Starting phenix.real_space_refine on Thu Dec 14 14:25:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmw_16126/12_2023/8bmw_16126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmw_16126/12_2023/8bmw_16126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmw_16126/12_2023/8bmw_16126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmw_16126/12_2023/8bmw_16126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmw_16126/12_2023/8bmw_16126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmw_16126/12_2023/8bmw_16126.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 47 5.49 5 S 107 5.16 5 C 18138 2.51 5 N 4786 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 19": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 111": "OD1" <-> "OD2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28658 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 957 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2121 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 258} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1585 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "N" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2029 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain: "R" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 971 Classifications: {'RNA': 48} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 26, 'rna3p_pur': 1, 'rna3p_pyr': 16} Link IDs: {'rna2p': 30, 'rna3p': 17} Chain: "G" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1877 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain breaks: 1 Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 230} Chain breaks: 1 Chain: "H" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2168 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "I" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2164 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 265} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 6678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6678 Classifications: {'peptide': 829} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 807} Chain: "M" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2383 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Time building chain proxies: 15.48, per 1000 atoms: 0.54 Number of scatterers: 28658 At special positions: 0 Unit cell: (126.566, 119.244, 242.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 47 15.00 O 5580 8.00 N 4786 7.00 C 18138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS J 223 " - pdb=" SG CYS J 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 75 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 180 " - pdb=" SG CYS L 185 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 80 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 82 " - pdb=" SG CYS H 123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 120 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 278 " distance=2.03 Simple disulfide: pdb=" SG CYS K 265 " - pdb=" SG CYS K 275 " distance=2.03 Simple disulfide: pdb=" SG CYS M 220 " - pdb=" SG CYS M 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.15 Conformation dependent library (CDL) restraints added in 5.3 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6496 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 35 sheets defined 44.3% alpha, 12.9% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 8.91 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.548A pdb=" N ILE A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 80 through 93 removed outlier: 4.634A pdb=" N ASP A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 117 Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.651A pdb=" N VAL A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.649A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 95 through 117 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 95 through 117 Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.508A pdb=" N LEU D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 95 through 117 Processing helix chain 'D' and resid 128 through 139 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 62 through 76 Processing helix chain 'E' and resid 80 through 91 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 96 through 117 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.613A pdb=" N VAL E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.714A pdb=" N LEU J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 removed outlier: 3.773A pdb=" N TYR J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 108 Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 255 through 266 Processing helix chain 'L' and resid 35 through 50 removed outlier: 3.597A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 82 Processing helix chain 'L' and resid 144 through 160 removed outlier: 3.697A pdb=" N ARG L 159 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 removed outlier: 3.754A pdb=" N VAL L 183 " --> pdb=" O ILE L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 198 removed outlier: 3.989A pdb=" N ARG L 198 " --> pdb=" O ASN L 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 59 Processing helix chain 'N' and resid 60 through 65 removed outlier: 3.594A pdb=" N GLU N 65 " --> pdb=" O GLU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 84 Processing helix chain 'N' and resid 84 through 96 Processing helix chain 'N' and resid 111 through 126 Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 195 through 208 removed outlier: 3.516A pdb=" N GLU N 207 " --> pdb=" O LYS N 