Starting phenix.real_space_refine on Wed Feb 14 01:59:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/02_2024/7fjd_31618_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/02_2024/7fjd_31618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/02_2024/7fjd_31618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/02_2024/7fjd_31618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/02_2024/7fjd_31618_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjd_31618/02_2024/7fjd_31618_updated.pdb" } resolution = 3.2 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= 0.006 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5341 2.51 5 N 1368 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 52": "NH1" <-> "NH2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "e ARG 115": "NH1" <-> "NH2" Residue "f ARG 155": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 185": "NH1" <-> "NH2" Residue "m ARG 253": "NH1" <-> "NH2" Residue "m ARG 269": "NH1" <-> "NH2" Residue "n PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 228": "NH1" <-> "NH2" Residue "n ARG 246": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8352 Number of models: 1 Model: "" Number of chains: 10 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "b" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "f" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 887 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1923 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2241 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.73, per 1000 atoms: 0.57 Number of scatterers: 8352 At special positions: 0 Unit cell: (89.1, 99, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1589 8.00 N 1368 7.00 C 5341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.04 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.03 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.04 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.04 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.04 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " 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: 3.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 19 sheets defined 23.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'a' and resid 29 through 53 removed outlier: 4.480A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 53 removed outlier: 3.532A pdb=" N TYR b 33 " --> pdb=" O LYS b 30 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU b 34 " --> pdb=" O LEU b 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU b 35 " --> pdb=" O CYS b 32 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE b 38 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU b 39 " --> pdb=" O ASP b 36 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE b 40 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR b 42 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU b 46 " --> pdb=" O GLY b 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU b 49 " --> pdb=" O LEU b 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 79 No H-bonds generated for 'chain 'd' and resid 77 through 79' Processing helix chain 'd' and resid 103 through 127 removed outlier: 4.076A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE d 125 " --> pdb=" O GLY d 121 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY d 127 " --> pdb=" O PHE d 123 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 107 No H-bonds generated for 'chain 'e' and resid 105 through 107' Processing helix chain 'e' and resid 127 through 153 removed outlier: 3.581A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 107 No H-bonds generated for 'chain 'f' and resid 105 through 107' Processing helix chain 'f' and resid 129 through 141 Processing helix chain 'f' and resid 144 through 153 Processing helix chain 'g' and resid 77 through 79 No H-bonds generated for 'chain 'g' and resid 77 through 79' Processing helix chain 'g' and resid 112 through 137 Processing helix chain 'm' and resid 232 through 234 No H-bonds generated for 'chain 'm' and resid 232 through 234' Processing helix chain 'm' and resid 241 through 272 removed outlier: 4.008A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) Processing helix chain 'n' and