " model vdw 1.948 2.170 nonbonded pdb=" O6 G 21196 " pdb="MG MG 21403 " model vdw 1.968 2.170 nonbonded pdb=" OP1 C 21277 " pdb="MG MG 21406 " model vdw 2.071 2.170 nonbonded pdb=" OP1 G 21171 " pdb="MG MG 21402 " model vdw 2.132 2.170 nonbonded pdb=" O2' G 21155 " pdb=" O5' G 21156 " model vdw 2.132 2.440 ... (remaining 187316 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: 1.970 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: 0.020 Extract box with map and model: 9.960 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 71.460 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.012 0.465 24156 Z= 0.783 Angle : 0.978 13.657 34954 Z= 0.514 Chirality : 0.055 0.444 4224 Planarity : 0.019 0.545 2642 Dihedral : 21.991 169.603 12627 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 1.17 % Allowed : 11.08 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.83 (0.17), residues: 1497 helix: -2.93 (0.17), residues: 510 sheet: -3.39 (0.29), residues: 183 loop : -3.42 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 64 HIS 0.010 0.002 HIS H 46 PHE 0.047 0.003 PHE H 180 TYR 0.020 0.003 TYR U 150 ARG 0.008 0.001 ARG K 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 310 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.7313 (mtt90) cc_final: 0.5244 (ppt170) REVERT: S 34 LYS cc_start: 0.8830 (tppp) cc_final: 0.8364 (tppt) REVERT: S 37 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7224 (mm-30) REVERT: Y 31 MET cc_start: 0.6659 (tpp) cc_final: 0.6247 (tpt) REVERT: Z 186 ASP cc_start: 0.7301 (p0) cc_final: 0.7010 (p0) REVERT: 3 32 ILE cc_start: 0.4356 (mm) cc_final: 0.3966 (mm) outliers start: 15 outliers final: 5 residues processed: 319 average time/residue: 0.4244 time to fit residues: 196.1651 Evaluate side-chains 238 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 6 residue 27 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 176 optimal weight: 0.0370 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 69 ASN H 94 ASN H 129 ASN K 117 HIS L 84 GLN S 30 HIS S 31 ASN S 48 ASN T 84 HIS U 18 GLN Z 72 GLN Z 95 GLN Z 123 ASN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24156 Z= 0.173 Angle : 0.709 15.293 34954 Z= 0.381 Chirality : 0.040 0.227 4224 Planarity : 0.006 0.117 2642 Dihedral : 22.435 170.359 9411 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.11 % Allowed : 15.52 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.19), residues: 1497 helix: -1.49 (0.22), residues: 512 sheet: -2.31 (0.31), residues: 201 loop : -2.87 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 51 HIS 0.003 0.001 HIS O 72 PHE 0.014 0.001 PHE Y 21 TYR 0.021 0.001 TYR Y 45 ARG 0.009 0.000 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 259 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.7192 (mtt90) cc_final: 0.5198 (ttp80) REVERT: Z 18 ASP cc_start: 0.7297 (t0) cc_final: 0.7057 (t0) REVERT: 3 32 ILE cc_start: 0.4838 (mm) cc_final: 0.4576 (mm) outliers start: 27 outliers final: 14 residues processed: 273 average time/residue: 0.3850 time to fit residues: 160.2759 Evaluate side-chains 252 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 190 optimal weight: 50.0000 chunk 157 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 141 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 58 GLN S 31 ASN U 18 GLN Y 19 ASN Z 72 GLN Z 123 ASN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24156 Z= 0.164 Angle : 0.651 14.520 34954 Z= 0.349 Chirality : 0.037 0.230 4224 Planarity : 0.006 0.124 2642 Dihedral : 22.325 174.598 9406 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.73 % Allowed : 16.46 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.20), residues: 1497 helix: -0.70 (0.23), residues: 519 sheet: -1.62 (0.33), residues: 207 loop : -2.51 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 5 HIS 0.003 0.001 HIS P 41 PHE 0.012 0.001 PHE Y 21 TYR 0.016 0.001 TYR Y 45 ARG 0.004 0.000 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.8731 (t) cc_final: 0.8411 (p) REVERT: H 215 ARG cc_start: 0.6906 (mtt90) cc_final: 0.4967 (ptt90) REVERT: L 3 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7274 (mmmt) REVERT: Y 31 MET cc_start: 0.6863 (tpp) cc_final: 0.5761 (tpp) REVERT: 3 32 ILE cc_start: 0.4540 (mm) cc_final: 0.4317 (mm) outliers start: 35 outliers final: 22 residues processed: 271 average time/residue: 0.3674 time to fit residues: 151.9222 Evaluate side-chains 263 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 13 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 92 optimal weight: 0.0470 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 31 ASN Y 3 GLN Z 72 GLN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24156 Z= 0.299 Angle : 0.713 14.628 34954 Z= 0.378 Chirality : 0.041 0.234 4224 Planarity : 0.006 0.129 2642 Dihedral : 22.353 172.047 9405 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.59 % Allowed : 17.47 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.21), residues: 1497 helix: -0.20 (0.24), residues: 510 