Starting phenix.real_space_refine on Tue Mar 19 00:42:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ud5_26454/03_2024/7ud5_26454_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ud5_26454/03_2024/7ud5_26454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ud5_26454/03_2024/7ud5_26454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ud5_26454/03_2024/7ud5_26454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ud5_26454/03_2024/7ud5_26454_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ud5_26454/03_2024/7ud5_26454_neut_updated.pdb" } resolution = 4.25 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 60 5.16 5 C 13457 2.51 5 N 4083 2.21 5 O 4820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22713 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1398 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 2382 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} bond proxies already assigned to first conformer: 2366 Chain: "M" Number of atoms: 2625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2625 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 24, 'TRANS': 303} Chain: "N" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2879 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain breaks: 2 Chain: "O" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "P" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 413 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 5, 'TRANS': 46} Chain: "Q" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 404 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 5, 'TRANS': 45} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13306 SG CYS K3959 58.276 81.672 16.227 1.00 68.53 S ATOM 13339 SG CYS K3964 57.281 80.118 14.907 1.00 51.13 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN L 225 " occ=0.91 ... (6 atoms not shown) pdb=" ND2 ASN L 225 " occ=0.91 residue: pdb=" N LEU O 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU O 73 " occ=0.45 residue: pdb=" N ARG O 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG O 74 " occ=0.45 residue: pdb=" N GLY O 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY O 75 " occ=0.25 Time building chain proxies: 12.76, per 1000 atoms: 0.56 Number of scatterers: 22713 At special positions: 0 Unit cell: (148.12, 155.526, 119.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 60 16.00 P 292 15.00 O 4820 8.00 N 4083 7.00 C 13457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.69 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3964 " 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 23 sheets defined 29.1% alpha, 10.9% beta 142 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 10.03 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.014A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.827A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 51 through 75 removed outlier: 4.024A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.861A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 101 through 119 removed outlier: 4.004A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.572A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 114 Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 51 through 75 removed outlier: 3.893A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 36 through 45 removed outlier: 3.535A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'K' and resid 3817 through 3824 removed outlier: 3.847A pdb=" N PHE K3820 " --> pdb=" O PRO K3817 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG K3821 " --> pdb=" O MET K3818 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS K3822 " --> pdb=" O ARG K3819 " (cutoff:3.500A) Processing helix chain 'K' and resid 3866 through 3878 removed outlier: 3.513A pdb=" N LYS K3870 " --> pdb=" O GLN K3867 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS K3878 " --> pdb=" O TYR K3875 " (cutoff:3.500A) Processing helix chain 'K' and resid 3901 through 3904 removed outlier: 3.698A pdb=" N PHE K3904 " --> pdb=" O ALA K3901 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3901 through 3904' Processing helix chain 'M' and resid 203 through 210 Processing helix chain 'M' and resid 435 through 