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 219 removed outlier: 3.571A pdb=" N GLY N 219 " --> pdb=" O LYS N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 252 Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.655A pdb=" N ASN G 73 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 240 through 244 Processing helix chain 'F' and resid 53 through 73 removed outlier: 3.595A pdb=" N ASN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 Processing helix chain 'F' and resid 180 through 200 Processing helix chain 'F' and resid 240 through 245 Processing helix chain 'H' and resid 58 through 77 Processing helix chain 'H' and resid 89 through 94 Processing helix chain 'H' and resid 96 through 106 removed outlier: 3.613A pdb=" N LYS H 105 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 removed outlier: 3.612A pdb=" N ALA H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 189 through 205 Processing helix chain 'H' and resid 253 through 270 Proline residue: H 263 - end of helix Processing helix chain 'I' and resid 58 through 77 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.738A pdb=" N ASN I 101 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS I 105 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 120 through 127 Processing helix chain 'I' and resid 189 through 206 Processing helix chain 'I' and resid 253 through 261 Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'K' and resid 17 through 44 removed outlier: 4.477A pdb=" N LYS K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 removed outlier: 3.503A pdb=" N TYR K 62 " --> pdb=" O ILE K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 115 through 136 removed outlier: 3.781A pdb=" N TYR K 123 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 165 removed outlier: 3.710A pdb=" N HIS K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 188 Processing helix chain 'K' and resid 191 through 207 Processing helix chain 'K' and resid 211 through 224 Processing helix chain 'K' and resid 230 through 245 Processing helix chain 'K' and resid 250 through 255 Processing helix chain 'K' and resid 271 through 283 Processing helix chain 'K' and resid 283 through 300 Processing helix chain 'K' and resid 323 through 329 Processing helix chain 'K' and resid 332 through 364 removed outlier: 3.982A pdb=" N TYR K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER K 351 " --> pdb=" O THR K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 374 removed outlier: 3.791A pdb=" N LEU K 374 " --> pdb=" O ALA K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 408 Processing helix chain 'K' and resid 430 through 441 Processing helix chain 'K' and resid 442 through 446 removed outlier: 4.096A pdb=" N TYR K 446 " --> pdb=" O SER K 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 442 through 446' Processing helix chain 'K' and resid 482 through 495 removed outlier: 4.512A pdb=" N ASN K 494 " --> pdb=" O ASP K 490 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG K 495 " --> pdb=" O LEU K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 502 Processing helix chain 'K' and resid 516 through 521 Processing helix chain 'K' and resid 534 through 541 Processing helix chain 'K' and resid 560 through 567 Processing helix chain 'K' and resid 570 through 598 Processing helix chain 'K' and resid 602 through 616 Processing helix chain 'K' and resid 633 through 643 Processing helix chain 'K' and resid 644 through 649 Processing helix chain 'K' and resid 665 through 680 Processing helix chain 'K' and resid 701 through 712 Processing helix chain 'K' and resid 726 through 736 Processing helix chain 'K' and resid 740 through 750 removed outlier: 3.638A pdb=" N ASN K 750 " --> pdb=" O GLU K 746 " (cutoff:3.500A) Processing helix chain 'K' and resid 750 through 775 removed outlier: 4.436A pdb=" N LYS K 756 " --> pdb=" O GLU K 752 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER K 764 " --> pdb=" O ASP K 760 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU K 765 " --> pdb=" O LYS K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 776 through 790 Processing helix chain 'K' and resid 795 through 806 removed outlier: 3.872A pdb=" N ARG K 799 " --> pdb=" O SER K 795 " (cutoff:3.500A) Processing helix chain 'K' and resid 815 through 829 removed outlier: 3.783A pdb=" N ILE K 825 " --> pdb=" O ILE K 821 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 829 " --> pdb=" O ILE K 825 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 47 Processing helix chain 'M' and resid 86 through 91 Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 179 through 185 removed outlier: 4.057A pdb=" N ASP M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.689A pdb=" N ILE M 299 " --> pdb=" O LEU M 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 90 through 91 removed outlier: 7.959A pdb=" N PHE J 170 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS J 199 " --> pdb=" O PHE J 170 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET J 172 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA J 197 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER J 174 " --> pdb=" O ILE J 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 90 through 91 removed outlier: 7.959A pdb=" N PHE J 170 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS J 199 " --> pdb=" O PHE J 170 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET J 172 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA J 197 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER J 174 " --> pdb=" O ILE J 195 