Starting phenix.real_space_refine on Mon Sep 30 05:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/09_2024/6ddg_7870_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/09_2024/6ddg_7870.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/09_2024/6ddg_7870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/09_2024/6ddg_7870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/09_2024/6ddg_7870_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddg_7870/09_2024/6ddg_7870_trim.cif" } 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= 0.001 sd= 0.008 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 2747 5.49 5 S 55 5.16 5 Cl 1 4.86 5 C 39210 2.51 5 N 14779 2.21 5 O 22791 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.91s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 79584 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2063 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain breaks: 1 Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "F" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 684 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "G" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 697 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "J" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "K" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 463 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1441 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "X" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1082 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "Y" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "Z" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 787 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 2 Chain: "1" Number of atoms: 56747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2646, 56747 Inner-chain residues flagged as termini: ['pdbres=" A 11459 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2646} Modifications used: {'5*END': 3, 'rna2p_pur': 266, 'rna2p_pyr': 132, 'rna3p_pur': 1258, 'rna3p_pyr': 990} Link IDs: {'rna2p': 398, 'rna3p': 2247} Chain breaks: 9 Chain: "2" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2214 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 45} Link IDs: {'rna2p': 13, 'rna3p': 90} Chain: "1" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'G6M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 32.52, per 1000 atoms: 0.41 Number of scatterers: 79584 At special positions: 0 Unit cell: (201.4, 221.54, 182.32, 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) Cl 1 17.00 S 55 16.00 P 2747 15.00 F 1 9.00 O 22791 8.00 N 14779 7.00 C 39210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 13.31 Conformation dependent library (CDL) restraints added in 2.9 seconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4782 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 25.6% alpha, 19.1% beta 817 base pairs and 1454 stacking pairs defined. Time for finding SS restraints: 29.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 197 through 203 removed outlier: 3.625A pdb=" N HIS B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 203 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'C' and resid 7 through 19 removed outlier: 4.298A pdb=" N ARG C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 70 removed outlier: 3.911A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'E' and resid 13 through 25 removed outlier: 4.396A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.732A pdb=" N ILE E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 removed outlier: 4.102A pdb=" N VAL E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.623A pdb=" N ALA F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 47 removed outlier: 3.525A pdb=" N LYS F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 23 Processing helix chain 'H' and resid 48 through 56 removed outlier: 4.272A pdb=" N GLU H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 removed outlier: 3.851A pdb=" N SER H 67 " --> pdb=" O GLY H 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'J' and resid 52 through 55 removed outlier: 3.859A pdb=" N LYS J 55 " --> pdb=" O ARG J 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 52 through 55' Processing helix chain 'K' and resid 10 through 22 Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 40 through 60 removed outlier: 3.819A pdb=" N ARG K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 79 Processing helix chain 'L' and resid 106 through 110 removed outlier: 3.570A pdb=" N THR L 109 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 135 Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 45 through 50 removed outlier: 3.708A pdb=" N LYS M 49 " --> pdb=" O GLY M 45 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL M 50 " --> pdb=" O GLN M 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 45 through 50' Processing helix chain 'N' and resid 9 through 17 removed outlier: 3.742A pdb=" N ASN N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 18 Processing helix chain 'P' and resid 18 through 23 Processing helix chain 'P' and resid 25 through 39 removed outlier: 3.618A pdb=" N LYS P 38 " --> pdb=" O ARG P 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.999A pdb=" N LYS Q 12 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.985A pdb=" N LYS Q 36 " --> pdb=" O PHE Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 42 Processing helix chain 'Q' and resid 51 through 58 Processing helix chain 'R' and resid 29 through 33 Processing helix chain 'S' and resid 29 through 43 removed outlier: 3.779A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 120 removed outlier: 3.902A pdb=" N LEU S 114 " --> pdb=" O LEU S 110 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 145 removed outlier: 3.812A pdb=" N PHE S 139 " --> pdb=" O LYS S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 168 removed outlier: 3.589A pdb=" N GLU S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU S 165 " --> pdb=" O VAL S 161 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER S 166 " --> pdb=" O ASN S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 181 No H-bonds generated for 'chain 'S' and resid 179 through 181' Processing helix chain 'S' and resid 182 through 189 removed outlier: 3.676A pdb=" N THR S 187 " --> pdb=" O VAL S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 197 through 206 Processing helix chain 'V' and resid 25 through 39 removed outlier: 4.116A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE V 36 " --> pdb=" O GLU V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 63 removed outlier: 4.073A pdb=" N ILE V 63 " --> pdb=" O ALA V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 95 removed outlier: 3.603A pdb=" N ARG V 95 " --> pdb=" O GLY V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 108 removed outlier: 4.125A pdb=" N GLU V 103 " --> pdb=" O GLU V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 121 removed outlier: 3.786A pdb=" N LYS V 121 " --> pdb=" O GLU V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 103 through 107 Processing helix chain 'W' and resid 111 through 118 Processing helix chain 'X' and resid 56 through 60 removed outlier: 3.864A pdb=" N ARG X 59 " --> pdb=" O PRO X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 99 removed outlier: 3.573A pdb=" N GLU X 98 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 94 through 99' Processing helix chain 'X' and resid 130 through 139 removed outlier: 3.735A pdb=" N GLU X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS X 139 " --> pdb=" O ALA X 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 58 removed outlier: 3.615A pdb=" N SER Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 123 removed outlier: 3.664A pdb=" N HIS Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 28 Processing helix chain 'Z' and resid 34 through 54 removed outlier: 4.392A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS Z 46 " --> pdb=" O SER Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 63 Processing helix chain 'Z' and resid 81 through 93 removed outlier: 4.145A pdb=" N ILE Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA Z 90 " --> pdb=" O PHE Z 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 19 removed outlier: 4.078A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 88 Processing helix chain 'a' and resid 103 through 115 removed outlier: 3.914A pdb=" N ALA a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG a 113 " --> pdb=" O ALA a 109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU a 114 " --> pdb=" O GLU a 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 8.838A pdb=" N GLY A 47 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ILE A 66 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL A 49 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 64 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 51 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 82 removed outlier: 6.689A pdb=" N LEU B 93 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 81 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.658A pdb=" N LEU B 173 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS B 167 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.867A pdb=" N PHE D 2 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL D 41 " --> pdb=" O PHE D 2 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE D 4 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 39 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 50 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 23 removed outlier: 6.391A pdb=" N THR D 96 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL D 62 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP D 98 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA D 60 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 62 " --> pdb=" O ASP D 31 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP D 31 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.341A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 10 removed outlier: 5.095A pdb=" N LYS E 4 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL E 107 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL E 6 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE E 105 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG E 8 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE E 103 " --> pdb=" O ARG E 8 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL E 71 " --> pdb=" O SER E 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 82 through 87 Processing sheet with id=AB2, first strand: chain 'F' and resid 7 through 10 removed outlier: 4.258A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE F 79 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL F 53 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR F 81 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 7 through 10 removed outlier: 4.258A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 75 " --> pdb=" O TYR F 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'G' and resid 26 through 27 removed outlier: 3.561A pdb=" N ARG G 32 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 40 through 43 Processing sheet with id=AB7, first strand: chain 'G' and resid 81 through 85 Processing sheet with id=AB8, first strand: chain 'H' and resid 40 through 44 removed outlier: 9.211A pdb=" N LYS H 26 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ILE H 89 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE H 91 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL H 30 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLN H 78 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.724A pdb=" N LEU I 67 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AC2, first strand: chain 'J' and resid 13 through 18 Processing sheet with id=AC3, first strand: chain 'J' and resid 33 through 38 Processing sheet with id=AC4, first strand: chain 'L' and resid 177 through 183 removed outlier: 4.087A pdb=" N ASN L 182 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE L 116 " --> pdb=" O ASN L 182 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS L 9 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU L 29 " --> pdb=" O LYS L 9 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY L 11 " --> pdb=" O VAL L 27 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN L 187 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS L 198 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL L 185 " --> pdb=" O LYS L 198 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 34 through 39 removed outlier: 6.458A pdb=" N GLN L 50 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS L 38 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA L 48 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN L 50 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU L 90 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY L 52 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE L 88 " --> pdb=" O GLY L 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 