438 Processing helix chain 'M' and resid 505 through 524 removed outlier: 4.622A pdb=" N GLU M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) Processing helix chain 'N' and resid 230 through 233 No H-bonds generated for 'chain 'N' and resid 230 through 233' Processing helix chain 'N' and resid 329 through 331 No H-bonds generated for 'chain 'N' and resid 329 through 331' Processing helix chain 'O' and resid 23 through 34 Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing helix chain 'P' and resid 53 through 59 Processing helix chain 'P' and resid 62 through 74 removed outlier: 4.768A pdb=" N GLN P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 90 Processing helix chain 'Q' and resid 53 through 59 Processing helix chain 'Q' and resid 65 through 73 Processing helix chain 'Q' and resid 80 through 90 Processing sheet with id= A, first strand: chain 'K' and resid 3831 through 3835 Processing sheet with id= B, first strand: chain 'K' and resid 3861 through 3864 Processing sheet with id= C, first strand: chain 'K' and resid 3917 through 3920 Processing sheet with id= D, first strand: chain 'L' and resid 60 through 63 removed outlier: 3.752A pdb=" N LYS L 81 " --> pdb=" O ILE L 71 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 93 through 95 Processing sheet with id= F, first strand: chain 'L' and resid 132 through 137 removed outlier: 6.841A pdb=" N GLY L 147 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N CYS L 135 " --> pdb=" O VAL L 145 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL L 145 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE L 144 " --> pdb=" O TRP L 156 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP L 156 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE L 155 " --> pdb=" O LYS L 165 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS L 165 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 174 through 179 removed outlier: 7.295A pdb=" N SER L 189 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL L 177 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL L 187 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE L 179 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU L 185 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG L 196 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS L 207 " --> pdb=" O ILE L 197 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP L 199 " --> pdb=" O CYS L 205 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N CYS L 205 " --> pdb=" O ASP L 199 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 228 through 231 removed outlier: 3.871A pdb=" N ALA L 231 " --> pdb=" O LYS L 239 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS L 239 " --> pdb=" O ALA L 231 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 264 through 267 removed outlier: 3.788A pdb=" N GLN L 295 " --> pdb=" O ILE L 285 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 36 through 41 removed outlier: 6.668A pdb=" N LEU L 329 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR L 40 " --> pdb=" O ILE L 327 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE L 327 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS L 328 " --> pdb=" O SER L 318 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER L 318 " --> pdb=" O LYS L 328 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN L 314 " --> pdb=" O SER L 332 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 247 through 250 removed outlier: 3.531A pdb=" N ILE M 250 " --> pdb=" O PHE M 426 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR M 425 " --> pdb=" O ILE M 418 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE M 418 " --> pdb=" O TYR M 425 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'M' and resid 314 through 316 Processing sheet with id= M, first strand: chain 'M' and resid 391 through 394 Processing sheet with id= N, first strand: chain 'M' and resid 373 through 375 Processing sheet with id= O, first strand: chain 'N' and resid 16 through 18 removed outlier: 3.941A pdb=" N ILE N 320 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'N' and resid 38 through 42 removed outlier: 3.661A pdb=" N LYS N 60 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'N' and