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU J 19 " --> pdb=" O SER J 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 37 through 40 removed outlier: 4.693A pdb=" N LYS J 40 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'L' and resid 91 through 95 Processing sheet with id=AA6, first strand: chain 'L' and resid 102 through 107 Processing sheet with id=AA7, first strand: chain 'N' and resid 142 through 144 Processing sheet with id=AA8, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AA9, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.479A pdb=" N ASP G 219 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG G 20 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU G 217 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU G 22 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE G 215 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE G 236 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AB3, first strand: chain 'G' and resid 132 through 137 Processing sheet with id=AB4, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.575A pdb=" N LYS F 18 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP F 219 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 20 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU F 217 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 236 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AB6, first strand: chain 'F' and resid 90 through 91 Processing sheet with id=AB7, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.532A pdb=" N LEU F 155 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AC1, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'H' and resid 147 through 152 removed outlier: 3.671A pdb=" N VAL H 168 " --> pdb=" O MET H 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 135 through 137 removed outlier: 3.559A pdb=" N LEU I 141 " --> pdb=" O SER I 180 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 135 through 137 removed outlier: 4.307A pdb=" N LYS I 225 " --> pdb=" O ASP I 21 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU I 23 " --> pdb=" O PHE I 223 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE I 223 " --> pdb=" O GLU I 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 147 through 151 Processing sheet with id=AC6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'K' and resid 382 through 387 removed outlier: 6.692A pdb=" N ALA K 311 " --> pdb=" O TYR K 424 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR K 424 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY K 313 " --> pdb=" O PHE K 422 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP K 319 " --> pdb=" O ASP K 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 447 through 448 removed outlier: 4.090A pdb=" N ILE M 239 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE M 234 " --> pdb=" O PHE M 276 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE M 276 " --> pdb=" O PHE M 234 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA M 236 " --> pdb=" O GLU M 274 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU M 274 " --> pdb=" O ALA M 236 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR M 238 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 271 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL M 273 " --> pdb=" O GLY M 216 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 505 through 507 Processing sheet with id=AD1, first strand: chain 'K' and resid 625 through 627 removed outlier: 3.697A pdb=" N ASN K 724 " --> pdb=" O ILE K 690 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 717 through 718 Processing sheet with id=AD3, first strand: chain 'M' and resid 60 through 61 Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.551A pdb=" N GLY M 10 " --> pdb=" O PHE M 169 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET M 160 " --> pdb=" O ALA M 148 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA M 148 " --> pdb=" O MET M 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS M 140 " --> pdb=" O GLU M 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.378A pdb=" N LYS M 133 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 227 through 228 Processing sheet with id=AD7, first strand: chain 'M' and resid 243 through 244 Processing sheet with id=AD8, first strand: chain 'M' and resid 247 through 249 removed outlier: 6.196A pdb=" N GLY M 248 " --> pdb=" O LYS M 259 " (cutoff:3.500A) 1291 hydrogen bonds defined for protein. 3747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 9.65 Time building geometry restraints manager: 12.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4873 1.32 - 1.45: 7460 1.45 - 1.57: 16633 1.57 - 1.69: 94 1.69 - 1.81: 177 Bond restraints: 29237 Sorted by residual: bond pdb=" N ILE I 57 " pdb=" CA ILE I 57 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.34e+01 bond pdb=" CA SER J 163 " pdb=" CB SER J 163 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.38e-02 5.25e+03 1.98e+01 bond pdb=" CA SER I 60 " pdb=" CB SER I 60 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.56e-02 4.11e+03 1.11e+01 bond pdb=" CA SER H 83 " pdb=" CB SER H 83 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.65e-02 3.67e+03 1.07e+01 bond pdb=" CA SER I 61 " pdb=" CB SER I 61 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 ... (remaining 29232 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.53: 816 106.53 - 113.41: 16205 113.41 - 120.30: 10436 120.30 - 127.18: 11929 127.18 - 134.07: 207 Bond angle restraints: 39593 Sorted by residual: angle pdb=" N SER L 24 " pdb=" CA SER L 24 " pdb=" C