Starting phenix.real_space_refine on Sat Apr 6 05:21:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja3_36124/04_2024/8ja3_36124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja3_36124/04_2024/8ja3_36124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja3_36124/04_2024/8ja3_36124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja3_36124/04_2024/8ja3_36124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja3_36124/04_2024/8ja3_36124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja3_36124/04_2024/8ja3_36124_updated.pdb" } resolution = 3.94 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= 0.013 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 8 5.49 5 S 23 5.16 5 C 4537 2.51 5 N 1222 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7130 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2118 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 291} Chain breaks: 4 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 233 Chain: "U" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'TPO:plan-1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 756 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "M" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 680 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2070 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 285} Chain breaks: 6 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 224 Chain: "V" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'TPO:plan-1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 684 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "L" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 660 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 94} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 4.80, per 1000 atoms: 0.67 Number of scatterers: 7130 At special positions: 0 Unit cell: (87.0348, 168.362, 79.9008, 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 23 16.00 P 8 15.00 O 1340 8.00 N 1222 7.00 C 4537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 23 sheets defined 4.8% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.587A pdb=" N LYS B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.561A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing sheet with id= A, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.522A pdb=" N VAL B 41 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 113 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.541A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 81 through 84 removed outlier: 3.925A pdb=" N THR B 58 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 59 through 62 Processing sheet with id= E, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= F, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.818A pdb=" N SER B 202 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 218 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 270 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 345 through 349 removed outlier: 4.185A pdb=" N GLY B 316 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 7 through 10 removed outlier: 3.931A pdb=" N LEU I 23 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 98 through 102 removed outlier: 3.864A pdb=" N ALA I 52 " --> pdb=" O TRP I 39 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 5 through 8 removed outlier: 4.054A pdb=" N SER M 8 " --> pdb=" O THR M 23 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR M 23 " --> pdb=" O SER M 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 86 through 91 removed outlier: 3.724A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 9 through 12 Processing sheet with id= M, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.540A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.562A pdb=" N VAL A 41 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR A 113 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.592A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= Q, first strand: chain 'A' and resid 184 through 186 Processing sheet with id= R, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.785A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 