resid 133 through 136 removed outlier: 3.591A pdb=" N LYS N 141 " --> pdb=" O THR N 136 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.690A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'N' and resid 222 through 226 Processing sheet with id= T, first strand: chain 'N' and resid 265 through 268 Processing sheet with id= U, first strand: chain 'N' and resid 90 through 93 removed outlier: 3.533A pdb=" N GLN N 102 " --> pdb=" O GLN N 92 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 114 through 116 removed outlier: 3.672A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS N 116 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS N 122 " --> pdb=" O HIS N 116 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 12 through 15 533 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 9.93 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5974 1.34 - 1.46: 5644 1.46 - 1.57: 11488 1.57 - 1.69: 582 1.69 - 1.81: 83 Bond restraints: 23771 Sorted by residual: bond pdb=" C ILE M 250 " pdb=" N LEU M 251 " ideal model delta sigma weight residual 1.334 1.389 -0.054 1.52e-02 4.33e+03 1.28e+01 bond pdb=" CA ASN M 243 " pdb=" CB ASN M 243 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 bond pdb=" C TYR M 249 " pdb=" N ILE M 250 " ideal model delta sigma weight residual 1.332 1.374 -0.042 1.37e-02 5.33e+03 9.49e+00 bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 23766 not shown) Histogram of bond angle deviations from ideal: 90.00 - 98.80: 5 98.80 - 107.59: 2752 107.59 - 116.38: 15102 116.38 - 125.18: 14352 125.18 - 133.97: 1191 Bond angle restraints: 33402 Sorted by residual: angle pdb=" CA PRO M 241 " pdb=" C PRO M 241 " pdb=" N PHE M 242 " ideal model delta sigma weight residual 115.50 121.22 -5.72 1.27e+00 6.20e-01 2.03e+01 angle pdb=" C ASN M 243 " pdb=" CA ASN M 243 " pdb=" CB ASN M 243 " ideal model delta sigma weight residual 110.79 118.18 -7.39 1.66e+00 3.63e-01 1.98e+01 angle pdb=" CA PRO M 241 " pdb=" C PRO M 241 " pdb=" O PRO M 241 " ideal model delta sigma weight residual 121.31 116.36 4.95 1.20e+00 6.94e-01 1.70e+01 angle pdb=" C GLY M 246 " pdb=" N TYR M 247 " pdb=" CA TYR M 247 " ideal model delta sigma weight residual 123.05 117.45 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" N PRO M 241 " pdb=" CA PRO M 241 " pdb=" C PRO M 241 " ideal model delta sigma weight residual 111.19 104.98 6.21 1.57e+00 4.06e-01 1.57e+01 ... (remaining 33397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.49: 11830 29.49 - 58.98: 1590 58.98 - 88.48: 122 88.48 - 117.97: 1 117.97 - 147.46: 3 Dihedral angle restraints: 13546 sinusoidal: 7411 harmonic: 6135 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" C4' DG J 244 " pdb=" C3' DG J 244 " pdb=" O3' DG J 244 " pdb=" P DG J 245 " ideal model delta sinusoidal sigma weight residual 220.00 72.54 147.46 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CA MET K3816 " pdb=" C MET K3816 " pdb=" N PRO K3817 " pdb=" CA PRO K3817 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 13543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3499 0.077 - 0.154: 246 0.154 - 0.231: 3 0.231 - 0.307: 0 0.307 - 0.384: 1 Chirality restraints: 3749 Sorted by residual: chirality pdb=" CA ASN M 243 " pdb=" N ASN M 243 " pdb=" C ASN M 243 " pdb=" CB ASN M 243 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ARG P 76 " pdb=" N ARG P 76 " pdb=" C ARG P 76 " pdb=" CB ARG P 76 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ASP M 223 " pdb=" N ASP M 223 " pdb=" C ASP M 223 " pdb=" CB ASP M 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 3746 not shown) Planarity restraints: 3230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 442 " -0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO M 443 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO M 443 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO M 443 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS M 240 " 0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C HIS M 240 " -0.061 2.00e-02 2.50e+03 pdb=" O HIS M 240 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO M 241 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 40 " 0.251 9.50e-02 