resid 102 through 104 No H-bonds generated for 'chain 'n' and resid 102 through 104' Processing helix chain 'n' and resid 151 through 156 Processing helix chain 'n' and resid 217 through 220 No H-bonds generated for 'chain 'n' and resid 217 through 220' Processing helix chain 'n' and resid 270 through 307 Processing sheet with id= A, first strand: chain 'd' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'd' and resid 85 through 89 removed outlier: 3.656A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'e' and resid 37 through 40 removed outlier: 3.656A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'e' and resid 57 through 61 removed outlier: 3.518A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.510A pdb=" N THR f 44 " --> pdb=" O SER f 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU f 47 " --> pdb=" O LEU f 82 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'f' and resid 57 through 61 removed outlier: 3.513A pdb=" N LEU f 114 " --> pdb=" O GLY f 94 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.785A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N CYS g 46 " --> pdb=" O LYS g 71 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS g 71 " --> pdb=" O CYS g 46 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'g' and resid 54 through 57 removed outlier: 3.633A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'm' and resid 33 through 36 Processing sheet with id= J, first strand: chain 'm' and resid 41 through 46 Processing sheet with id= K, first strand: chain 'm' and resid 108 through 114 removed outlier: 3.874A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET m 70 " --> pdb=" O TRP m 57 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG m 59 " --> pdb=" O LEU m 68 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU m 68 " --> pdb=" O ARG m 59 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'm' and resid 140 through 143 removed outlier: 4.093A pdb=" N ALA m 140 " --> pdb=" O THR m 158 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'm' and resid 180 through 184 Processing sheet with id= N, first strand: chain 'n' and resid 24 through 26 Processing sheet with id= O, first strand: chain 'n' and resid 29 through 33 removed outlier: 6.697A pdb=" N ARG n 129 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU n 32 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR n 131 " --> pdb=" O LEU n 32 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'n' and resid 38 through 40 removed outlier: 3.632A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN n 84 " --> pdb=" O ARG n 96 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'n' and resid 54 through 56 removed outlier: 3.570A pdb=" N PHE n 109 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.543A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'n' and resid 174 through 180 295 hydrogen bonds defined for protein. 798 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: 2.07 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2067 1.33 - 1.46: 2117 1.46 - 1.58: 4275 1.58 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8535 Sorted by residual: bond pdb=" CG LEU a 27 " pdb=" CD2 LEU a 27 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.30e-02 5.92e+03 7.41e+00 bond pdb=" N ILE n 253 " pdb=" CA ILE n 253 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.29e-02 6.01e+03 6.39e+00 bond pdb=" N CYS b 32 " pdb=" CA CYS b 32 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.23e+00 bond pdb=" CB ARG e 117 " pdb=" CG ARG e 117 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.12e+00 ... (remaining 8530 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.85: 189 105.85 - 113.09: 4483 113.09 - 120.32: 3465 120.32 - 127.56: 3378 127.56 - 134.79: 71 Bond angle restraints: 11586 Sorted by residual: angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.02e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.79 -12.99 2.44e+00 1.68e-01 2.83e+01 angle pdb=" CA TYR n 50 " pdb=" CB TYR n 50 " pdb=" CG TYR n 50 " ideal model delta sigma weight residual 113.90 123.18 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" N ASP m 159 " pdb=" CA ASP m 159 " pdb=" C ASP m 159 " ideal model delta sigma weight residual 