322 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 236 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 254 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= T, first strand: chain 'H' and resid 96 through 100 removed outlier: 3.846A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER H 55 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 74 through 76 Processing sheet with id= V, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.569A pdb=" N PHE L 72 " --> pdb=" O CYS L 24 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 86 through 88 removed outlier: 3.540A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2126 1.33 - 1.46: 1243 1.46 - 1.58: 3860 1.58 - 1.70: 17 1.70 - 1.82: 28 Bond restraints: 7274 Sorted by residual: bond pdb=" C LEU A 33 " pdb=" N VAL A 34 " ideal model delta sigma weight residual 1.330 1.470 -0.140 1.97e-02 2.58e+03 5.04e+01 bond pdb=" OG1 TPO V 463 " pdb=" P TPO V 463 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" OG1 TPO V 466 " pdb=" P TPO V 466 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" OG1 TPO U 463 " pdb=" P TPO U 463 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" OG1 TPO U 466 " pdb=" P TPO U 466 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 7269 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.49: 294 106.49 - 113.40: 4004 113.40 - 120.30: 2375 120.30 - 127.21: 3244 127.21 - 134.12: 91 Bond angle restraints: 10008 Sorted by residual: angle pdb=" C LEU A 33 " pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 122.91 133.35 -10.44 1.43e+00 4.89e-01 5.33e+01 angle pdb=" N SEP U 465 " pdb=" CA SEP U 465 " pdb=" C SEP U 465 " ideal model delta sigma weight residual 111.20 127.20 -16.00 2.80e+00 1.28e-01 3.27e+01 angle pdb=" O LEU A 33 " pdb=" C LEU A 33 " pdb=" N VAL A 34 " ideal model delta sigma weight residual 123.17 117.27 5.90 1.21e+00 6.83e-01 2.37e+01 angle pdb=" N ARG U 464 " pdb=" CA ARG U 464 " pdb=" C ARG U 464 " ideal model delta sigma weight residual 111.00 124.31 -13.31 2.80e+00 1.28e-01 2.26e+01 angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 116.54 111.36 5.18 1.15e+00 7.56e-01 2.03e+01 ... (remaining 10003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3891 17.26 - 34.53: 300 34.53 - 51.79: 53 51.79 - 69.05: 14 69.05 - 86.31: 4 Dihedral angle restraints: 4262 sinusoidal: 1196 harmonic: 3066 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 39.38 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA ARG B 169 " pdb=" C ARG B 169 " pdb=" N LYS B 170 " pdb=" CA LYS B 170 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LEU I 110 " pdb=" C LEU I 110 " pdb=" N ASP I 111 " pdb=" CA ASP I 111 " ideal model delta harmonic sigma weight residual 180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 4259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1036 0.069 - 0.137: 166 0.137 - 0.206: 11 0.206 - 0.275: 3 0.275 - 0.344: 1 Chirality restraints: 1217 Sorted by residual: chirality pdb=" CA SEP U 465 " pdb=" N SEP U 465 " pdb=" C SEP U 465 " pdb=" CB SEP U 465 " both_signs ideal model delta sigma weight residual False 2.50 2.16 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ARG U 464 " pdb=" N ARG U 464 " pdb=" C ARG U 464 " pdb=" CB ARG U 464 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB TPO U 463 " pdb=" CA TPO U 463 " pdb=" OG1 TPO U 463 " pdb=" CG2 TPO U 463 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1214 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER I 102 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C SER I 102 " 0.082 2.00e-02 2.50e+03 pdb=" O SER I 102 " -0.030 2.00e-02 2.50e+03 pdb=" N ARG I 103 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 462 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C LEU U 462 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU U 462 " -0.031 2.00e-02 2.50e+03 pdb=" N TPO U 463 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP U 459 " 0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C SEP U 459 " -0.064 2.00e-02 2.50e+03 pdb=" O SEP U 459 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU U 460 " 