1.11e+02 1.13e-01 8.24e+00 pdb=" NE ARG F 40 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 40 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG F 40 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 40 " 0.013 2.00e-02 2.50e+03 ... (remaining 3227 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 829 2.70 - 3.25: 21731 3.25 - 3.80: 39852 3.80 - 4.35: 50554 4.35 - 4.90: 75301 Nonbonded interactions: 188267 Sorted by model distance: nonbonded pdb=" OD1 ASN M 397 " pdb=" OH TYR M 450 " model vdw 2.144 2.440 nonbonded pdb=" N ASP M 410 " pdb=" OD1 ASP M 410 " model vdw 2.172 2.520 nonbonded pdb=" OH TYR K3875 " pdb=" OD1 ASP K3894 " model vdw 2.182 2.440 nonbonded pdb=" OE2 GLU M 330 " pdb=" ND2 ASN M 483 " model vdw 2.195 2.520 nonbonded pdb=" OD1 ASN L 34 " pdb=" OG SER L 332 " model vdw 2.199 2.440 ... (remaining 188262 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = (chain 'P' and resid 46 through 96) selection = chain 'Q' } 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 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: 1.250 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: 6.730 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 72.440 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 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 0.059 23771 Z= 0.164 Angle : 0.586 11.770 33402 Z= 0.344 Chirality : 0.039 0.384 3749 Planarity : 0.005 0.113 3230 Dihedral : 22.038 147.460 9592 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.50 % Allowed : 6.37 % Favored : 92.13 % 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: -2.04 (0.18), residues: 2061 helix: 0.54 (0.21), residues: 631 sheet: -1.87 (0.28), residues: 320 loop : -2.42 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 35 HIS 0.006 0.000 HIS M 240 PHE 0.012 0.001 PHE M 464 TYR 0.009 0.001 TYR L 243 ARG 0.012 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 2.055 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: A 45 THR cc_start: 0.7817 (p) cc_final: 0.7535 (p) REVERT: A 60 LEU cc_start: 0.6597 (tp) cc_final: 0.6270 (pt) REVERT: D 76 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.7605 (ttp80) REVERT: F 63 GLU cc_start: 0.8019 (pp20) cc_final: 0.7709 (pp20) REVERT: M 410 ASP cc_start: 0.1509 (OUTLIER) cc_final: 0.0899 (t0) REVERT: N 13 TYR cc_start: 0.6773 (p90) cc_final: 0.6479 (p90) REVERT: N 310 ILE cc_start: 0.7184 (pt) cc_final: 0.6250 (tt) outliers start: 26 outliers final: 0 residues processed: 295 average time/residue: 0.4498 time to fit residues: 187.6512 Evaluate side-chains 138 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 10.0000 chunk 175 optimal weight: 0.3980 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 118 optimal weight: 0.0270 chunk 93 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 overall best weight: 3.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 112 GLN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3822 HIS K3906 ASN ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 375 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23771 Z= 0.321 Angle : 0.654 9.782 33402 Z= 0.363 Chirality : 0.042 0.253 3749 Planarity : 0.006 0.144 3230 Dihedral : 26.875 151.524 5509 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.17 % Allowed : 4.10 % Favored : 95.73 % 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: -2.25 (0.18), residues: 2061 helix: 0.18 (0.20), residues: 632 sheet: -1.86 (0.28), residues: 331 loop : -2.47 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 35 HIS 0.008 0.002 HIS F 75 PHE 0.015 0.002 PHE F 61 TYR 0.025 0.002 TYR P 87 ARG 0.026 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7891 (p) cc_final: 0.7625 (p) REVERT: A 60 LEU cc_start: 0.6709 (tp) cc_final: 0.6099 (mt) REVERT: B 26 ILE cc_start: 0.8387 (mm) cc_final: 0.8038 (pt) REVERT: B 44 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7125 (mttt) REVERT: F 63 GLU cc_start: 0.8253 (pp20) cc_final: 0.7800 (pp20) REVERT: K 3822 HIS cc_start: 0.5723 (OUTLIER) cc_final: 0.5392 (t-170) REVERT: M 284 TYR cc_start: 0.3009 (m-10) cc_final: 0.2425 (m-80) REVERT: N 26 MET cc_start: 0.7805 (pmm) cc_final: 0.7217 (pmm) REVERT: N 310 ILE cc_start: 0.7357 (pt) cc_final: 0.6963 (tt) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.3867 time to fit residues: 93.6250 Evaluate side-chains 116 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 210 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23771 Z= 0.263 Angle : 0.618 10.104 33402 Z= 0.345 Chirality : 0.041 0.177 3749 Planarity : 0.005 0.143 3230 Dihedral : 26.811 153.411 5509 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % 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: -2.24 (0.18), residues: 2061 helix: 0.21 (0.20), residues: 629 sheet: -1.85 (0.28), residues: 331 loop : -2.48 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 35 HIS 0.007 0.001 HIS N 304 PHE 0.014 0.002 PHE E 84 TYR 0.027 0.002 TYR G 50 ARG 0.012 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.6718 (tp) cc_final: 0.6126 (mt) REVERT: B 26 ILE cc_start: 0.8412 (mm) cc_final: 0.8106 (pt) REVERT: B 44 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7233 (mttt) REVERT: F 63 GLU cc_start: 0.8232 (pp20) cc_final: 0.7766 (pp20) REVERT: M 284 TYR cc_start: 0.3125 (m-10) cc_final: 0.2407 (m-80) REVERT: N 26 MET cc_start: 0.7906 (pmm) cc_final: 0.7308 (pmm) REVERT: N 310 ILE cc_start: 0.7580 (pt) cc_final: 0.6886 (tt) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.3740 time to fit residues: 92.2028 Evaluate side-chains 117 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3822 HIS K3925 HIS L 225 ASN ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23771 Z= 0.333 Angle : 0.681 10.267 33402 Z= 0.377 Chirality : 0.043 0.256 3749 Planarity : 0.006 0.159 3230 Dihedral : 26.902 156.225 5509 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.07 % 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: -2.54 (0.17), residues: 2061 helix: -0.15 (0.20), residues: 625 sheet: -2.00 (0.27), residues: 332 loop : -2.58 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 35 HIS 0.008 0.002 HIS C 31 PHE 0.017 0.002 PHE E 104 TYR 0.026 0.002 TYR F 98 ARG 0.014 0.001 ARG K3765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8044 (p) cc_final: 0.7770 (p) REVERT: A 60 LEU cc_start: 0.6775 (tp) cc_final: 0.6304 (mt) REVERT: B 44 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7314 (mttt) REVERT: F 63 GLU cc_start: 0.8309 (pp20) cc_final: 0.8013 (pp20) REVERT: K 3854 MET cc_start: 0.7573 (tmm) cc_final: 0.6927 (tmm) REVERT: M 284 TYR cc_start: 0.3508 (m-10) cc_final: 0.2617 (m-80) REVERT: N 26 MET cc_start: 0.8121 (pmm) cc_final: 0.7527 (pmm) REVERT: N 310 ILE cc_start: 0.7588 (pt) cc_final: 0.7054 (tt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3911 time to fit residues: 86.2932 Evaluate side-chains 107 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 3 optimal weight: 0.0770 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 overall best weight: 4.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23771 Z= 0.377 Angle : 0.724 9.543 33402 Z= 0.399 Chirality : 0.044 0.195 3749 Planarity : 0.006 0.144 3230 Dihedral : 27.082 157.631 5509 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % 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: -2.74 (0.17), residues: 2061 helix: -0.41 (0.20), residues: 622 sheet: -2.10 (0.29), residues: 297 loop : -2.65 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP N 303 HIS 0.009 0.002 HIS K3769 PHE 0.019 0.002 PHE E 104 TYR 0.028 0.002 TYR F 98 ARG 0.031 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8104 (p) cc_final: 0.7776 (p) REVERT: A 60 LEU cc_start: 0.7146 (tp) cc_final: 0.6563 (mt) REVERT: B 44 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7436 (mttt) REVERT: F 63 GLU cc_start: 0.8228 (pp20) cc_final: 0.7952 (pp20) REVERT: G 50 TYR cc_start: 0.8248 (t80) cc_final: 0.7755 (t80) REVERT: N 26 MET cc_start: 0.8194 (pmm) cc_final: 0.7724 (pmm) REVERT: N 310 ILE cc_start: 0.7696 (pt) cc_final: 0.7254 (tt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3949 time to fit residues: 83.1128 Evaluate side-chains 101 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3822 HIS ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23771 Z= 0.268 Angle : 0.649 10.103 33402 Z= 0.361 Chirality : 0.042 0.288 3749 Planarity : 0.005 0.109 3230 Dihedral : 26.982 