SER L 24 " ideal model delta sigma weight residual 114.62 106.54 8.08 1.14e+00 7.69e-01 5.02e+01 angle pdb=" N ARG J 164 " pdb=" CA ARG J 164 " pdb=" C ARG J 164 " ideal model delta sigma weight residual 113.19 104.91 8.28 1.19e+00 7.06e-01 4.84e+01 angle pdb=" C PRO H 189 " pdb=" CA PRO H 189 " pdb=" CB PRO H 189 " ideal model delta sigma weight residual 111.23 103.69 7.54 1.28e+00 6.10e-01 3.47e+01 angle pdb=" C TYR K 282 " pdb=" CA TYR K 282 " pdb=" CB TYR K 282 " ideal model delta sigma weight residual 109.07 117.25 -8.18 1.68e+00 3.54e-01 2.37e+01 angle pdb=" N LEU I 112 " pdb=" CA LEU I 112 " pdb=" C LEU I 112 " ideal model delta sigma weight residual 111.07 105.90 5.17 1.07e+00 8.73e-01 2.33e+01 ... (remaining 39588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 17617 35.71 - 71.42: 202 71.42 - 107.14: 9 107.14 - 142.85: 0 142.85 - 178.56: 11 Dihedral angle restraints: 17839 sinusoidal: 7722 harmonic: 10117 Sorted by residual: dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 120 " pdb=" CB CYS H 120 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" O4' U R 23 " pdb=" C1' U R 23 " pdb=" N1 U R 23 " pdb=" C2 U R 23 " ideal model delta sinusoidal sigma weight residual 200.00 28.17 171.83 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CB CYS L 75 " pdb=" SG CYS L 75 " pdb=" SG CYS L 78 " pdb=" CB CYS L 78 " ideal model delta sinusoidal sigma weight residual 93.00 9.89 83.11 1 1.00e+01 1.00e-02 8.45e+01 ... (remaining 17836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3706 0.050 - 0.099: 648 0.099 - 0.149: 146 0.149 - 0.198: 14 0.198 - 0.248: 10 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CA ARG J 164 " pdb=" N ARG J 164 " pdb=" C ARG J 164 " pdb=" CB ARG J 164 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO H 189 " pdb=" N PRO H 189 " pdb=" C PRO H 189 " pdb=" CB PRO H 189 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE I 114 " pdb=" N ILE I 114 " pdb=" C ILE I 114 " pdb=" CB ILE I 114 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 4521 not shown) Planarity restraints: 4852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 88 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ASP H 88 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP H 88 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR H 89 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 82 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C CYS H 82 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS H 82 " -0.017 2.00e-02 2.50e+03 pdb=" N SER H 83 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 115 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C PHE I 115 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE I 115 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP I 116 " -0.012 2.00e-02 2.50e+03 ... (remaining 4849 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2440 2.74 - 3.28: 30904 3.28 - 3.82: 49718 3.82 - 4.36: 57607 4.36 - 4.90: 98284 Nonbonded interactions: 238953 Sorted by model distance: nonbonded pdb=" OG1 THR L 38 " pdb=" OP1 U R 9 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR K 173 " pdb=" OD1 ASN K 213 " model vdw 2.198 2.440 nonbonded pdb=" O2' U R 23 " pdb=" O PHE G 113 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP L 94 " pdb=" OG1 THR L 137 " model vdw 2.201 2.440 nonbonded pdb=" O LEU L 151 " pdb=" OG SER L 154 " model vdw 2.201 2.440 ... (remaining 238948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 137) selection = chain 'B' selection = (chain 'C' and resid 19 through 137) selection = (chain 'D' and resid 19 through 137) selection = (chain 'E' and resid 19 through 137) } ncs_group { reference = (chain 'F' and resid 4 through 244) selection = (chain 'G' and (resid 4 through 94 or resid 101 through 244)) } ncs_group { reference = (chain 'H' and (resid 4 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 119 or (resid 120 and \ (name N or name CA or name C or name O or name CB )) or resid 121 through 122 or \ (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 4 through 278)) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.300 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 82.950 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.003 0.061 29237 Z= 0.206 Angle : 0.537 8.282 39593 Z= 0.330 Chirality : 0.042 0.248 4524 Planarity : 0.003 0.043 4852 Dihedral : 12.220 178.559 11298 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 0.49 % Allowed : 11.33 % Favored : 88.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3441 helix: 2.45 (0.14), residues: 1468 sheet: 0.20 (0.25), residues: 449 loop : -1.57 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 249 HIS 0.004 0.001 HIS K 225 PHE 0.014 0.001 PHE G 144 TYR 0.016 0.001 TYR H 195 ARG 0.008 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 865 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 876 average time/residue: 0.4803 time to fit residues: 635.5961 Evaluate side-chains 512 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 508 time to evaluate : 3.676 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4270 time to fit residues: 7.5325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 7.9990 chunk 262 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** N 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN K 734 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29237 Z= 0.272 Angle : 0.668 11.366 39593 Z= 0.349 Chirality : 0.043 0.189 4524 Planarity : 0.004 0.056 4852 Dihedral : 11.582 178.824 4398 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 