0.021 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1433 2.77 - 3.30: 7007 3.30 - 3.84: 11116 3.84 - 4.37: 12563 4.37 - 4.90: 21638 Nonbonded interactions: 53757 Sorted by model distance: nonbonded pdb=" N GLY L 17 " pdb=" O LEU L 79 " model vdw 2.242 2.520 nonbonded pdb=" O ASN H 80 " pdb=" OD1 ASN H 80 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLN B 172 " pdb=" OG1 THR B 304 " model vdw 2.260 2.440 nonbonded pdb=" O PHE H 30 " pdb=" ND2 ASN H 80 " model vdw 2.271 2.520 nonbonded pdb=" O THR A 221 " pdb=" OG1 THR A 221 " model vdw 2.289 2.440 ... (remaining 53752 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 7 through 45 or (resid 46 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 through 100 or (resid 101 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thro \ ugh 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) o \ r resid 124 through 184 or (resid 185 and (name N or name CA or name C or name O \ or name CB )) or resid 186 through 193 or (resid 194 through 195 and (name N or \ name CA or name C or name O or name CB )) or resid 196 through 209 or (resid 21 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 220 or (resid 221 through 222 and (name N or name CA or name C or name O or \ name CB )) or resid 223 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB )) or resid 229 through 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 through 247 \ or (resid 248 through 251 and (name N or name CA or name C or name O or name CB \ )) or resid 252 through 255 or (resid 256 through 261 and (name N or name CA or \ name C or name O or name CB )) or resid 262 through 266 or (resid 267 and (name \ N or name CA or name C or name O or name CB )) or resid 268 through 288 or (resi \ d 289 through 290 and (name N or name CA or name C or name O or name CB )) or re \ sid 291 through 299 or (resid 300 through 301 and (name N or name CA or name C o \ r name O or name CB )) or resid 302 through 325 or (resid 326 through 327 and (n \ ame N or name CA or name C or name O or name CB )) or resid 328 through 357)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 41 or resid 45 through 47 or (resid 48 through 51 and (name \ N or name CA or name C or name O or name CB )) or resid 52 through 61 or resid \ 77 through 89 or (resid 92 through 95 and (name N or name CA or name C or name O \ or name CB )) or resid 96 through 121 or (resid 122 through 123 and (name N or \ name CA or name C or name O or name CB )) or resid 124 through 131 or (resid 139 \ through 145 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 46 through 148 or (resid 149 through 157 and (name N or name CA or name C or nam \ e O or name CB )) or resid 158 through 160 or (resid 161 and (name N or name CA \ or name C or name O or name CB )) or resid 162 through 189 or (resid 190 and (na \ me N or name CA or name C or name O or name CB )) or resid 193 through 198 or (r \ esid 199 through 201 and (name N or name CA or name C or name O or name CB )) or \ resid 202 through 205 or (resid 206 through 207 and (name N or name CA or name \ C or name O or name CB )) or resid 208 through 217 or (resid 218 through 219 and \ (name N or name CA or name C or name O or name CB )) or resid 220 through 226 o \ r (resid 227 through 228 and (name N or name CA or name C or name O or name CB ) \ ) or resid 229 through 240 or (resid 241 and (name N or name CA or name C or nam \ e O or name CB )) or resid 242 through 286 or (resid 287 through 290 and (name N \ or name CA or name C or name O or name CB )) or resid 291 through 349 or (resid \ 350 and (name N or name CA or name C or name O or name CB )) or resid 351 throu \ gh 357)) } ncs_group { reference = (chain 'H' and (resid 5 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 47 or (resid 48 through 49 and (name \ N or name CA or name C or name O or name CB )) or resid 50 through 69 or (resid \ 70 and (name N or name CA or name C or name O or name CB )) or resid 71 through \ 103 or resid 106 through 111 or (resid 112 and (name N or name CA or name C or \ name O or name CB )) or resid 113 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 