157.021 5509 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.29 % 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: -2.57 (0.17), residues: 2061 helix: -0.14 (0.20), residues: 628 sheet: -2.07 (0.30), residues: 284 loop : -2.61 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 35 HIS 0.007 0.001 HIS K3822 PHE 0.014 0.002 PHE K3844 TYR 0.019 0.002 TYR H 80 ARG 0.016 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7919 (p) cc_final: 0.7560 (p) REVERT: A 60 LEU cc_start: 0.6830 (tp) cc_final: 0.6301 (mt) REVERT: B 44 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7297 (mttt) REVERT: F 59 LYS cc_start: 0.8377 (tppt) cc_final: 0.8163 (tppt) REVERT: F 63 GLU cc_start: 0.8224 (pp20) cc_final: 0.7815 (pp20) REVERT: G 50 TYR cc_start: 0.8121 (t80) cc_final: 0.7551 (t80) REVERT: K 3854 MET cc_start: 0.7678 (tmm) cc_final: 0.7449 (tmm) REVERT: N 26 MET cc_start: 0.8166 (pmm) cc_final: 0.7700 (pmm) REVERT: N 310 ILE cc_start: 0.7710 (pt) cc_final: 0.7177 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.3877 time to fit residues: 86.3591 Evaluate side-chains 108 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 255 HIS ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 375 HIS ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23771 Z= 0.337 Angle : 0.696 10.470 33402 Z= 0.385 Chirality : 0.044 0.261 3749 Planarity : 0.006 0.119 3230 Dihedral : 27.035 157.426 5509 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.79 % 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: -2.72 (0.17), residues: 2061 helix: -0.40 (0.20), residues: 627 sheet: -1.94 (0.31), residues: 267 loop : -2.70 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 35 HIS 0.008 0.002 HIS C 31 PHE 0.025 0.002 PHE A 67 TYR 0.037 0.002 TYR M 284 ARG 0.018 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8000 (p) cc_final: 0.7631 (p) REVERT: B 44 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7329 (mttt) REVERT: E 97 GLU cc_start: 0.8756 (mp0) cc_final: 0.8528 (mp0) REVERT: F 59 LYS cc_start: 0.8453 (tppt) cc_final: 0.8245 (tppt) REVERT: F 63 GLU cc_start: 0.8283 (pp20) cc_final: 0.7827 (pp20) REVERT: G 50 TYR cc_start: 0.8117 (t80) cc_final: 0.7522 (t80) REVERT: K 3854 MET cc_start: 0.7909 (tmm) cc_final: 0.7633 (tmm) REVERT: K 3931 MET cc_start: 0.4386 (pmm) cc_final: 0.4163 (tpt) REVERT: N 310 ILE cc_start: 0.7783 (pt) cc_final: 0.7197 (tt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3901 time to fit residues: 84.8983 Evaluate side-chains 100 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 141 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 202 optimal weight: 0.9980 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3822 HIS ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23771 Z= 0.186 Angle : 0.615 10.031 33402 Z= 0.341 Chirality : 0.040 0.257 3749 Planarity : 0.005 0.088 3230 Dihedral : 26.837 156.267 5509 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.06 % Allowed : 0.72 % Favored : 99.22 % 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: -2.31 (0.18), residues: 2061 helix: 0.23 (0.21), residues: 626 sheet: -1.97 (0.29), residues: 291 loop : -2.55 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP N 303 HIS 0.007 0.001 HIS K3822 PHE 0.011 0.001 PHE N 213 TYR 0.020 0.001 TYR H 80 ARG 0.014 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7826 (p) cc_final: 0.7477 (p) REVERT: B 26 ILE cc_start: 0.8352 (mm) cc_final: 0.7971 (pt) REVERT: B 44 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7346 (mttt) REVERT: C 88 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7891 (mmt180) REVERT: E 97 GLU cc_start: 0.8683 (mp0) cc_final: 0.8417 (mp0) REVERT: F 59 LYS cc_start: 0.8350 (tppt) cc_final: 0.8099 (tppt) REVERT: F 63 GLU cc_start: 0.8254 (pp20) cc_final: 0.7736 (pp20) REVERT: G 50 TYR cc_start: 0.8020 (t80) cc_final: 0.7569 (t80) REVERT: K 3854 MET cc_start: 0.7596 (tmm) cc_final: 0.7356 (tmm) REVERT: K 3931 MET cc_start: 0.4374 (pmm) cc_final: 0.4148 (tpp) REVERT: N 26 MET cc_start: 0.7685 (pmm) cc_final: 0.7311 (pmm) REVERT: N 310 ILE cc_start: 0.7563 (pt) cc_final: 0.6800 (tt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3756 time to fit residues: 87.7102 