3.72 % Allowed : 19.48 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3441 helix: 2.00 (0.14), residues: 1469 sheet: 0.19 (0.25), residues: 455 loop : -1.64 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 749 HIS 0.004 0.001 HIS K 225 PHE 0.030 0.001 PHE K 245 TYR 0.025 0.002 TYR E 105 ARG 0.013 0.001 ARG K 786 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 588 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 53 residues processed: 662 average time/residue: 0.4040 time to fit residues: 425.8762 Evaluate side-chains 541 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 488 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2992 time to fit residues: 32.0064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 340 optimal weight: 0.0050 chunk 280 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN J 181 ASN N 59 ASN ** N 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** K 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29237 Z= 0.225 Angle : 0.642 8.689 39593 Z= 0.332 Chirality : 0.043 0.202 4524 Planarity : 0.004 0.044 4852 Dihedral : 11.655 179.386 4398 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.52 % Favored : 94.36 % Rotamer: Outliers : 2.69 % Allowed : 19.74 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3441 helix: 1.75 (0.14), residues: 1468 sheet: 0.01 (0.24), residues: 464 loop : -1.63 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 182 HIS 0.004 0.001 HIS L 70 PHE 0.039 0.002 PHE E 56 TYR 0.025 0.002 TYR L 104 ARG 0.006 0.000 ARG K 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 546 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 31 residues processed: 608 average time/residue: 0.3923 time to fit residues: 384.5411 Evaluate side-chains 496 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 465 time to evaluate : 3.303 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2557 time to fit residues: 19.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 334 optimal weight: 1.9990 chunk 165 optimal weight: 0.0970 chunk 299 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29237 Z= 0.220 Angle : 0.657 12.679 39593 Z= 0.335 Chirality : 0.043 0.342 4524 Planarity : 0.004 0.048 4852 Dihedral : 11.686 178.848 4398 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 2.52 % Allowed : 21.29 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3441 helix: 1.57 (0.14), residues: 1469 sheet: 0.00 (0.23), residues: 469 loop : -1.65 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 182 HIS 0.004 0.001 HIS L 70 PHE 0.030 0.001 PHE E 56 TYR 0.026 0.002 TYR E 69 ARG 0.006 0.000 ARG J 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 511 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 30 residues processed: 562 average time/residue: 0.4004 time to fit residues: 367.2801 Evaluate side-chains 494 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 464 time to evaluate : 3.293 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2673 time to fit residues: 19.4463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 285 optimal weight: 6.9990 chunk 231 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 300 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN C 58 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29237 Z= 0.188 Angle : 0.649 11.608 39593 Z= 0.330 Chirality : 0.043 0.254 4524 Planarity : 0.004 0.048 4852 Dihedral : 11.709 179.695 4398 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.29 % Favored : 94.59 % Rotamer: Outliers : 1.81 % Allowed : 22.49 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3441 helix: 1.51 (0.14), residues: 1474 sheet: 0.12 (0.23), residues: 462 loop : -1.66 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 182 HIS 0.004 0.001 HIS L 70 PHE 0.040 0.001 PHE K 245 TYR 0.037 0.001 TYR K 62 ARG 0.007 0.000 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 526 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 28 residues processed: 560 average time/residue: 0.3905 time to fit residues: 357.3420 Evaluate side-chains 497 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 469 time to evaluate : 3.422 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2929 time to fit residues: 19.5009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 3.9990 chunk 301 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 chunk 277 optimal weight: 0.0970 chunk 154 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 overall best weight: 1.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** N 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29237 Z= 0.208 Angle : 0.647 14.013 39593 Z= 0.331 Chirality : 0.043 0.252 4524 Planarity : 0.004 0.051 4852 Dihedral : 11.749 179.795 4398 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 1.97 % Allowed : 23.50 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3441 helix: 1.47 (0.14), residues: 1475 sheet: 0.23 (0.23), residues: 453 loop : -1.62 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 182 HIS 0.006 0.001 HIS L 70 PHE 0.051 0.002 PHE A 129 TYR 0.035 0.002 TYR K 62 ARG 0.008 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 499 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 533 average time/residue: 0.4006 time to fit residues: 344.8809 Evaluate side-chains 495 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 464 time to evaluate : 3.592 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2909 time to fit residues: 21.1972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 281 optimal weight: 0.0980 chunk 186 optimal weight: 0.9990 chunk 333 