110.42 117.93 -7.51 1.46e+00 4.69e-01 2.65e+01 angle pdb=" CA LEU m 182 " pdb=" CB LEU m 182 " pdb=" CG LEU m 182 " ideal model delta sigma weight residual 116.30 134.30 -18.00 3.50e+00 8.16e-02 2.65e+01 ... (remaining 11581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4888 17.13 - 34.26: 236 34.26 - 51.39: 70 51.39 - 68.52: 16 68.52 - 85.65: 9 Dihedral angle restraints: 5219 sinusoidal: 2143 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.81 52.19 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual 93.00 178.65 -85.65 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CA MET g 103 " pdb=" C MET g 103 " pdb=" N CYS g 104 " pdb=" CA CYS g 104 " ideal model delta harmonic sigma weight residual 180.00 -135.19 -44.81 0 5.00e+00 4.00e-02 8.03e+01 ... (remaining 5216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1113 0.095 - 0.191: 181 0.191 - 0.286: 9 0.286 - 0.382: 1 0.382 - 0.477: 1 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CG LEU f 90 " pdb=" CB LEU f 90 " pdb=" CD1 LEU f 90 " pdb=" CD2 LEU f 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1302 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR n 50 " -0.043 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR n 50 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR n 50 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR n 50 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.027 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR e 111 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.026 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR d 90 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.002 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1303 2.76 - 3.30: 6868 3.30 - 3.83: 12126 3.83 - 4.37: 13548 4.37 - 4.90: 24918 Nonbonded interactions: 58763 Sorted by model distance: nonbonded pdb=" NZ LYS b 30 " pdb=" O1 CLR b 201 " model vdw 2.229 2.520 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.305 2.520 nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.310 2.440 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.408 2.520 nonbonded pdb=" N ASP g 39 " pdb=" OD1 ASP g 39 " model vdw 2.409 2.520 ... (remaining 58758 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 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 54)) selection = (chain 'b' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 77 or (resid 78 and (nam \ e N or name CA or name C or name O or name CB )) or resid 79 through 155)) selection = (chain 'f' and resid 33 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.000 Extract box with map and model: 4.090 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.890 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.011 0.120 8535 Z= 0.681 Angle : 1.240 18.002 11586 Z= 0.666 Chirality : 0.068 0.477 1305 Planarity : 0.008 0.073 1466 Dihedral : 11.941 82.404 3206 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.94 % Favored : 90.87 % Rotamer: Outliers : 0.87 % Allowed : 6.19 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.22), residues: 1040 helix: -1.03 (0.28), residues: 237 sheet: -1.35 (0.29), residues: 292 loop : -3.79 (0.19), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP e 59 HIS 0.018 0.005 HIS f 61 PHE 0.041 0.005 PHE f 110 TYR 0.063 0.005 TYR d 90 ARG 0.015 0.002 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 0.954 Fit side-chains REVERT: e 41 SER cc_start: 0.9071 (t) cc_final: 0.8756 (p) REVERT: e 57 ILE cc_start: 0.8760 (mp) cc_final: 0.8355 (tt) REVERT: f 117 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8258 (ttm170) REVERT: g 32 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8215 (mptt) REVERT: g 53 ILE cc_start: 0.7888 (mm) cc_final: 0.7685 (mt) REVERT: m 99 ARG cc_start: 0.7189 (ptp90) cc_final: 0.6860 (mtm-85) REVERT: m 173 ASP cc_start: 0.7734 (m-30) cc_final: 0.7082 (p0) REVERT: m 211 ASN cc_start: 0.8609 (t160) cc_final: 0.8401 (t0) REVERT: n 33 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7531 (ptmt) REVERT: n 92 ASP cc_start: 0.7574 (m-30) cc_final: 0.6680 (t70) REVERT: n 96 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7403 (mtt90) REVERT: n 113 ARG cc_start: 0.6255 (mtp180) cc_final: 0.5994 (mtm180) REVERT: n 121 