124 through 128 removed outlier: 3.910A pdb=" N PHE L 127 " --> pdb=" O GLY L 171 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY L 171 " --> pdb=" O PHE L 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 34 through 36 Processing sheet with id=AC8, first strand: chain 'N' and resid 27 through 29 Processing sheet with id=AC9, first strand: chain 'O' and resid 6 through 7 Processing sheet with id=AD1, first strand: chain 'O' and resid 32 through 36 Processing sheet with id=AD2, first strand: chain 'Q' and resid 14 through 16 removed outlier: 3.694A pdb=" N LYS Q 15 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Q 48 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 15 through 19 removed outlier: 3.536A pdb=" N GLN R 34 " --> pdb=" O VAL R 25 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 173 through 177 removed outlier: 6.341A pdb=" N LEU S 153 " --> pdb=" O VAL S 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 123 through 125 removed outlier: 6.234A pdb=" N TYR V 17 " --> pdb=" O ILE V 56 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE V 58 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE V 19 " --> pdb=" O ILE V 58 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP V 16 " --> pdb=" O GLU V 139 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 74 through 78 Processing sheet with id=AD7, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.867A pdb=" N VAL W 40 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL W 24 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL W 38 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS W 59 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N CYS W 84 " --> pdb=" O ARG W 7 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS W 9 " --> pdb=" O CYS W 84 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE W 86 " --> pdb=" O LYS W 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 75 through 77 removed outlier: 6.019A pdb=" N ALA X 75 " --> pdb=" O LYS X 110 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 88 through 91 removed outlier: 3.537A pdb=" N THR X 122 " --> pdb=" O THR X 89 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 63 through 66 removed outlier: 6.634A pdb=" N ILE Y 102 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA Y 36 " --> pdb=" O ILE Y 102 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE Y 104 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 40 through 43 removed outlier: 5.250A pdb=" N VAL Y 90 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS Y 76 " --> pdb=" O VAL Y 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY Y 92 " --> pdb=" O TYR Y 74 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 29 through 33 Processing sheet with id=AE4, first strand: chain 'Z' and resid 29 through 33 removed outlier: 6.408A pdb=" N SER Z 116 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 70 through 71 removed outlier: 3.707A pdb=" N GLN Z 79 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 43 through 45 620 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2056 hydrogen bonds 3320 hydrogen bond angles 0 basepair planarities 817 basepair parallelities 1454 stacking parallelities Total time for adding SS restraints: 124.82 Time building geometry restraints manager: 16.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12563 1.33 - 1.46: 38494 1.46 - 1.58: 30326 1.58 - 1.71: 5429 1.71 - 1.83: 97 Bond restraints: 86909 Sorted by residual: bond pdb=" C12 G6M 13001 " pdb=" O11 G6M 13001 " ideal model delta sigma weight residual 1.339 1.447 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C1' U 2 68 " pdb=" N1 U 2 68 " ideal model delta sigma weight residual 1.480 1.561 -0.081 1.50e-02 4.44e+03 2.91e+01 bond pdb=" C12 G6M 13001 " pdb=" N8 G6M 13001 " ideal model delta sigma weight residual 1.364 1.311 0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C ARG M 20 " pdb=" O ARG M 20 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.22e+00 bond pdb=" O5' A 11926 " pdb=" C5' A 11926 " ideal model delta sigma weight residual 1.420 1.451 -0.031 1.50e-02 4.44e+03 4.18e+00 ... (remaining 86904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 130141 3.26 - 6.53: 695 6.53 - 9.79: 28 9.79 - 13.05: 6 13.05 - 16.31: 4 Bond angle restraints: 130874 Sorted by residual: angle pdb=" O2' C 2 91 " pdb=" C2' C 2 91 " pdb=" C1' C 2 91 " ideal model delta sigma weight residual 108.40 92.09 16.31 1.50e+00 4.44e-01 1.18e+02 angle pdb=" O2' G 11924 " pdb=" C2' G 11924 " pdb=" C1' G 11924 " ideal model delta sigma weight residual 108.40 92.42 15.98 1.50e+00 4.44e-01 1.13e+02 angle pdb=" O2' A 11954 " pdb=" C2' A 11954 " pdb=" C1' A 11954 " ideal model delta sigma weight residual 108.40 92.54 15.86 1.50e+00 4.44e-01 1.12e+02 angle pdb=" O2' U 2 90 " pdb=" C2' U 2 90 " pdb=" C1' U 2 90 " ideal model delta sigma weight residual 108.40 94.60 13.80 1.50e+00 4.44e-01 8.46e+01 angle pdb=" C4' G 11867 " pdb=" C3' G 11867 " pdb=" O3' G 11867 " ideal model delta sigma weight residual 113.00 125.16 -12.16 1.50e+00 4.44e-01 6.58e+01 ... (remaining 130869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48663 35.95 - 71.89: 6160 71.89 - 107.84: 668 107.84 - 143.78: 20 143.78 - 179.73: 37 Dihedral angle restraints: 55548 sinusoidal: 48104 harmonic: 7444 Sorted by residual: dihedral pdb=" O4' U 1 403 " pdb=" C1' U 1 403 " pdb=" N1 U 1 403 " pdb=" C2 U 1 403 " ideal model delta sinusoidal sigma weight residual 200.00 20.27 179.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12607 " pdb=" C1' U 12607 " pdb=" N1 U 12607 " pdb=" C2 U 12607 " ideal model delta sinusoidal sigma weight residual -160.00 18.46 -178.46 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 12639 " pdb=" C1' C 12639 " pdb=" N1 C 12639 " pdb=" C2 C 12639 " ideal model delta sinusoidal sigma weight residual 200.00 23.60 176.40 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 55545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 15374 0.075 - 0.150: 1353 0.150 - 0.226: 114 0.226 - 0.301: 18 0.301 - 0.376: 4 Chirality restraints: 16863 Sorted by residual: chirality pdb=" C1' A 1 125 " pdb=" O4' A 1 125 " pdb=" C2' A 1 125 " pdb=" N9 A 1 125 " both_signs ideal model delta sigma weight residual False 2.46 2.08 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C3' G 11930 " pdb=" C4' G 11930 " pdb=" O3' G 11930 " pdb=" C2' G 11930 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' G 11866 " pdb=" C4' G 11866 " pdb=" O3' G 11866 " pdb=" C2' G 11866 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 