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 134 ASN C 58 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29237 Z= 0.232 Angle : 0.679 14.110 39593 Z= 0.345 Chirality : 0.043 0.351 4524 Planarity : 0.004 0.054 4852 Dihedral : 11.804 179.925 4398 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.81 % Favored : 94.07 % Rotamer: Outliers : 1.17 % Allowed : 24.92 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3441 helix: 1.37 (0.14), residues: 1477 sheet: 0.18 (0.23), residues: 460 loop : -1.59 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 182 HIS 0.005 0.001 HIS L 70 PHE 0.042 0.001 PHE A 129 TYR 0.024 0.001 TYR K 62 ARG 0.008 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 488 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 509 average time/residue: 0.4064 time to fit residues: 335.1432 Evaluate side-chains 474 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 452 time to evaluate : 3.397 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2696 time to fit residues: 15.8062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 262 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN K 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29237 Z= 0.200 Angle : 0.694 13.499 39593 Z= 0.352 Chirality : 0.044 0.358 4524 Planarity : 0.004 0.056 4852 Dihedral : 11.799 179.774 4398 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 1.04 % Allowed : 25.50 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3441 helix: 1.31 (0.14), residues: 1471 sheet: 0.32 (0.24), residues: 453 loop : -1.58 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 182 HIS 0.006 0.001 HIS L 70 PHE 0.038 0.001 PHE A 129 TYR 0.028 0.001 TYR B 105 ARG 0.006 0.000 ARG K 644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 496 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 510 average time/residue: 0.4145 time to fit residues: 345.3126 Evaluate side-chains 481 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 461 time to evaluate : 3.720 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3102 time to fit residues: 15.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 135 optimal weight: 0.0020 chunk 244 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 134 ASN C 58 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN J 26 GLN ** N 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29237 Z= 0.240 Angle : 0.713 13.698 39593 Z= 0.363 Chirality : 0.044 0.309 4524 Planarity : 0.004 0.057 4852 Dihedral : 11.856 179.973 4398 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.87 % Rotamer: Outliers : 1.04 % Allowed : 25.89 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3441 helix: 1.29 (0.14), residues: 1477 sheet: 0.29 (0.24), residues: 454 loop : -1.55 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 182 HIS 0.006 0.001 HIS K 153 PHE 0.041 0.002 PHE E 129 TYR 0.055 0.001 TYR B 105 ARG 0.009 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 467 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 484 average time/residue: 0.3999 time to fit residues: 321.9015 Evaluate side-chains 465 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 446 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4383 time to fit residues: 21.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 10.0000 chunk 328 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 212 optimal weight: 0.0980 chunk 168 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29237 Z= 0.208 Angle : 0.728 14.362 39593 Z= 0.368 Chirality : 0.044 0.301 4524 Planarity : 0.004 0.055 4852 Dihedral : 11.847 179.247 4398 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 0.42 % Allowed : 26.50 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3441 helix: 1.24 (0.14), residues: 1475 sheet: 0.40 (0.24), residues: 452 loop : -1.54 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 182 HIS 0.004 0.001 HIS L 70 PHE 0.037 0.001 PHE J 141 TYR 0.045 0.001 TYR B 105 ARG 0.014 0.000 ARG K 644 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 480 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 486 average time/residue: 0.3941 time to fit residues: 314.5204 Evaluate side-chains 460 residues out of total 3097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 456 time to evaluate : 3.695 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3165 time to fit residues: 7.2942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 115 optimal weight: 0.0870 chunk 282 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 269 ASN K 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.053704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045429 restraints weight = 144896.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.047166 restraints weight = 74096.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.048368 restraints weight = 46223.659| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29237 Z= 0.290 Angle : 0.756 14.687 39593 Z= 0.385 Chirality : 0.044 0.286 4524 Planarity : 0.004 0.056 4852 Dihedral : 11.938 179.736 4398 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.68 % Favored : 93.20 % Rotamer: Outliers : 0.71 % Allowed : 27.06 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3441 helix: 1.21 (0.14), residues: 1469 sheet: 0.27 (0.24), residues: 442 loop : -1.52 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 182 HIS 0.004 0.001 HIS M 68 PHE 0.047 0.002 PHE K 245 TYR 0.048 0.002 TYR B 105 ARG 0.010 0.000 ARG K 644 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6948.16 seconds wall clock time: 127 minutes 42.88 seconds (7662.88 seconds total)