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6581 (mp0) REVERT: n 183 LYS cc_start: 0.7914 (mttt) cc_final: 0.7421 (mtpp) outliers start: 8 outliers final: 1 residues processed: 202 average time/residue: 0.2486 time to fit residues: 65.1215 Evaluate side-chains 135 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 ASN m 168 GLN n 47 ASN n 122 GLN n 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8535 Z= 0.160 Angle : 0.594 8.553 11586 Z= 0.315 Chirality : 0.043 0.210 1305 Planarity : 0.005 0.049 1466 Dihedral : 7.019 55.103 1275 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.26 % Allowed : 7.93 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % 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: -1.86 (0.25), residues: 1040 helix: 1.73 (0.34), residues: 233 sheet: -0.25 (0.32), residues: 275 loop : -3.37 (0.21), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 197 HIS 0.005 0.001 HIS f 81 PHE 0.019 0.001 PHE m 157 TYR 0.030 0.002 TYR n 50 ARG 0.002 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 0.881 Fit side-chains REVERT: b 30 LYS cc_start: 0.8009 (mttm) cc_final: 0.7708 (mtmm) REVERT: b 34 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7946 (mt) REVERT: d 27 GLU cc_start: 0.8001 (pt0) cc_final: 0.7753 (pt0) REVERT: d 99 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6854 (pp) REVERT: e 41 SER cc_start: 0.9043 (t) cc_final: 0.8828 (p) REVERT: e 57 ILE cc_start: 0.8793 (mp) cc_final: 0.8351 (tt) REVERT: e 80 ASP cc_start: 0.8351 (p0) cc_final: 0.8143 (p0) REVERT: f 39 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8108 (m) REVERT: f 80 ASP cc_start: 0.7980 (t70) cc_final: 0.7564 (t0) REVERT: f 101 ARG cc_start: 0.7756 (tpp-160) cc_final: 0.7537 (tpp-160) REVERT: g 30 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7330 (mp) REVERT: g 60 LYS cc_start: 0.7219 (pttp) cc_final: 0.7006 (ptpp) REVERT: m 173 ASP cc_start: 0.7530 (m-30) cc_final: 0.7008 (p0) REVERT: n 33 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7358 (ptmt) REVERT: n 92 ASP cc_start: 0.7530 (m-30) cc_final: 0.6721 (t70) REVERT: n 96 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7185 (mtt90) REVERT: n 183 LYS cc_start: 0.7898 (mttt) cc_final: 0.7503 (mtpp) REVERT: n 302 MET cc_start: 0.7295 (ttp) cc_final: 0.5670 (mmt) outliers start: 30 outliers final: 14 residues processed: 182 average time/residue: 0.2370 time to fit residues: 56.6044 Evaluate side-chains 157 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 95 SER Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS g 52 ASN m 211 ASN n 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8535 Z= 0.157 Angle : 0.554 9.132 11586 Z= 0.291 Chirality : 0.041 0.184 1305 Planarity : 0.004 0.044 1466 Dihedral : 6.010 48.563 1275 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.80 % Allowed : 11.29 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % 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: -1.16 (0.26), residues: 1040 helix: 2.47 (0.34), residues: 233 sheet: 0.15 (0.32), residues: 295 loop : -3.11 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.005 0.001 HIS n 173 PHE 0.015 0.001 PHE m 157 TYR 0.021 0.001 TYR n 50 ARG 0.003 0.000 ARG m 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: b 30 LYS cc_start: 0.8058 (mttm) cc_final: 0.7767 (mtmm) REVERT: b 34 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7940 (mt) REVERT: d 29 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7270 (mm) REVERT: d 99 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6949 (pp) REVERT: d 117 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7193 (tp) REVERT: e 57 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8318 (tt) REVERT: e 123 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7563 (ptp) REVERT: f 39 SER cc_start: 0.8334 (t) cc_final: 0.8084 (m) REVERT: f 80 ASP cc_start: 0.8002 (t70) cc_final: 0.7556 (t0) REVERT: f 106 GLU cc_start: 0.7937 (pt0) cc_final: 0.7349 (pt0) REVERT: f 117 ARG cc_start: 0.8364 (ttm170) cc_final: 0.8088 (ttm170) REVERT: m 173 ASP cc_start: 0.7680 (m-30) cc_final: 0.7088 (p0) REVERT: n 33 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7481 (ptmt) REVERT: n 38 MET cc_start: 0.7522 (tpt) cc_final: 0.7211 (tmm) REVERT: n 46 MET cc_start: 0.4090 (tmm) cc_final: 0.3154 (tmm) REVERT: n 50 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5437 (p90) REVERT: n 92 ASP cc_start: 0.7570 (m-30) cc_final: 0.6759 (t70) REVERT: n 96 ARG cc_start: 0.7506 (mtt180) cc_final: 0.7232 (mtt90) REVERT: n 121 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6569 (mp0) REVERT: n 183 LYS cc_start: 0.7925 (mttt) cc_final: 0.7497 (mtpp) outliers start: 35 outliers final: 18 residues processed: 172 average time/residue: 0.2158 time to fit residues: 49.7581 Evaluate side-chains 156 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8535 Z= 0.246 Angle : 0.611 9.259 11586 Z= 0.321 Chirality : 0.044 0.199 1305 Planarity : 0.005 0.045 1466 Dihedral : 5.992 48.663 1275 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.89 % Allowed : 11.83 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % 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: -1.06 (0.26), residues: 1040 helix: 2.44 (0.34), residues: 234 sheet: 0.28 (0.32), residues: 293 loop : -3.04 (0.22), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.005 0.001 HIS n 173 PHE 0.013 0.002 PHE f 110 TYR 0.025 0.002 TYR n 50 ARG 0.003 0.000 ARG m 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: b 30 LYS cc_start: 0.8140 (mttm) cc_final: 0.7874 (mtmm) REVERT: b 31 LEU cc_start: 0.8712 (tp) cc_final: 0.8492 (mm) REVERT: b 34 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7791 (mt) REVERT: d 29 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7351 (mm) REVERT: d 99 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6648 (pp) REVERT: d 117 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7238 (tp) REVERT: e 57 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8249 (tt) REVERT: f 80 ASP cc_start: 0.7982 (t70) cc_final: 0.7596 (t0) REVERT: f 106 GLU cc_start: 0.8046 (pt0) cc_final: 0.7495 (pt0) REVERT: f 117 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8115 (ttm170) REVERT: m 113 MET cc_start: 0.7282 (mtm) cc_final: 0.6653 (mtm) REVERT: m 159 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6150 (p0) REVERT: m 173 ASP cc_start: 0.7683 (m-30) cc_final: 0.7072 (p0) REVERT: n 33 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7460 (ptmt) REVERT: n 50 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5329 (p90) REVERT: n 92 ASP cc_start: 0.7557 (m-30) cc_final: 0.6658 (t70) REVERT: n 96 ARG cc_start: 0.7464 (mtt180) cc_final: 0.7238 (mtt90) REVERT: n 121 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6507 (mp0) REVERT: n 183 LYS cc_start: 0.7991 (mttt) cc_final: 0.7562 (mtpp) outliers start: 45 outliers final: 30 residues processed: 169 average time/residue: 0.2446 time to fit residues: 54.2413 Evaluate side-chains 170 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.0170 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS m 28 GLN n 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8535 Z= 0.122 Angle : 0.499 8.670 11586 Z= 0.262 Chirality : 0.040 0.176 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.266 45.990 1275 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.15 % Allowed : 13.57 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % 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: -0.56 (0.27), residues: 1040 helix: 3.06 (0.34), residues: 232 sheet: 0.56 (0.32), residues: 296 loop : -2.80 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 259 HIS 0.003 0.001 HIS n 173 PHE 0.012 0.001 PHE m 157 TYR 0.020 0.001 TYR n 50 ARG 0.003 0.000 ARG m 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 30 LYS cc_start: 0.8033 (mttm) cc_final: 0.7739 (mtmm) REVERT: b 31 LEU cc_start: 0.8719 (tp) cc_final: 0.8499 (mm) REVERT: b 34 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (mt) REVERT: d 99 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6886 (pp) REVERT: d 117 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7260 (tp) REVERT: e 79 GLU cc_start: 0.7715 (pm20) cc_final: 0.7493 (pm20) REVERT: e 104 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7452 (ttpt) REVERT: e 123 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7536 (ptp) REVERT: e 128 MET cc_start: 0.6379 (mmm) cc_final: 0.6177 (mmp) REVERT: f 80 ASP cc_start: 0.7993 (t70) cc_final: 