16860 not shown) Planarity restraints: 6328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 11867 " -0.040 2.00e-02 2.50e+03 2.33e-02 1.63e+01 pdb=" N9 G 11867 " 0.068 2.00e-02 2.50e+03 pdb=" C8 G 11867 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G 11867 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 11867 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G 11867 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G 11867 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G 11867 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G 11867 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 11867 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G 11867 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 11867 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 557 " 0.048 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" N9 G 1 557 " -0.050 2.00e-02 2.50e+03 pdb=" C8 G 1 557 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 1 557 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 557 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 1 557 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G 1 557 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G 1 557 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G 1 557 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G 1 557 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 557 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G 1 557 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 91 " 0.035 2.00e-02 2.50e+03 2.20e-02 1.08e+01 pdb=" N1 C 2 91 " -0.055 2.00e-02 2.50e+03 pdb=" C2 C 2 91 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C 2 91 " -0.000 2.00e-02 2.50e+03 pdb=" N3 C 2 91 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C 2 91 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C 2 91 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C 2 91 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C 2 91 " -0.000 2.00e-02 2.50e+03 ... (remaining 6325 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1814 2.61 - 3.18: 63126 3.18 - 3.76: 153916 3.76 - 4.33: 223718 4.33 - 4.90: 294857 Nonbonded interactions: 737431 Sorted by model distance: nonbonded pdb=" OH TYR Y 57 " pdb=" OE1 GLU Y 116 " model vdw 2.040 3.040 nonbonded pdb=" O2' U 11510 " pdb=" O4' C 11511 " model vdw 2.040 3.040 nonbonded pdb=" OP1 U 11063 " pdb=" O2' U 11079 " model vdw 2.044 3.040 nonbonded pdb=" O2' A 1 645 " pdb=" O2' G 1 647 " model vdw 2.044 3.040 nonbonded pdb=" O2' A 12740 " pdb=" OP2 C 12742 " model vdw 2.049 3.040 ... (remaining 737426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.110 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: 0.090 Extract box with map and model: 2.330 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 238.580 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.230 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: 0.030 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.007 0.108 86909 Z= 0.419 Angle : 0.779 16.314 130874 Z= 0.414 Chirality : 0.044 0.376 16863 Planarity : 0.005 0.059 6328 Dihedral : 23.682 179.725 50760 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.13), residues: 2575 helix: -2.72 (0.16), residues: 625 sheet: -2.67 (0.20), residues: 480 loop : -3.22 (0.13), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP B 213 HIS 0.013 0.002 HIS B 53 PHE 0.042 0.003 PHE K 30 TYR 0.040 0.003 TYR F 58 ARG 0.023 0.002 ARG X 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 739 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7141 (mtm180) cc_final: 0.6711 (mtt180) REVERT: B 77 LYS cc_start: 0.7533 (tppt) cc_final: 0.7303 (tptt) REVERT: B 171 TYR cc_start: 0.8141 (m-80) cc_final: 0.7642 (m-80) REVERT: D 81 ASN cc_start: 0.7442 (m-40) cc_final: 0.7241 (m-40) REVERT: E 27 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8403 (mmtm) REVERT: F 49 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7602 (mmmm) REVERT: F 65 MET cc_start: 0.4649 (ptm) cc_final: 0.4297 (mmm) REVERT: H 18 LEU cc_start: 0.8369 (mt) cc_final: 0.8096 (mt) REVERT: H 23 LYS cc_start: 0.7528 (mptp) cc_final: 0.7162 (tptt) REVERT: I 84 LYS cc_start: 0.7915 (mttp) cc_final: 0.7602 (mtmm) REVERT: K 14 ILE cc_start: 0.7447 (mm) cc_final: 0.7106 (tt) REVERT: K 20 SER cc_start: 0.8587 (m) cc_final: 0.8365 (m) REVERT: M 44 ARG cc_start: 0.7720 (tpp80) cc_final: 0.7519 (mmm-85) REVERT: O 1 MET cc_start: 0.4680 (ptp) cc_final: 0.4337 (mtp) REVERT: O 40 ASN cc_start: 0.8435 (t0) cc_final: 0.8137 (t0) REVERT: W 5 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7723 (mm-30) REVERT: W 31 LYS cc_start: 0.8234 (pmmt) cc_final: 0.8034 (ptpp) REVERT: X 15 GLU cc_start: 0.6374 (pt0) cc_final: 0.5869 (mt-10) REVERT: Z 89 ILE cc_start: 0.8710 (mm) cc_final: 0.8318 (mt) REVERT: a 38 LYS cc_start: 0.6578 (pttt) cc_final: 0.6296 (mptt) REVERT: a 99 TYR cc_start: 0.7084 (m-80) cc_final: 0.6805 (m-80) outliers start: 1 outliers final: 1 residues processed: 740 average time/residue: 0.8703 time to fit residues: 1041.4650 Evaluate side-chains 554 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 553 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 6.9990 chunk 400 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 213 optimal weight: 0.0870 chunk 413 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 479 optimal weight: 5.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 4 HIS ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 70 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 38 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 57 ASN E 65 ASN F 54 ASN G 44 HIS H 38 ASN H 85 GLN H 88 HIS J 16 ASN K 17 GLN K 27 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 HIS L 146 HIS L 182 ASN M 52 HIS O 45 HIS P 7 GLN P 9 ASN P 17 HIS Q 7 HIS Q 31 HIS Q 35 ASN ** S 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN S 75 GLN S 148 GLN S 169 ASN S 188 ASN V 8 ASN V 24 GLN V 48 HIS X 4 HIS X 17 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 71 HIS Y 123 HIS Z 83 GLN a 39 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 86909 Z= 0.471 Angle : 0.831 12.026 130874 Z= 0.414 Chirality : 0.047 0.379 16863 Planarity : 0.007 0.071 6328 Dihedral : 24.256 179.401 45447 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.00 % Allowed : 11.46 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.14), residues: 2575 helix: -1.82 (0.18), residues: 635 sheet: -2.29 (0.21), residues: 484 loop : -2.76 (0.13), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 