5 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 19 or (resid 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 or (resid 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 33 or (resid 34 through 36 and (name N or name CA or name C or name O or name \ CB )) or resid 37 through 55 or (resid 56 through 58 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 59 through 61 and (name N or name CA or \ name C or name O or name CB )) or resid 62 through 67 or (resid 68 and (name N o \ r name CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 \ through 76 and (name N or name CA or name C or name O or name CB )) or resid 77 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )) or resid 93 or (resid 94 through 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 through 115)) } ncs_group { reference = (chain 'L' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 17 or (resid 18 through 2 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 24 through 2 \ 6 or (resid 27 through 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 39 or (resid 40 and (name N or name CA or name C or name \ O or name CB )) or resid 41 through 73 or (resid 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 82 through 87 and \ (name N or name CA or name C or name O or name CB )) or resid 88 through 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 2 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 28 or (resid 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 throug \ h 33 and (name N or name CA or name C or name O or name CB )) or resid 34 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 45 or (resid 46 and (name N or name CA or name C or na \ me O or name CB )) or resid 47 through 67 or (resid 68 and (name N or name CA or \ name C or name O or name CB )) or resid 69 through 79 or (resid 82 through 87 a \ nd (name N or name CA or name C or name O or name CB )) or resid 88 through 93 o \ r (resid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 \ through 104 or (resid 105 through 106 and (name N or name CA or name C or name \ O or name CB )))) } ncs_group { reference = chain 'U' selection = chain 'V' } 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: 0.880 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: 0.010 Extract box with map and model: 3.710 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.870 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 7274 Z= 0.480 Angle : 0.941 16.005 10008 Z= 0.508 Chirality : 0.051 0.344 1217 Planarity : 0.007 0.082 1284 Dihedral : 14.002 86.312 2256 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.26 % Allowed : 17.01 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.46 (0.26), residues: 987 helix: -1.26 (0.98), residues: 22 sheet: -0.94 (0.26), residues: 391 loop : -0.92 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.011 0.002 HIS I 38 PHE 0.018 0.002 PHE B 349 TYR 0.032 0.003 TYR B 321 ARG 0.005 0.001 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 ILE cc_start: 0.7224 (mm) cc_final: 0.6869 (mt) REVERT: I 78 SER cc_start: 0.7651 (m) cc_final: 0.7294 (p) REVERT: I 103 ARG cc_start: 0.3686 (OUTLIER) cc_final: 0.3454 (ttp80) REVERT: M 49 ILE cc_start: 0.7847 (mt) cc_final: 0.7322 (mp) REVERT: M 90 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 103 ARG cc_start: 0.3486 (OUTLIER) cc_final: 0.2304 (mtm-85) REVERT: A 169 ARG cc_start: 0.6389 (mtp180) cc_final: 0.6076 (mtp-110) REVERT: A 326 LYS cc_start: 0.5016 (OUTLIER) cc_final: 0.3323 (tptt) REVERT: L 49 ILE cc_start: 0.7721 (mm) cc_final: 0.7361 (mm) outliers start: 13 outliers final: 5 residues processed: 150 average time/residue: 0.2361 time to fit residues: 45.0866 Evaluate side-chains 130 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain H residue 31 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7274 Z= 0.252 Angle : 0.696 11.259 10008 Z= 0.355 Chirality : 0.046 0.227 1217 Planarity : 0.005 0.055 1284 Dihedral : 7.809 69.005 1135 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.86 % Allowed : 18.40 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 987 helix: 0.12 (1.07), residues: 22 sheet: -0.71 (0.26), residues: 411 loop : -0.65 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 39 HIS 0.006 0.001 HIS I 38 PHE 0.018 0.002 PHE B 349 TYR 0.021 0.002 TYR A 54 ARG 0.005 0.001 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 0.814 Fit side-chains REVERT: B 275 THR cc_start: 0.5441 (m) cc_final: 0.5164 (m) REVERT: I 78 SER cc_start: 0.7495 (m) cc_final: 0.7096 (p) REVERT: I 103 ARG cc_start: 0.3263 (OUTLIER) cc_final: 0.2471 (ttt180) REVERT: I 110 LEU cc_start: 0.7233 (tt) cc_final: 0.7025 (tt) REVERT: M 49 ILE cc_start: 0.7808 (mt) cc_final: 0.7212 (mp) REVERT: M 90 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 103 ARG cc_start: 0.3865 (OUTLIER) cc_final: 0.2457 (mtm-85) REVERT: A 169 ARG cc_start: 0.6325 (mtp180) cc_final: 0.6016 (mtp-110) REVERT: H 50 TRP cc_start: 0.6911 (t60) cc_final: 0.6654 (t60) outliers start: 28 outliers final: 22 residues processed: 150 average time/residue: 0.2101 time to fit residues: 40.9554 Evaluate side-chains 154 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 245 ASN I 38 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 7274 Z= 0.541 Angle : 0.912 12.236 10008 Z= 0.469 Chirality : 0.053 0.259 1217 Planarity : 0.007 0.077 1284 Dihedral : 8.305 64.254 1125 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 9.03 % Allowed : 20.49 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.27), residues: 987 helix: -1.15 (0.95), residues: 22 sheet: -1.09 (0.27), residues: 394 loop : -1.21 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP I 39 HIS 0.009 0.002 HIS A 210 PHE 0.018 0.003 PHE H 71 TYR 0.037 0.004 TYR H 98 ARG 0.015 0.001 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 142 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: B 7 ARG cc_start: 0.6176 (tmt170) cc_final: 0.5852 (tmt170) REVERT: B 233 ILE cc_start: 0.1433 (OUTLIER) cc_final: 0.0926 (mm) REVERT: B 280 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7211 (p0) REVERT: B 295 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.6513 (t-90) REVERT: I 78 SER cc_start: 0.7611 (m) cc_final: 0.7140 (p) REVERT: I 103 ARG cc_start: 0.3924 (OUTLIER) cc_final: 0.0587 (ttt90) REVERT: M 49 ILE cc_start: 0.8046 (mt) cc_final: 0.7482 (tt) REVERT: M 78 SER cc_start: 0.5994 (p) cc_final: 0.5791 (t) REVERT: M 90 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6625 (tm-30) REVERT: A 103 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.3881 (mtp-110) REVERT: A 169 ARG cc_start: 0.6459 (mtp180) cc_final: 0.6074 (mtp-110) REVERT: A 173 TYR cc_start: 0.6426 (m-80) cc_final: 0.5445 (m-10) REVERT: H 50 TRP cc_start: 0.7204 (t60) cc_final: 0.6945 (t60) REVERT: H 62 TYR cc_start: 0.6319 (m-80) cc_final: 0.6059 (m-10) REVERT: L 38 GLN cc_start: 0.5079 (tt0) cc_final: 0.4006 (mm-40) REVERT: L 49 ILE cc_start: 0.7633 (mp) cc_final: 0.7090 (tt) outliers start: 52 outliers final: 35 residues processed: 173 average time/residue: 0.1984 time to fit residues: 45.1940 Evaluate side-chains 178 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0000 chunk 48 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.0870 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7274 Z= 0.185 Angle : 0.624 9.419 10008 Z= 0.315 Chirality : 0.044 0.184 1217 Planarity : 0.005 0.052 1284 Dihedral : 7.041 67.991 1125 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 6.42 % Allowed : 23.96 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.28 (0.28), residues: 987 helix: 0.88 (1.16), residues: 22 sheet: -0.88 (0.26), residues: 416 loop : -0.81 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 39 HIS 0.005 0.001 HIS I 38 PHE 0.020 0.001 PHE B 349 TYR 0.015 0.002 TYR B 321 ARG 0.011 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 0.814 Fit side-chains REVERT: B 173 TYR cc_start: 0.6479 (m-80) cc_final: 0.5535 (m-10) REVERT: B 203 LEU cc_start: 0.6415 (mt) cc_final: 0.6093 (mp) REVERT: B 295 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6121 (t-90) REVERT: I 55 SER cc_start: 0.6683 (t) cc_final: 0.6347 (p) REVERT: I 78 SER cc_start: 0.7554 (m) cc_final: 0.7175 (p) REVERT: I 110 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6740 (tt) REVERT: M 49 ILE cc_start: 0.7754 (mt) cc_final: 0.7204 (tt) REVERT: M 90 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6631 (tm-30) REVERT: A 10 LYS cc_start: 0.7105 (pptt) cc_final: 0.6842 (tptt) REVERT: A 320 SER cc_start: 0.7650 (t) cc_final: 0.7389 (t) REVERT: H 50 TRP cc_start: 0.6940 (t60) cc_final: 0.6498 (t60) REVERT: L 38 GLN cc_start: 0.4821 (tt0) cc_final: 0.3874 (mm-40) REVERT: L 49 ILE cc_start: 0.7412 (mp) cc_final: 0.6947 (tt) outliers start: 37 outliers final: 25 residues processed: 161 average time/residue: 0.1831 time to fit residues: 39.5867 Evaluate side-chains 158 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7274 Z= 0.216 Angle : 0.605 8.945 10008 Z= 0.305 Chirality : 0.043 0.186 1217 Planarity : 0.005 0.049 1284 Dihedral : 6.462 68.226 1117 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 6.77 % Allowed : 25.00 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.16 (0.28), residues: 987 helix: 1.16 (1.18), residues: 22 sheet: -0.78 (0.26), residues: 414 loop : -0.76 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 39 HIS 0.004 0.001 HIS I 38 PHE 0.015 0.001 PHE B 349 TYR 0.017 0.002 TYR I 98 ARG 0.009 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 0.734 Fit side-chains REVERT: B 173 TYR cc_start: 0.6422 (m-80) cc_final: 0.5524 (m-10) REVERT: B 295 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6193 (t-90) REVERT: I 55 SER cc_start: 0.6651 (t) cc_final: 0.5984 (p) REVERT: I 78 SER cc_start: 0.7502 (m) cc_final: 0.7083 (p) REVERT: I 110 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6472 (tt) REVERT: M 49 ILE cc_start: 0.7800 (mt) cc_final: 0.7310 (tt) REVERT: M 90 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 320 SER cc_start: 0.7693 (t) cc_final: 0.7420 (t) REVERT: H 50 TRP cc_start: 0.6799 (t60) cc_final: 0.6381 (t60) REVERT: L 38 GLN cc_start: 0.4870 (tt0) cc_final: 0.3920 (mm-40) REVERT: L 49 ILE cc_start: 0.7447 (mp) cc_final: 0.6978 (tt) outliers start: 39 outliers final: 26 residues processed: 155 average time/residue: 0.1746 time to fit residues: 36.8961 Evaluate side-chains 158 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7274 Z= 0.201 Angle : 0.591 8.479 10008 Z= 0.298 Chirality : 0.044 0.184 1217 Planarity : 0.005 0.047 1284 Dihedral : 6.165 67.868 1115 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.12 % Allowed : 25.69 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.13 (0.28), residues: 987 helix: 1.50 (1.18), residues: 22 sheet: -0.68 (0.27), residues: 406 loop : -0.83 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 39 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE B 349 TYR 0.015 0.002 TYR I 98 ARG 0.008 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 0.816 Fit side-chains REVERT: B 173 TYR cc_start: 0.6462 (m-80) cc_final: 0.5216 (m-10) REVERT: B 233 ILE cc_start: 0.0305 (OUTLIER) cc_final: -0.0029 (mt) REVERT: B 295 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6441 (t-90) REVERT: I 55 SER cc_start: 0.6691 (t) cc_final: 0.6233 (p) REVERT: I 78 SER cc_start: 0.7580 (m) cc_final: 0.7155 (p) REVERT: M 49 ILE cc_start: 0.7792 (mt) cc_final: 0.7295 (tt) REVERT: M 90 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 10 LYS cc_start: 0.7106 (pptt) cc_final: 0.6850 (tptt) REVERT: A 169 ARG cc_start: 0.6465 (mtp180) cc_final: 0.6131 (mtp-110) REVERT: A 172 GLN cc_start: 0.6303 (tm-30) cc_final: 0.6067 (tm-30) REVERT: A 320 SER cc_start: 0.7779 (t) cc_final: 0.7555 (t) REVERT: H 50 TRP cc_start: 0.6753 (t60) cc_final: 0.6305 (t60) REVERT: L 38 GLN cc_start: 0.4841 (tt0) cc_final: 0.3984 (mm-40) REVERT: L 49 ILE cc_start: 0.7426 (mp) cc_final: 0.6972 (tt) outliers start: 41 outliers final: 32 residues processed: 166 average time/residue: 0.1910 time to fit residues: 43.1425 Evaluate side-chains 170 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 61 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7274 Z= 0.198 Angle : 0.591 8.199 10008 Z= 0.297 Chirality : 0.043 0.191 1217 Planarity : 0.005 0.049 1284 Dihedral : 6.028 67.239 1114 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 7.47 % Allowed : 26.04 