Evaluate side-chains 112 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.0770 chunk 194 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23771 Z= 0.348 Angle : 0.709 10.017 33402 Z= 0.389 Chirality : 0.044 0.264 3749 Planarity : 0.006 0.098 3230 Dihedral : 26.988 157.351 5509 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.84 % 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: -2.60 (0.17), residues: 2061 helix: -0.24 (0.20), residues: 626 sheet: -1.91 (0.31), residues: 266 loop : -2.65 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 303 HIS 0.009 0.002 HIS C 31 PHE 0.017 0.002 PHE F 61 TYR 0.018 0.002 TYR M 386 ARG 0.019 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7915 (p) cc_final: 0.7555 (p) REVERT: B 44 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7432 (mttt) REVERT: B 84 MET cc_start: 0.6577 (tmm) cc_final: 0.6244 (tmm) REVERT: E 97 GLU cc_start: 0.8759 (mp0) cc_final: 0.8528 (mp0) REVERT: F 59 LYS cc_start: 0.8460 (tppt) cc_final: 0.8237 (tppt) REVERT: F 63 GLU cc_start: 0.8272 (pp20) cc_final: 0.7827 (pp20) REVERT: G 50 TYR cc_start: 0.8096 (t80) cc_final: 0.7561 (t80) REVERT: K 3854 MET cc_start: 0.7888 (tmm) cc_final: 0.7628 (tmm) REVERT: K 3931 MET cc_start: 0.4633 (pmm) cc_final: 0.4391 (tpp) REVERT: N 26 MET cc_start: 0.7914 (pmm) cc_final: 0.7431 (pmm) REVERT: N 310 ILE cc_start: 0.7578 (pt) cc_final: 0.6718 (tt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3609 time to fit residues: 75.5486 Evaluate side-chains 105 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 141 optimal weight: 0.0470 chunk 112 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3822 HIS ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23771 Z= 0.243 Angle : 0.645 10.118 33402 Z= 0.356 Chirality : 0.042 0.269 3749 Planarity : 0.005 0.083 3230 Dihedral : 26.923 156.892 5509 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.67 % 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: -2.46 (0.18), residues: 2061 helix: 0.01 (0.20), residues: 627 sheet: -1.93 (0.30), residues: 280 loop : -2.62 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP N 303 HIS 0.005 0.001 HIS N 274 PHE 0.016 0.001 PHE D 67 TYR 0.018 0.002 TYR G 50 ARG 0.016 0.000 ARG F 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7876 (p) cc_final: 0.7523 (p) REVERT: B 26 ILE cc_start: 0.8418 (mm) cc_final: 0.8024 (pt) REVERT: B 44 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7401 (mttt) REVERT: C 88 ARG cc_start: 0.8068 (mmt180) cc_final: 0.7844 (mmt180) REVERT: E 97 GLU cc_start: 0.8722 (mp0) cc_final: 0.8502 (mp0) REVERT: F 59 LYS cc_start: 0.8454 (tppt) cc_final: 0.8188 (tppt) REVERT: F 63 GLU cc_start: 0.8184 (pp20) cc_final: 0.7780 (pp20) REVERT: G 50 TYR cc_start: 0.7988 (t80) cc_final: 0.7456 (t80) REVERT: K 3931 MET cc_start: 0.4547 (pmm) cc_final: 0.4340 (tpp) REVERT: N 26 MET cc_start: 0.7827 (pmm) cc_final: 0.7347 (pmm) REVERT: N 310 ILE cc_start: 0.7505 (pt) cc_final: 0.6583 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.3802 time to fit residues: 84.8792 Evaluate side-chains 116 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 168 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.117803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.103283 restraints weight = 191264.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.102318 restraints weight = 237456.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.101396 restraints weight = 156372.228| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23771 Z= 0.206 Angle : 0.615 10.058 33402 Z= 0.340 Chirality : 0.040 0.259 3749 Planarity : 0.004 0.067 3230 Dihedral : 26.759 156.233 5509 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.06 % Allowed : 0.22 % Favored : 99.72 % 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: -2.26 (0.18), residues: 2061 helix: 0.31 (0.21), residues: 627 sheet: -1.96 (0.30), residues: 284 loop : -2.53 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 303 HIS 0.006 0.001 HIS N 304 PHE 0.011 0.001 PHE N 213 TYR 0.025 0.002 TYR M 284 ARG 0.012 0.000 ARG F 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.03 seconds wall clock time: 64 minutes 35.44 seconds (3875.44 seconds total)