213 HIS 0.012 0.002 HIS A 4 PHE 0.042 0.003 PHE Z 86 TYR 0.035 0.003 TYR F 58 ARG 0.011 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 534 time to evaluate : 3.158 Fit side-chains revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7037 (mtm180) cc_final: 0.6629 (mtt180) REVERT: B 77 LYS cc_start: 0.7709 (tppt) cc_final: 0.7424 (tptp) REVERT: B 134 ASN cc_start: 0.7852 (m-40) cc_final: 0.7479 (m110) REVERT: D 15 GLU cc_start: 0.6913 (mp0) cc_final: 0.6631 (mp0) REVERT: D 18 GLN cc_start: 0.7814 (tt0) cc_final: 0.7417 (tt0) REVERT: E 90 GLN cc_start: 0.8313 (mt0) cc_final: 0.8052 (mt0) REVERT: F 8 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7988 (mtmp) REVERT: F 65 MET cc_start: 0.4416 (ptm) cc_final: 0.4104 (mmm) REVERT: I 84 LYS cc_start: 0.7922 (mttp) cc_final: 0.7630 (mtmm) REVERT: K 14 ILE cc_start: 0.7602 (mm) cc_final: 0.7073 (tt) REVERT: K 37 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6947 (tp) REVERT: L 116 ILE cc_start: 0.8794 (pp) cc_final: 0.8556 (pt) REVERT: M 6 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8174 (mt) REVERT: M 44 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7620 (mmm-85) REVERT: N 15 LYS cc_start: 0.9021 (mttt) cc_final: 0.8687 (mttm) REVERT: O 1 MET cc_start: 0.4891 (ptp) cc_final: 0.4499 (mtp) REVERT: X 15 GLU cc_start: 0.6641 (pt0) cc_final: 0.6067 (mt-10) REVERT: Y 54 MET cc_start: 0.6523 (mtm) cc_final: 0.6301 (mtp) REVERT: Z 61 ASN cc_start: 0.7975 (m110) cc_final: 0.7752 (m110) outliers start: 66 outliers final: 47 residues processed: 568 average time/residue: 0.9443 time to fit residues: 900.5002 Evaluate side-chains 540 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 490 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 51 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 480 optimal weight: 6.9990 chunk 518 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 476 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 385 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 57 ASN H 85 GLN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 ASN S 29 ASN V 104 ASN Y 12 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 86909 Z= 0.400 Angle : 0.756 12.991 130874 Z= 0.381 Chirality : 0.044 0.351 16863 Planarity : 0.006 0.070 6328 Dihedral : 24.117 178.871 45445 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.23 % Allowed : 13.78 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.14), residues: 2575 helix: -1.34 (0.19), residues: 631 sheet: -1.99 (0.21), residues: 509 loop : -2.52 (0.14), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 213 HIS 0.007 0.002 HIS E 102 PHE 0.033 0.003 PHE Z 86 TYR 0.027 0.003 TYR F 58 ARG 0.007 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 495 time to evaluate : 3.142 Fit side-chains revert: symmetry clash REVERT: B 77 LYS cc_start: 0.7691 (tppt) cc_final: 0.7378 (tptp) REVERT: D 15 GLU cc_start: 0.6897 (mp0) cc_final: 0.6531 (mp0) REVERT: D 18 GLN cc_start: 0.7907 (tt0) cc_final: 0.7415 (tt0) REVERT: E 38 LEU cc_start: 0.8368 (mt) cc_final: 0.7975 (mt) REVERT: E 90 GLN cc_start: 0.8287 (mt0) cc_final: 0.8066 (mt0) REVERT: F 8 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7881 (mtmp) REVERT: F 65 MET cc_start: 0.4710 (ptm) cc_final: 0.4203 (mmm) REVERT: I 84 LYS cc_start: 0.7934 (mttp) cc_final: 0.7633 (mtmm) REVERT: K 14 ILE cc_start: 0.7513 (mm) cc_final: 0.6977 (tt) REVERT: K 17 GLN cc_start: 0.7849 (tm130) cc_final: 0.7584 (tm-30) REVERT: L 103 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6054 (pm20) REVERT: M 6 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8141 (mt) REVERT: N 15 LYS cc_start: 0.8936 (mttt) cc_final: 0.8562 (mttm) REVERT: N 22 ILE cc_start: 0.8114 (pt) cc_final: 0.7693 (pt) REVERT: O 1 MET cc_start: 0.4681 (ptp) cc_final: 0.4183 (mtp) REVERT: O 40 ASN cc_start: 0.8422 (t0) cc_final: 0.8202 (t0) REVERT: S 40 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: W 37 ASP cc_start: 0.6825 (m-30) cc_final: 0.6614 (m-30) REVERT: W 63 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7946 (m) REVERT: X 15 GLU cc_start: 0.6631 (pt0) cc_final: 0.6149 (mt-10) REVERT: Y 54 MET cc_start: 0.6448 (mtm) cc_final: 0.6231 (mtp) REVERT: Z 16 MET cc_start: 0.7920 (tpp) cc_final: 0.7575 (tpp) REVERT: a 82 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5711 (mppt) outliers start: 93 outliers final: 62 residues processed: 548 average time/residue: 0.9544 time to fit residues: 862.2195 Evaluate side-chains 547 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 479 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 183 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain Y residue 12 GLN Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 322 optimal weight: 5.9990 chunk 482 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 chunk 456 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 85 GLN K 27 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 86909 Z= 0.350 Angle : 0.715 12.868 130874 Z= 0.362 Chirality : 0.042 0.348 16863 Planarity : 0.006 0.070 6328 Dihedral : 24.033 178.684 45445 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.87 % Allowed : 14.92 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.15), residues: 2575 helix: -1.04 (0.20), residues: 627 sheet: -1.74 (0.21), residues: 512 loop : -2.35 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 213 HIS 0.006 0.001 HIS E 102 PHE 0.027 0.002 PHE Z 86 TYR 0.024 0.002 TYR a 101 ARG 0.006 0.001 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 494 time to evaluate : 3.434 Fit side-chains revert: symmetry clash REVERT: B 77 LYS cc_start: 0.7684 (tppt) cc_final: 0.7371 (tptp) REVERT: D 15 GLU cc_start: 0.6751 (mp0) cc_final: 0.6350 (mp0) REVERT: D 18 GLN cc_start: 0.7862 (tt0) cc_final: 0.7370 (tt0) REVERT: D 67 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7628 (ptm160) REVERT: E 38 LEU cc_start: 0.8345 (mt) cc_final: 0.7921 (mt) REVERT: F 8 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7846 (mtmp) REVERT: F 20 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6564 (mtt) REVERT: F 65 MET cc_start: 0.4912 (ptm) cc_final: 0.4349 (mmm) REVERT: H 42 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8028 (mtmm) REVERT: I 84 LYS cc_start: 0.7942 (mttp) cc_final: 0.7640 (mtmm) REVERT: K 14 ILE cc_start: 0.7404 (mm) cc_final: 0.6884 (tt) REVERT: L 103 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: L 162 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.6445 (ppt-90) REVERT: M 6 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8147 (mt) REVERT: M 56 VAL cc_start: 0.8244 (p) cc_final: 0.7992 (t) REVERT: N 15 LYS cc_start: 0.8926 (mttt) cc_final: 0.8567 (mttm) REVERT: N 22 ILE cc_start: 0.8089 (pt) cc_final: 0.7679 (pt) REVERT: O 1 MET cc_start: 0.4757 (ptp) cc_final: 0.4356 (mtp) REVERT: O 40 ASN cc_start: 0.8324 (t0) cc_final: 0.8088 (t0) REVERT: S 40 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: W 75 SER cc_start: 0.8293 (m) cc_final: 0.8018 (p) REVERT: W 87 ILE cc_start: 0.8757 (tt) cc_final: 0.8407 (pt) REVERT: X 15 GLU cc_start: 0.6671 (pt0) cc_final: 0.6146 (mt-10) REVERT: X 47 ARG cc_start: 0.4867 (mtt180) cc_final: 0.4488 (ttm170) REVERT: X 51 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6299 (pt0) outliers start: 107 outliers final: 75 residues processed: 557 average time/residue: 0.8887 time to fit residues: 823.3516 Evaluate side-chains 565 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 482 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 51 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 380 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 435 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 458 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 134 ASN B 226 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 90 GLN H 85 GLN K 27 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 86909 Z= 0.447 Angle : 0.796 12.713 130874 Z= 0.397 Chirality : 0.046 0.366 16863 Planarity : 0.006 0.071 6328 Dihedral : 24.077 178.967 45445 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 5.37 % Allowed : 15.83 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.15), residues: 2575 helix: -1.07 (0.19), residues: 628 sheet: -1.82 (0.21), residues: 510 loop : -2.29 (0.14), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 213 HIS 0.007 0.002 HIS X 35 PHE 0.030 0.003 PHE Z 86 TYR 0.025 0.003 TYR a 101 ARG 0.007 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 485 time to evaluate : 3.301 Fit side-chains revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7037 (mtm180) cc_final: 0.6606 (mtt180) REVERT: B 77 LYS cc_start: 0.7736 (tppt) cc_final: 0.7442 (tptp) REVERT: B 185 LEU cc_start: 0.8837 (tp) cc_final: 0.8368 (mp) REVERT: B 260 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.5535 (tmt90) REVERT: C 19 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8165 (mtpt) REVERT: D 15 GLU cc_start: 0.6846 (mp0) cc_final: 0.6465 (mp0) REVERT: D 18 GLN cc_start: 0.7879 (tt0) cc_final: 0.7451 (tt0) REVERT: D 67 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7561 (ptm160) REVERT: F 8 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7901 (mtmp) REVERT: F 20 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6720 (mtt) REVERT: F 65 MET cc_start: 0.4613 (ptm) cc_final: 0.4125 (mmm) REVERT: H 42 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8077 (mtmm) REVERT: I 84 LYS cc_start: 0.7963 (mttp) cc_final: 0.7604 (mtmm) REVERT: K 14 ILE cc_start: 0.7481 (mm) cc_final: 0.6912 (tt) REVERT: L 103 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: L 162 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.6871 (ppt-90) REVERT: M 6 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8223 (mt) REVERT: N 15 LYS cc_start: 0.8990 (mttt) cc_final: 0.8597 (mttm) REVERT: O 1 MET cc_start: 0.4791 (ptp) cc_final: 0.4342 (mtp) REVERT: O 40 ASN cc_start: 0.8367 (t0) cc_final: 0.8148 (t0) REVERT: S 40 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: W 5 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7546 (mm-30) REVERT: W 87 ILE cc_start: 0.8862 (tt) cc_final: 0.8461 (pt) REVERT: X 15 GLU cc_start: 0.6704 (pt0) cc_final: 0.6234 (mt-10) REVERT: X 18 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8153 (mtm180) REVERT: Y 83 MET cc_start: 0.8568 (mmp) cc_final: 0.8065 (mmp) REVERT: a 82 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5650 (mppt) outliers start: 118 outliers final: 87 residues processed: 556 average time/residue: 0.9183 time to fit residues: 853.3702 Evaluate side-chains 574 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 476 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 2.9990 chunk 459 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 510 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 85 GLN K 27 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 76 HIS S 38 ASN V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 86909 Z= 0.266 Angle : 0.652 12.800 130874 Z= 0.333 Chirality : 0.039 0.369 16863 Planarity : 0.005 0.069 6328 Dihedral : 23.934 179.370 45445 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.82 % Allowed : 17.37 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.15), residues: 2575 helix: -0.80 (0.20), residues: 631 sheet: -1.71 (0.21), residues: 515 loop : -2.09 (0.14), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 213 HIS 0.006 0.001 HIS C 29 PHE 0.021 0.002 PHE Z 86 TYR 0.025 0.002 TYR a 101 ARG 0.005 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 498 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6577 (mtt180) REVERT: B 77 LYS cc_start: 0.7724 (tppt) cc_final: 0.7433 (tptp) REVERT: B 260 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.5504 (tmt90) REVERT: C 19 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8123 (mtpt) REVERT: D 15 GLU cc_start: 0.6751 (mp0) cc_final: 0.6330 (mp0) REVERT: D 18 GLN cc_start: 0.7954 (tt0) cc_final: 0.7518 (tt0) REVERT: D 67 ARG cc_start: 0.8147 (mtm180) cc_final: 0.7609 (ptm160) REVERT: E 38 LEU cc_start: 0.8297 (mt) cc_final: 0.7878 (mt) REVERT: F 20 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6626 (mtt) REVERT: F 22 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5687 (mm-30) REVERT: F 43 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6192 (mt-10) REVERT: H 42 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7999 (mtmm) REVERT: I 84 LYS cc_start: 0.7925 (mttp) cc_final: 0.7603 (mtmm) REVERT: K 14 ILE cc_start: 0.7394 (mm) cc_final: 0.6865 (tt) REVERT: L 162 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.6758 (ppt-90) REVERT: M 6 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8148 (mt) REVERT: N 15 LYS cc_start: 0.8908 (mttt) cc_final: 0.8560 (mttm) REVERT: O 1 MET cc_start: 0.4792 (ptp) cc_final: 0.4436 (mtp) REVERT: O 40 ASN cc_start: 0.8264 (t0) cc_final: 0.8005 (t0) REVERT: S 40 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: V 3 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: W 75 SER cc_start: 0.8249 (m) cc_final: 0.8014 (p) REVERT: W 87 ILE cc_start: 0.8836 (tt) cc_final: 0.8442 (pt) REVERT: X 15 GLU cc_start: 0.6566 (pt0) cc_final: 0.6270 (mt-10) REVERT: X 47 ARG cc_start: 0.4788 (mtt180) cc_final: 0.4409 (ttm170) REVERT: Y 83 MET cc_start: 0.8599 (mmp) cc_final: 0.8075 (mmp) REVERT: Y 134 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6123 (ttm170) REVERT: a 82 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5538 (mppt) outliers start: 106 outliers final: 77 residues processed: 561 average time/residue: 0.8688 time to fit residues: 808.4597 Evaluate side-chains 574 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 486 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Y residue 134 ARG Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 508 optimal weight: 9.9990 chunk 318 optimal weight: 7.9990 chunk 310 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN B 200 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 85 GLN K 27 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN O 25 ASN Q 40 GLN V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 12 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 86909 Z= 0.625 Angle : 0.949 12.656 130874 Z= 0.463 Chirality : 0.053 0.403 16863 Planarity : 0.008 0.101 6328 Dihedral : 24.181 179.840 45445 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 6.09 % Allowed : 16.92 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.15), residues: 2575 helix: -1.18 (0.19), residues: 630 sheet: -1.82 (0.21), residues: 507 loop : -2.25 (0.14), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 213 HIS 0.008 0.002 HIS Q 31 PHE 0.033 0.003 PHE Z 86 TYR 0.028 0.004 TYR a 101 ARG 0.008 0.001 ARG N 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 474 time to evaluate : 3.111 Fit side-chains revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7058 (mtm180) cc_final: 0.6659 (mtt180) REVERT: B 77 LYS cc_start: 0.7858 (tppt) cc_final: 0.7555 (tptp) REVERT: B 260 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.5558 (tmt90) REVERT: C 19 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8234 (mtpt) REVERT: D 18 GLN cc_start: 0.7924 (tt0) cc_final: 0.7671 (tt0) REVERT: D 67 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7597 (ptm160) REVERT: E 20 VAL cc_start: 0.9075 (m) cc_final: 0.8871 (m) REVERT: F 65 MET cc_start: 0.5079 (ptm) cc_final: 0.4473 (mmm) REVERT: K 14 ILE cc_start: 0.7505 (mm) cc_final: 0.6906 (tt) REVERT: L 37 GLN cc_start: 0.8576 (tt0) cc_final: 0.8339 (tt0) REVERT: L 104 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: L 162 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.7011 (ppt-90) REVERT: M 6 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8186 (mt) REVERT: S 40 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: S 168 ARG cc_start: 0.8050 (ppt-90) cc_final: 0.7808 (tmm-80) REVERT: V 94 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7768 (ttp80) REVERT: W 5 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7485 (mm-30) REVERT: W 37 ASP cc_start: 0.7651 (t0) cc_final: 0.7435 (t0) REVERT: W 112 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.5691 (mmm) REVERT: X 15 GLU cc_start: 0.6809 (pt0) cc_final: 0.6406 (mt-10) REVERT: X 18 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8151 (mtm180) REVERT: Y 83 MET cc_start: 0.8555 (mmp) cc_final: 0.8070 (mmp) REVERT: Y 134 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6099 (ttm170) REVERT: a 82 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5643 (mppt) outliers start: 134 outliers final: 105 residues processed: 552 average time/residue: 0.8665 time to fit residues: 790.1214 Evaluate side-chains 575 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 460 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 41 CYS Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 112 MET Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 109 ILE Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Y residue 134 ARG Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.6980 chunk 203 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 323 optimal weight: 0.7980 chunk 346 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 400 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 85 GLN K 27 ASN L 33 ASN L 37 GLN M 40 ASN S 38 ASN V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 86909 Z= 0.157 Angle : 0.585 12.861 130874 Z= 0.302 Chirality : 0.036 0.399 16863 Planarity : 0.005 0.068 6328 Dihedral : 23.843 179.756 45445 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.27 % Allowed : 20.28 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 2575 helix: -0.51 (0.20), residues: 630 sheet: -1.55 (0.21), residues: 515 loop : -1.92 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 213 HIS 0.007 0.001 HIS C 29 PHE 0.016 0.001 PHE D 40 TYR 0.024 0.001 TYR a 101 ARG 0.005 0.000 ARG N 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 507 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.6942 (mtm180) cc_final: 0.6548 (mtt180) REVERT: B 77 LYS cc_start: 0.7677 (tppt) cc_final: 0.7383 (tptp) REVERT: B 177 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6752 (tpt-90) REVERT: B 180 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: C 19 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7953 (mtpt) REVERT: D 1 MET cc_start: 0.6075 (tpt) cc_final: 0.5041 (tpt) REVERT: D 15 GLU cc_start: 0.6618 (mp0) cc_final: 0.6131 (mp0) REVERT: D 18 GLN cc_start: 0.7943 (tt0) cc_final: 0.7430 (tt0) REVERT: D 67 ARG cc_start: 0.8091 (mtm180) cc_final: 0.7521 (ptm160) REVERT: E 38 LEU cc_start: 0.8212 (mt) cc_final: 0.7807 (mt) REVERT: I 84 LYS cc_start: 0.7887 (mttp) cc_final: 0.7579 (mtmm) REVERT: L 104 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: N 15 LYS cc_start: 0.8864 (mttt) cc_final: 0.8536 (mttm) REVERT: O 40 ASN cc_start: 0.8215 (t0) cc_final: 0.7954 (t0) REVERT: Q 21 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: S 40 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: W 13 ASN cc_start: 0.8247 (p0) cc_final: 0.7976 (p0) REVERT: W 75 SER cc_start: 0.8179 (m) cc_final: 0.7972 (p) REVERT: Y 83 MET cc_start: 0.8591 (mmp) cc_final: 0.7980 (mmp) REVERT: a 82 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5313 (mmmt) outliers start: 72 outliers final: 48 residues processed: 551 average time/residue: 0.8568 time to fit residues: 775.7862 Evaluate side-chains 544 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 489 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 444 optimal weight: 6.9990 chunk 474 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 206 optimal weight: 0.1980 chunk 372 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 448 optimal weight: 8.9990 chunk 472 optimal weight: 8.