sheet: -1.35 (0.33), residues: 219 loop : -2.32 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 77 HIS 0.004 0.001 HIS T 84 PHE 0.017 0.002 PHE H 180 TYR 0.012 0.001 TYR Y 45 ARG 0.005 0.000 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.7221 (mtt90) cc_final: 0.5215 (ptt90) REVERT: O 15 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7968 (pp) REVERT: X 42 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8205 (ttm170) REVERT: X 59 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6816 (mt-10) REVERT: Y 18 LYS cc_start: 0.8008 (tppp) cc_final: 0.7778 (ttmt) REVERT: Y 31 MET cc_start: 0.6407 (tpp) cc_final: 0.5546 (tpp) REVERT: Y 45 TYR cc_start: 0.6923 (m-80) cc_final: 0.6719 (m-10) outliers start: 46 outliers final: 34 residues processed: 273 average time/residue: 0.3619 time to fit residues: 149.7369 Evaluate side-chains 272 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 42 ARG Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 51 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 13 VAL Chi-restraints excluded: chain 6 residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.0000 chunk 168 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 2 GLN U 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24156 Z= 0.147 Angle : 0.655 14.109 34954 Z= 0.350 Chirality : 0.037 0.216 4224 Planarity : 0.006 0.122 2642 Dihedral : 22.317 174.398 9405 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.89 % Allowed : 19.34 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1497 helix: 0.19 (0.24), residues: 509 sheet: -0.98 (0.35), residues: 210 loop : -2.14 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 5 HIS 0.003 0.001 HIS P 41 PHE 0.011 0.001 PHE Z 7 TYR 0.012 0.001 TYR S 53 ARG 0.004 0.000 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.7041 (mtt90) cc_final: 0.5141 (ptt90) REVERT: Y 18 LYS cc_start: 0.7927 (tppp) cc_final: 0.7723 (ttmt) REVERT: Y 31 MET cc_start: 0.6270 (tpp) cc_final: 0.6034 (tpp) outliers start: 37 outliers final: 28 residues processed: 274 average time/residue: 0.3734 time to fit residues: 155.2291 Evaluate side-chains 273 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 245 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 126 SER Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 92 ILE Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 13 VAL Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 82 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 0.0030 chunk 187 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 2.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 2 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24156 Z= 0.339 Angle : 0.730 14.458 34954 Z= 0.385 Chirality : 0.042 0.232 4224 Planarity : 0.006 0.129 2642 Dihedral : 22.331 171.834 9405 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.90 % Allowed : 19.03 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.22), residues: 1497 helix: 0.28 (0.24), residues: 514 sheet: -0.92 (0.34), residues: 218 loop : -2.02 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 77 HIS 0.004 0.001 HIS T 84 PHE 0.017 0.002 PHE H 180 TYR 0.024 0.002 TYR Z 6 ARG 0.008 0.000 ARG 6 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.7133 (mtt90) cc_final: 0.5242 (ptt90) REVERT: Y 18 LYS cc_start: 0.7989 (tppp) cc_final: 0.7701 (ttmt) REVERT: Y 31 MET cc_start: 0.6369 (tpp) cc_final: 0.6131 (tpp) REVERT: Z 18 ASP cc_start: 0.7423 (t0) cc_final: 0.7147 (t0) outliers start: 50 outliers final: 40 residues processed: 262 average time/residue: 0.3719 time to fit residues: 147.5298 Evaluate side-chains 267 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain T residue 126 SER Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 51 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 92 ILE Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 13 VAL Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 117 optimal weight: 0.5980 chunk 113 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 18 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24156 Z= 0.151 Angle : 0.659 14.019 34954 Z= 0.351 Chirality : 0.037 0.204 4224 Planarity : 0.006 0.122 2642 Dihedral : 22.293 174.122 9405 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.96 % Allowed : 21.37 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1497 helix: 0.59 (0.25), residues: 510 sheet: -0.60 (0.35), residues: 210 loop : -1.92 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 5 HIS 0.003 0.001 HIS P 41 PHE 0.015 0.001 PHE Y 21 TYR 0.012 0.001 TYR S 53 ARG 0.005 0.000 ARG S 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 245 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.8898 (t) cc_final: 0.8697 (p) REVERT: H 215 ARG cc_start: 0.6737 (mtt90) cc_final: 0.5161 (ttt-90) REVERT: X 59 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6882 (mt-10) REVERT: Y 18 LYS cc_start: 0.7891 (tppp) cc_final: 0.7654 (ttmt) outliers start: 38 outliers final: 31 residues processed: 264 average time/residue: 