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.99 (0.28), residues: 987 helix: 1.74 (1.16), residues: 22 sheet: -0.50 (0.27), residues: 395 loop : -0.82 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 39 HIS 0.003 0.001 HIS A 198 PHE 0.015 0.001 PHE B 349 TYR 0.013 0.002 TYR H 112 ARG 0.007 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 0.851 Fit side-chains REVERT: B 173 TYR cc_start: 0.6369 (m-80) cc_final: 0.5140 (m-10) REVERT: B 233 ILE cc_start: 0.0090 (OUTLIER) cc_final: -0.0239 (mt) REVERT: B 295 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6122 (t-90) REVERT: I 55 SER cc_start: 0.6685 (t) cc_final: 0.5954 (p) REVERT: I 78 SER cc_start: 0.7587 (m) cc_final: 0.7169 (p) REVERT: I 110 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6497 (tt) REVERT: M 49 ILE cc_start: 0.7802 (mt) cc_final: 0.7343 (tt) REVERT: M 90 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6564 (tm-30) REVERT: M 95 VAL cc_start: 0.7159 (OUTLIER) cc_final: 0.6867 (m) REVERT: A 10 LYS cc_start: 0.7109 (pptt) cc_final: 0.6859 (tptt) REVERT: A 169 ARG cc_start: 0.6385 (mtp180) cc_final: 0.6051 (mtp-110) REVERT: A 278 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6718 (pp) REVERT: A 320 SER cc_start: 0.7920 (t) cc_final: 0.7663 (t) REVERT: A 346 GLU cc_start: 0.6181 (mp0) cc_final: 0.5859 (mp0) REVERT: H 50 TRP cc_start: 0.6738 (t60) cc_final: 0.6356 (t60) REVERT: L 38 GLN cc_start: 0.4728 (tt0) cc_final: 0.3906 (mm-40) REVERT: L 49 ILE cc_start: 0.7418 (mp) cc_final: 0.6993 (tt) outliers start: 43 outliers final: 34 residues processed: 167 average time/residue: 0.1653 time to fit residues: 38.0851 Evaluate side-chains 176 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 62 ARG Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.0050 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7274 Z= 0.231 Angle : 0.630 11.307 10008 Z= 0.311 Chirality : 0.044 0.239 1217 Planarity : 0.005 0.053 1284 Dihedral : 6.093 66.842 1114 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 7.99 % Allowed : 24.65 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.13 (0.28), residues: 987 helix: 1.76 (1.16), residues: 22 sheet: -0.57 (0.27), residues: 395 loop : -0.95 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 39 HIS 0.004 0.001 HIS A 198 PHE 0.016 0.002 PHE H 71 TYR 0.016 0.002 TYR I 98 ARG 0.008 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 140 time to evaluate : 0.807 Fit side-chains REVERT: B 173 TYR cc_start: 0.6386 (m-80) cc_final: 0.5075 (m-10) REVERT: B 233 ILE cc_start: 0.0298 (OUTLIER) cc_final: -0.0050 (mt) REVERT: B 295 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6179 (t-90) REVERT: I 78 SER cc_start: 0.7603 (m) cc_final: 0.7184 (p) REVERT: I 110 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6334 (tt) REVERT: M 49 ILE cc_start: 0.7834 (mt) cc_final: 0.7419 (tt) REVERT: M 90 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6545 (tm-30) REVERT: A 278 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6805 (pp) REVERT: A 320 SER cc_start: 0.7985 (t) cc_final: 0.7699 (t) REVERT: H 50 TRP cc_start: 0.6710 (t60) cc_final: 0.6445 (t60) REVERT: L 38 GLN cc_start: 0.4896 (tt0) cc_final: 0.4028 (mm-40) REVERT: L 49 ILE cc_start: 0.7436 (mp) cc_final: 0.7012 (tt) outliers start: 46 outliers final: 38 residues processed: 171 average time/residue: 0.1704 time to fit residues: 40.1914 Evaluate side-chains 179 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 62 ARG Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7274 Z= 0.223 Angle : 0.615 9.365 10008 Z= 0.306 Chirality : 0.044 0.216 1217 Planarity : 0.005 0.049 1284 Dihedral : 6.028 66.420 1114 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 8.33 % Allowed : 23.78 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.16 (0.28), residues: 987 helix: 1.88 (1.17), residues: 22 sheet: -0.61 (0.27), residues: 393 loop : -0.96 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 39 HIS 0.003 0.001 HIS A 198 PHE 0.013 0.002 PHE H 71 TYR 0.015 0.002 TYR H 98 ARG 0.008 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 0.806 Fit side-chains REVERT: B 173 TYR cc_start: 0.6632 (m-80) cc_final: 0.5521 (m-10) REVERT: B 233 ILE cc_start: 0.0093 (OUTLIER) cc_final: -0.0261 (mt) REVERT: B 295 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.6151 (t-90) REVERT: I 55 SER cc_start: 0.6874 (t) cc_final: 0.6015 (p) REVERT: I 78 SER cc_start: 0.7567 (m) cc_final: 0.7125 (p) REVERT: I 110 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6245 (tt) REVERT: M 49 ILE cc_start: 0.7867 (mt) cc_final: 0.7418 (tt) REVERT: M 90 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6555 (tm-30) REVERT: A 117 PHE cc_start: 0.4821 (OUTLIER) cc_final: 0.4423 (m-10) REVERT: A 278 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6749 (pp) REVERT: A 320 SER cc_start: 0.7962 (t) cc_final: 0.7729 (t) REVERT: H 50 TRP cc_start: 0.6699 (t60) cc_final: 0.6351 (t60) REVERT: L 38 GLN cc_start: 0.4891 (tt0) cc_final: 0.4041 (mm-40) REVERT: L 49 ILE cc_start: 0.7424 (mp) cc_final: 0.7019 (tt) outliers start: 48 outliers final: 39 residues processed: 171 average time/residue: 0.1648 time to fit residues: 39.1252 Evaluate side-chains 177 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.0570 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 280 ASN A 237 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7274 Z= 0.175 Angle : 0.587 11.736 10008 Z= 0.288 Chirality : 0.043 0.172 1217 Planarity : 0.004 0.048 1284 Dihedral : 5.778 66.211 1114 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.25 % Allowed : 26.91 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.04 (0.28), residues: 987 helix: 2.13 (1.18), residues: 22 sheet: -0.51 (0.27), residues: 394 loop : -0.90 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 39 HIS 0.002 0.001 HIS H 38 PHE 0.013 0.001 PHE A 277 TYR 0.014 0.001 TYR H 112 ARG 0.007 0.001 ARG I 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 0.743 Fit side-chains REVERT: B 173 TYR cc_start: 0.6387 (m-80) cc_final: 0.5603 (m-10) REVERT: B 233 ILE cc_start: 0.0081 (OUTLIER) cc_final: -0.0262 (mt) REVERT: B 295 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6246 (t-90) REVERT: B 320 SER cc_start: 0.7566 (t) cc_final: 0.7241 (p) REVERT: I 55 SER cc_start: 0.6766 (t) cc_final: 0.6213 (p) REVERT: I 78 SER cc_start: 0.7610 (m) cc_final: 0.7197 (p) REVERT: I 110 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6323 (tt) REVERT: M 49 ILE cc_start: 0.7784 (mt) cc_final: 0.7347 (tt) REVERT: M 90 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6577 (tm-30) REVERT: A 10 LYS cc_start: 0.7090 (pptt) cc_final: 0.6830 (tptt) REVERT: A 278 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6730 (pp) REVERT: A 320 SER cc_start: 0.7927 (t) cc_final: 0.7710 (t) REVERT: H 50 TRP cc_start: 0.6662 (t60) cc_final: 0.6385 (t60) REVERT: H 78 SER cc_start: 0.7879 (m) cc_final: 0.7491 (p) REVERT: L 38 GLN cc_start: 0.4636 (tt0) cc_final: 0.4020 (mm-40) REVERT: L 49 ILE cc_start: 0.7334 (mp) cc_final: 0.7003 (tt) outliers start: 36 outliers final: 30 residues processed: 157 average time/residue: 0.1721 time to fit residues: 37.2129 Evaluate side-chains 167 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0570 chunk 81 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.180746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.167445 restraints weight = 12963.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.169358 restraints weight = 9845.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.170794 restraints weight = 7882.126| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7274 Z= 0.183 Angle : 0.583 10.683 10008 Z= 0.286 Chirality : 0.043 0.183 1217 Planarity : 0.004 0.050 1284 Dihedral : 5.746 66.290 1114 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.60 % Allowed : 26.91 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.01 (0.28), residues: 987 helix: 2.22 (1.16), residues: 22 sheet: -0.48 (0.27), residues: 395 loop : -0.89 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 39 HIS 0.002 0.001 HIS H 38 PHE 0.012 0.001 PHE A 277 TYR 0.014 0.001 TYR H 112 ARG 0.007 0.000 ARG I 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.52 seconds wall clock time: 33 minutes 59.40 seconds (2039.40 seconds total)