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN K 27 ASN V 119 GLN X 81 GLN ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 86909 Z= 0.565 Angle : 0.891 12.915 130874 Z= 0.436 Chirality : 0.050 0.390 16863 Planarity : 0.007 0.082 6328 Dihedral : 24.041 179.542 45445 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 4.68 % Allowed : 18.83 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 2575 helix: -0.89 (0.19), residues: 631 sheet: -1.65 (0.21), residues: 518 loop : -2.13 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 213 HIS 0.007 0.002 HIS Q 31 PHE 0.031 0.003 PHE Z 86 TYR 0.029 0.003 TYR a 101 ARG 0.006 0.001 ARG L 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 476 time to evaluate : 3.091 Fit side-chains revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7053 (mtm180) cc_final: 0.6646 (mtt180) REVERT: B 75 ASN cc_start: 0.7279 (m-40) cc_final: 0.6973 (m-40) REVERT: B 77 LYS cc_start: 0.7858 (tppt) cc_final: 0.7542 (tptp) REVERT: B 177 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6907 (tpt-90) REVERT: B 180 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7056 (tp30) REVERT: C 19 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8247 (mtpt) REVERT: D 18 GLN cc_start: 0.7880 (tt0) cc_final: 0.7617 (tt0) REVERT: D 67 ARG cc_start: 0.8175 (mtm180) cc_final: 0.7610 (ptm160) REVERT: J 34 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: L 104 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: N 15 LYS cc_start: 0.9015 (mttt) cc_final: 0.8675 (mttm) REVERT: O 40 ASN cc_start: 0.8330 (t0) cc_final: 0.8083 (t0) REVERT: S 40 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: W 5 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7541 (mm-30) REVERT: Y 83 MET cc_start: 0.8569 (mmp) cc_final: 0.8050 (mmp) REVERT: Y 134 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6064 (ttm170) REVERT: Z 71 ILE cc_start: 0.6285 (mt) cc_final: 0.5825 (mt) REVERT: a 82 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5559 (mppt) outliers start: 103 outliers final: 84 residues processed: 533 average time/residue: 0.8650 time to fit residues: 761.6041 Evaluate side-chains 559 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 467 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 41 CYS Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Y residue 134 ARG Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 1.9990 chunk 501 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 348 optimal weight: 3.9990 chunk 526 optimal weight: 10.0000 chunk 484 optimal weight: 5.9990 chunk 418 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 256 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 85 GLN K 27 ASN V 3 GLN Y 12 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 86909 Z= 0.163 Angle : 0.582 12.756 130874 Z= 0.301 Chirality : 0.036 0.404 16863 Planarity : 0.005 0.068 6328 Dihedral : 23.819 179.500 45445 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.91 % Allowed : 20.83 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2575 helix: -0.42 (0.20), residues: 632 sheet: -1.53 (0.21), residues: 514 loop : -1.90 (0.14), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 213 HIS 0.007 0.001 HIS C 29 PHE 0.018 0.002 PHE D 40 TYR 0.026 0.002 TYR a 101 ARG 0.007 0.000 ARG V 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 485 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.6865 (mtm180) cc_final: 0.6525 (mtt180) REVERT: B 77 LYS cc_start: 0.7691 (tppt) cc_final: 0.7402 (tptp) REVERT: B 177 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6779 (tpt-90) REVERT: B 180 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6999 (tp30) REVERT: B 260 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.5381 (tmt90) REVERT: C 19 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7926 (mtpt) REVERT: D 1 MET cc_start: 0.6147 (tpt) cc_final: 0.5030 (tpt) REVERT: D 15 GLU cc_start: 0.6648 (mp0) cc_final: 0.6157 (mp0) REVERT: D 18 GLN cc_start: 0.7811 (tt0) cc_final: 0.7438 (tt0) REVERT: D 67 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7510 (ptm160) REVERT: E 38 LEU cc_start: 0.8222 (mt) cc_final: 0.7838 (mt) REVERT: F 43 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6532 (mt-10) REVERT: I 84 LYS cc_start: 0.7877 (mttp) cc_final: 0.7538 (mtmm) REVERT: L 78 LYS cc_start: 0.7311 (mmmt) cc_final: 0.7061 (tppt) REVERT: L 104 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: L 162 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.6692 (ppt-90) REVERT: N 15 LYS cc_start: 0.8877 (mttt) cc_final: 0.8553 (mttm) REVERT: S 40 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: W 5 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7504 (mm-30) REVERT: W 13 ASN cc_start: 0.8257 (p0) cc_final: 0.7991 (p0) REVERT: W 75 SER cc_start: 0.8201 (m) cc_final: 0.7994 (p) REVERT: a 82 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5336 (mmmt) outliers start: 64 outliers final: 50 residues processed: 522 average time/residue: 0.8498 time to fit residues: 734.5702 Evaluate side-chains 539 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 481 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 6.9990 chunk 446 optimal weight: 6.9990 chunk 128 optimal weight: 0.0470 chunk 386 optimal weight: 20.0000 chunk 61 optimal weight: 0.0970 chunk 116 optimal weight: 8.9990 chunk 419 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 430 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 4.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN K 27 ASN L 37 GLN L 200 ASN O 25 ASN V 3 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122784 restraints weight = 104663.877| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 0.53 r_work: 0.3044 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 86909 Z= 0.379 Angle : 0.726 12.177 130874 Z= 0.364 Chirality : 0.042 0.366 16863 Planarity : 0.006 0.071 6328 Dihedral : 23.881 178.349 45445 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.64 % Allowed : 20.42 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2575 helix: -0.57 (0.20), residues: 635 sheet: -1.59 (0.21), residues: 542 loop : -1.96 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 213 HIS 0.006 0.001 HIS C 29 PHE 0.024 0.002 PHE Z 86 TYR 0.028 0.003 TYR a 101 ARG 0.008 0.001 ARG V 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14648.81 seconds wall clock time: 257 minutes 10.15 seconds (15430.15 seconds total)