0.7508 (t0) REVERT: f 106 GLU cc_start: 0.7791 (pt0) cc_final: 0.7096 (pt0) REVERT: f 117 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8101 (ttm170) REVERT: m 113 MET cc_start: 0.6917 (mtm) cc_final: 0.6173 (mtt) REVERT: n 33 LYS cc_start: 0.7772 (ttpt) cc_final: 0.7468 (ptmt) REVERT: n 50 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.5535 (p90) REVERT: n 92 ASP cc_start: 0.7509 (m-30) cc_final: 0.6690 (t70) REVERT: n 96 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7315 (mtt90) REVERT: n 121 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6494 (mp0) REVERT: n 183 LYS cc_start: 0.7925 (mttt) cc_final: 0.7519 (mtpp) REVERT: n 302 MET cc_start: 0.6736 (ttp) cc_final: 0.6436 (ttm) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.2386 time to fit residues: 52.3058 Evaluate side-chains 163 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8535 Z= 0.219 Angle : 0.578 8.924 11586 Z= 0.302 Chirality : 0.043 0.189 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.522 47.361 1275 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.78 % Allowed : 14.12 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.66 (0.27), residues: 1040 helix: 2.63 (0.34), residues: 240 sheet: 0.50 (0.32), residues: 309 loop : -2.85 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.004 0.001 HIS n 173 PHE 0.013 0.002 PHE f 110 TYR 0.024 0.001 TYR n 50 ARG 0.003 0.000 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: b 31 LEU cc_start: 0.8773 (tp) cc_final: 0.8512 (mm) REVERT: b 34 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7787 (mt) REVERT: d 29 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7239 (mm) REVERT: d 99 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6661 (pp) REVERT: d 117 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7305 (tp) REVERT: d 123 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.5972 (t80) REVERT: e 57 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8248 (tt) REVERT: e 90 LEU cc_start: 0.8501 (tp) cc_final: 0.8251 (tp) REVERT: e 104 LYS cc_start: 0.7989 (mmtp) cc_final: 0.7486 (ttpt) REVERT: e 128 MET cc_start: 0.6683 (mmm) cc_final: 0.6435 (mmp) REVERT: f 80 ASP cc_start: 0.8193 (t70) cc_final: 0.7667 (t0) REVERT: f 106 GLU cc_start: 0.7822 (pt0) cc_final: 0.7049 (pt0) REVERT: f 117 ARG cc_start: 0.8413 (ttm170) cc_final: 0.8106 (ttm170) REVERT: m 78 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5828 (tmtt) REVERT: m 113 MET cc_start: 0.6490 (mtm) cc_final: 0.5924 (mtm) REVERT: m 159 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.6005 (p0) REVERT: m 173 ASP cc_start: 0.7685 (m-30) cc_final: 0.7062 (p0) REVERT: n 32 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7830 (pp) REVERT: n 33 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7464 (ptmt) REVERT: n 50 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5401 (p90) REVERT: n 92 ASP cc_start: 0.7509 (m-30) cc_final: 0.6640 (t70) REVERT: n 96 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7321 (mtt90) REVERT: n 121 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6466 (mp0) REVERT: n 183 LYS cc_start: 0.8017 (mttt) cc_final: 0.7606 (mtpp) outliers start: 44 outliers final: 24 residues processed: 173 average time/residue: 0.2348 time to fit residues: 53.4090 Evaluate side-chains 172 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 78 LYS Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 112 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8535 Z= 0.181 Angle : 0.550 8.961 11586 Z= 0.288 Chirality : 0.042 0.188 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.440 47.243 1275 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.91 % Allowed : 14.88 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.52 (0.27), residues: 1040 helix: 2.79 (0.34), residues: 238 sheet: 0.56 (0.32), residues: 309 loop : -2.75 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.004 0.001 HIS n 173 PHE 0.011 0.001 PHE f 110 TYR 0.024 0.001 TYR n 50 ARG 0.004 0.000 ARG n 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: b 31 LEU cc_start: 0.8781 (tp) cc_final: 0.8495 (mm) REVERT: b 34 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7823 (mt) REVERT: d 29 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7204 (mm) REVERT: d 99 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6624 (pp) REVERT: d 117 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7308 (tp) REVERT: d 123 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5907 (t80) REVERT: e 90 LEU cc_start: 0.8491 (tp) cc_final: 0.8241 (tp) REVERT: e 104 LYS cc_start: 0.7972 (mmtp) cc_final: 0.7480 (ttpt) REVERT: f 80 ASP cc_start: 0.8050 (t70) cc_final: 0.7573 (t0) REVERT: f 106 GLU cc_start: 0.7745 (pt0) cc_final: 0.7077 (pt0) REVERT: f 117 ARG cc_start: 0.8415 (ttm170) cc_final: 0.8099 (ttm170) REVERT: m 113 MET cc_start: 0.6411 (mtm) cc_final: 0.5901 (mtm) REVERT: n 32 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7801 (pp) REVERT: n 33 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7449 (ptmt) REVERT: n 50 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5291 (p90) REVERT: n 92 ASP cc_start: 0.7485 (m-30) cc_final: 0.6626 (t70) REVERT: n 96 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7311 (mtt90) REVERT: n 121 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6516 (mp0) REVERT: n 183 LYS cc_start: 0.8007 (mttt) cc_final: 0.7612 (mtpp) outliers start: 36 outliers final: 23 residues processed: 163 average time/residue: 0.2158 time to fit residues: 46.8808 Evaluate side-chains 166 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 128 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8535 Z= 0.310 Angle : 0.654 9.352 11586 Z= 0.340 Chirality : 0.045 0.211 1305 Planarity : 0.005 0.041 1466 Dihedral : 5.964 49.566 1275 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.13 % Allowed : 14.88 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.74 (0.26), residues: 1040 helix: 2.38 (0.33), residues: 240 sheet: 0.58 (0.32), residues: 297 loop : -2.81 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP m 197 HIS 0.005 0.001 HIS n 226 PHE 0.015 0.002 PHE f 110 TYR 0.028 0.002 TYR n 50 ARG 0.005 0.001 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7832 (mt) REVERT: d 29 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7435 (mm) REVERT: d 99 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6676 (pp) REVERT: d 117 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7286 (tp) REVERT: d 123 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.5706 (t80) REVERT: e 90 LEU cc_start: 0.8575 (tp) cc_final: 0.8344 (tp) REVERT: e 128 MET cc_start: 0.6824 (mmm) cc_final: 0.6550 (mmp) REVERT: f 80 ASP cc_start: 0.8179 (t70) cc_final: 0.7690 (t0) REVERT: f 106 GLU cc_start: 0.7921 (pt0) cc_final: 0.7360 (pt0) REVERT: m 113 MET cc_start: 0.7127 (mtm) cc_final: 0.6394 (mtm) REVERT: m 173 ASP cc_start: 0.7687 (m-30) cc_final: 0.7070 (p0) REVERT: n 32 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7738 (pp) REVERT: n 33 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7431 (ptmt) REVERT: n 50 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.5341 (p90) REVERT: n 92 ASP cc_start: 0.7521 (m-30) cc_final: 0.6621 (t70) REVERT: n 96 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7321 (mtt90) REVERT: n 121 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6445 (mp0) REVERT: n 183 LYS cc_start: 0.8060 (mttt) cc_final: 0.7637 (mtpp) outliers start: 38 outliers final: 25 residues processed: 164 average time/residue: 0.2762 time to fit residues: 59.1789 Evaluate side-chains 168 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8535 Z= 0.304 Angle : 0.653 10.519 11586 Z= 0.338 Chirality : 0.045 0.212 1305 Planarity : 0.005 0.041 1466 Dihedral : 6.106 50.258 1275 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.23 % Allowed : 15.20 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.83 (0.26), residues: 1040 helix: 2.35 (0.33), residues: 239 sheet: 0.54 (0.33), residues: 284 loop : -2.81 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP m 197 HIS 0.004 0.001 HIS n 226 PHE 0.016 0.002 PHE f 110 TYR 0.027 0.002 TYR n 50 ARG 0.005 0.001 ARG n 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7838 (mt) REVERT: d 29 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7415 (mm) REVERT: d 99 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6792 (pp) REVERT: d 117 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7274 (tp) REVERT: d 123 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6272 (t80) REVERT: e 90 LEU cc_start: 0.8586 (tp) cc_final: 0.8354 (tp) REVERT: f 80 ASP cc_start: 0.8063 (t70) cc_final: 0.7617 (t0) REVERT: m 99 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.6571 (ptt-90) REVERT: m 113 MET cc_start: 0.7311 (mtm) cc_final: 0.6599 (mtt) REVERT: m 173 ASP cc_start: 0.7669 (m-30) cc_final: 0.7061 (p0) REVERT: n 32 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7730 (pp) REVERT: n 33 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7443 (ptmt) REVERT: n 50 TYR cc_start: 0.6565 (OUTLIER) cc_final: 0.5099 (p90) REVERT: n 92 ASP cc_start: 0.7511 (m-30) cc_final: 0.6605 (t70) REVERT: n 96 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7314 (mtt90) REVERT: n 121 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6456 (mp0) REVERT: n 183 LYS cc_start: 0.7982 (mttt) cc_final: 0.7574 (mtpp) outliers start: 39 outliers final: 26 residues processed: 162 average time/residue: 0.2399 time to fit residues: 50.9503 Evaluate side-chains 166 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 79 GLU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain m residue 239 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8535 Z= 0.178 Angle : 0.557 9.387 11586 Z= 0.290 Chirality : 0.042 0.194 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.588 49.074 1275 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.15 % Allowed : 16.72 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.48 (0.27), residues: 1040 helix: 2.82 (0.33), residues: 238 sheet: 0.55 (0.31), residues: 309 loop : -2.70 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 259 HIS 0.004 0.001 HIS n 173 PHE 0.011 0.001 PHE f 110 TYR 0.023 0.001 TYR n 50 ARG 0.005 0.000 ARG n 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7850 (mt) REVERT: d 29 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7388 (mm) REVERT: d 99 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6863 (pp) REVERT: d 117 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7278 (tp) REVERT: d 123 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5635 (t80) REVERT: e 90 LEU cc_start: 0.8527 (tp) cc_final: 0.8288 (tp) REVERT: e 104 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7472 (ttpt) REVERT: e 128 MET cc_start: 0.6681 (mmm) cc_final: 0.6427 (mmp) REVERT: f 80 ASP cc_start: 0.8059 (t70) cc_final: 0.7570 (t0) REVERT: m 99 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.6539 (ptt-90) REVERT: m 113 MET cc_start: 0.7317 (mtm) cc_final: 0.6669 (mtm) REVERT: m 173 ASP cc_start: 0.7669 (m-30) cc_final: 0.7108 (p0) REVERT: n 32 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7781 (pp) REVERT: n 33 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7461 (ptmt) REVERT: n 50 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5404 (p90) REVERT: n 92 ASP cc_start: 0.7532 (m-30) cc_final: 0.6655 (t70) REVERT: n 96 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7318 (mtt90) REVERT: n 121 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6541 (mp0) REVERT: n 183 LYS cc_start: 0.7999 (mttt) cc_final: 0.7600 (mtpp) outliers start: 29 outliers final: 19 residues processed: 159 average time/residue: 0.2358 time to fit residues: 49.2719 Evaluate side-chains 160 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.149472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113168 restraints weight = 9780.430| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.85 r_work: 0.2857 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8535 Z= 0.227 Angle : 0.597 9.732 11586 Z= 0.308 Chirality : 0.043 0.188 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.682 49.480 1275 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.37 % Allowed : 16.18 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.53 (0.27), residues: 1040 helix: 2.73 (0.33), residues: 239 sheet: 0.64 (0.33), residues: 289 loop : -2.67 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 197 HIS 0.004 0.001 HIS n 173 PHE 0.013 0.002 PHE f 110 TYR 0.025 0.002 TYR n 50 ARG 0.005 0.000 ARG n 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.90 seconds wall clock time: 38 minutes 58.24 seconds (2338.24 seconds total)