0.3935 time to fit residues: 159.0209 Evaluate side-chains 269 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 SER Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 13 VAL Chi-restraints excluded: chain 6 residue 59 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 18 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24156 Z= 0.327 Angle : 0.727 14.379 34954 Z= 0.383 Chirality : 0.041 0.236 4224 Planarity : 0.006 0.128 2642 Dihedral : 22.308 172.147 9405 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.21 % Allowed : 20.51 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1497 helix: 0.54 (0.24), residues: 519 sheet: -0.49 (0.35), residues: 214 loop : -1.93 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 77 HIS 0.004 0.001 HIS P 41 PHE 0.016 0.002 PHE H 180 TYR 0.017 0.001 TYR S 53 ARG 0.007 0.000 ARG S 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 234 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.7070 (mtt90) cc_final: 0.5338 (ptt90) REVERT: Y 1 MET cc_start: 0.1527 (mtm) cc_final: 0.0765 (ttm) REVERT: Z 186 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6806 (p0) outliers start: 54 outliers final: 39 residues processed: 262 average time/residue: 0.3609 time to fit residues: 145.1435 Evaluate side-chains 268 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 228 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 SER Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.0970 chunk 174 optimal weight: 0.4980 chunk 179 optimal weight: 6.9990 chunk 104 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 18 GLN Z 148 GLN ** 3 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 24156 Z= 0.151 Angle : 0.671 13.846 34954 Z= 0.356 Chirality : 0.037 0.255 4224 Planarity : 0.006 0.120 2642 Dihedral : 22.271 175.115 9405 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.96 % Allowed : 22.39 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.22), residues: 1497 helix: 0.73 (0.25), residues: 513 sheet: -0.35 (0.36), residues: 210 loop : -1.84 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 5 HIS 0.003 0.001 HIS P 41 PHE 0.010 0.001 PHE Y 21 TYR 0.010 0.001 TYR S 53 ARG 0.006 0.000 ARG S 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.6600 (mtt90) cc_final: 0.5321 (ttt-90) REVERT: S 22 ASN cc_start: 0.7738 (p0) cc_final: 0.7483 (p0) REVERT: T 17 MET cc_start: 0.6886 (tpt) cc_final: 0.6536 (tpt) REVERT: Z 186 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6533 (p0) REVERT: 3 15 LEU cc_start: 0.6476 (pt) cc_final: 0.5630 (mt) outliers start: 38 outliers final: 35 residues processed: 267 average time/residue: 0.3577 time to fit residues: 145.6100 Evaluate side-chains 272 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 SER Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 66 LEU Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 94 optimal weight: 0.0030 chunk 122 optimal weight: 4.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 31 ASN U 18 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 24156 Z= 0.462 Angle : 0.811 14.572 34954 Z= 0.422 Chirality : 0.045 0.249 4224 Planarity : 0.007 0.132 2642 Dihedral : 22.351 170.089 9405 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.43 % Allowed : 22.39 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1497 helix: 0.50 (0.24), residues: 521 sheet: -0.36 (0.35), residues: 217 loop : -1.95 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 77 HIS 0.006 0.002 HIS T 84 PHE 0.022 0.002 PHE H 180 TYR 0.020 0.002 TYR S 53 ARG 0.007 0.001 ARG S 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 215 ARG cc_start: 0.7085 (mtt90) cc_final: 0.5503 (ttp-170) REVERT: X 59 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6801 (mt-10) REVERT: Z 186 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6954 (p0) outliers start: 44 outliers final: 34 residues processed: 245 average time/residue: 0.3720 time to fit residues: 139.7428 Evaluate side-chains 248 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 126 SER Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 0.0770 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 31 ASN ** 3 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049573 restraints weight = 75490.738| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.56 r_work: 0.2686 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 24156 Z= 0.155 Angle : 0.686 14.009 34954 Z= 0.364 Chirality : 0.037 0.192 4224 Planarity : 0.006 0.119 2642 Dihedral : 22.283 173.395 9405 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.73 % Allowed : 23.17 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1497 helix: 0.81 (0.25), residues: 515 sheet: -0.28 (0.36), residues: 207 loop : -1.81 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 48 HIS 0.003 0.001 HIS H 51 PHE 0.020 0.001 PHE Y 21 TYR 0.010 0.001 TYR P 6 ARG 0.008 0.000 ARG 6 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4569.70 seconds wall clock time: 83 minutes 52.85 seconds (5032.85 seconds total)