Starting phenix.real_space_refine on Thu Oct 10 05:00:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjm_43289/10_2024/8vjm_43289.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjm_43289/10_2024/8vjm_43289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjm_43289/10_2024/8vjm_43289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjm_43289/10_2024/8vjm_43289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjm_43289/10_2024/8vjm_43289.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjm_43289/10_2024/8vjm_43289.cif" } resolution = 4.0 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= 0.021 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 1 5.49 5 S 28 5.16 5 C 4423 2.51 5 N 1083 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 6667 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 185 Unusual residues: {'LMN': 2, 'PEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.95, per 1000 atoms: 0.74 Number of scatterers: 6667 At special positions: 0 Unit cell: (88.2648, 78.9291, 129.002, 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 28 16.00 P 1 15.00 O 1132 8.00 N 1083 7.00 C 4423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 67.2% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 4.143A pdb=" N LEU A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.954A pdb=" N TRP A 18 " --> pdb=" O HIS A 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 54 removed outlier: 3.943A pdb=" N PHE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.871A pdb=" N GLU A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.772A pdb=" N LEU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.646A pdb=" N PHE A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 4.865A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 178 Processing helix chain 'A' and resid 181 through 201 removed outlier: 4.007A pdb=" N TRP A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.801A pdb=" N VAL A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'B' and resid 33 through 47 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.682A pdb=" N ARG B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.670A pdb=" N ALA B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 94 Processing helix chain 'B' and resid 102 through 126 Processing helix chain 'C' and resid 2 through 9 removed outlier: 4.393A pdb=" N ASP C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 7 " --> pdb=" O LYS C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 27 Processing helix chain 'C' and resid 30 through 54 removed outlier: 3.729A pdb=" N LEU C 34 " --> pdb=" O MET C 30 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 51 " --> pdb=" O HIS C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.631A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.945A pdb=" N LEU C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 93 through 105 removed outlier: 3.511A pdb=" N MET C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 4.027A pdb=" N PHE C 115 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 150 removed outlier: 4.213A pdb=" N GLN C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.692A pdb=" N LEU C 160 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 201 removed outlier: 3.511A pdb=" N TRP C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.660A pdb=" N VAL C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 removed outlier: 4.062A pdb=" N GLU C 241 " --> pdb=" O HIS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.595A pdb=" N LEU C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 48 removed outlier: 3.919A pdb=" N LYS D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP D 48 " --> pdb=" O MET D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.924A pdb=" N ASN D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.666A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 94 removed outlier: 3.656A pdb=" N LEU D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 126 removed outlier: 3.585A pdb=" N TYR D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 7.252A pdb=" N HIS A 12 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 22 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 5.707A pdb=" N LEU A 227 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU A 253 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 229 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 250 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 261 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 252 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 64 removed outlier: 6.818A pdb=" N GLU C 71 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL C 61 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 69 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU C 63 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 22 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 70 " --> pdb=" O TYR D 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 227 through 230 372 hydrogen bonds defined for protein. 1101 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: 1.73 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1004 1.31 - 1.44: 1844 1.44 - 1.56: 3922 1.56 - 1.69: 26 1.69 - 1.82: 44 Bond restraints: 6840 Sorted by residual: bond pdb=" C1 LMN A 401 " pdb=" O5 LMN A 401 " ideal model delta sigma weight residual 1.403 1.538 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C1 LMN A 403 " pdb=" O5 LMN A 403 " ideal model delta sigma weight residual 1.403 1.535 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" CBS LMN A 401 " pdb=" CCM LMN A 401 " ideal model delta sigma weight residual 1.529 1.631 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C4 LMN A 403 " pdb=" O4 LMN A 403 " ideal model delta sigma weight residual 1.409 1.510 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" CBS LMN A 403 " pdb=" CCM LMN A 403 " ideal model delta sigma weight residual 1.529 1.629 -0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 6835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 9096 3.10 - 6.21: 146 6.21 - 9.31: 13 9.31 - 12.42: 3 12.42 - 15.52: 1 Bond angle restraints: 9259 Sorted by residual: angle pdb=" O3P PEF A 402 " pdb=" P PEF A 402 " pdb=" O4P PEF A 402 " ideal model delta sigma weight residual 93.96 109.48 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" N VAL C 107 " pdb=" CA VAL C 107 " pdb=" C VAL C 107 " ideal model delta sigma weight residual 112.98 108.06 4.92 1.25e+00 6.40e-01 1.55e+01 angle pdb=" C4 LMN A 401 " pdb=" O4 LMN A 401 " pdb=" CCR LMN A 401 " ideal model delta sigma weight residual 120.22 109.38 10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1P PEF A 402 " pdb=" P PEF A 402 " pdb=" O2P PEF A 402 " ideal model delta sigma weight residual 119.53 109.50 10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CCQ LMN A 401 " pdb=" OCB LMN A 401 " pdb=" CCS LMN A 401 " ideal model delta sigma weight residual 119.65 109.82 9.83 3.00e+00 1.11e-01 1.07e+01 ... (remaining 9254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.63: 3781 24.63 - 49.25: 307 49.25 - 73.88: 60 73.88 - 98.50: 22 98.50 - 123.13: 35 Dihedral angle restraints: 4205 sinusoidal: 1841 harmonic: 2364 Sorted by residual: dihedral pdb=" CCD LMN A 403 " pdb=" CCS LMN A 403 " pdb=" OBZ LMN A 403 " pdb=" OCB LMN A 403 " ideal model delta sinusoidal sigma weight residual 60.96 -175.91 -123.13 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O2 LMN A 403 " pdb=" C2 LMN A 403 " pdb=" C3 LMN A 403 " pdb=" O3 LMN A 403 " ideal model delta sinusoidal sigma weight residual 295.11 172.74 122.37 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" CCD LMN A 403 " pdb=" CCS LMN A 403 " pdb=" OBZ LMN A 403 " pdb=" CCW LMN A 403 " ideal model delta sinusoidal sigma weight residual -59.55 61.55 -121.10 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 4202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 806 0.041 - 0.082: 201 0.082 - 0.123: 53 0.123 - 0.164: 6 0.164 - 0.205: 5 Chirality restraints: 1071 Sorted by residual: chirality pdb=" C1 LMN A 403 " pdb=" C2 LMN A 403 " pdb=" O1 LMN A 403 " pdb=" O5 LMN A 403 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C1 LMN A 401 " pdb=" C2 LMN A 401 " pdb=" O1 LMN A 401 " pdb=" O5 LMN A 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.48 0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CCV LMN A 401 " pdb=" CCR LMN A 401 " pdb=" CCT LMN A 401 " pdb=" OAU LMN A 401 " both_signs ideal model delta sigma weight residual False 2.28 2.46 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1068 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 225 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 226 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 90 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 91 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO C 179 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.023 5.00e-02 4.00e+02 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1182 2.77 - 3.30: 6438 3.30 - 3.83: 10474 3.83 - 4.37: 11155 4.37 - 4.90: 19505 Nonbonded interactions: 48754 Sorted by model distance: nonbonded pdb=" OG SER A 280 " pdb=" OE1 GLU A 283 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN A 129 " pdb=" OG SER B 21 " model vdw 2.299 3.120 nonbonded pdb=" O PRO D 29 " pdb=" NH1 ARG D 61 " model vdw 2.309 3.120 nonbonded pdb=" O ARG C 78 " pdb=" NH2 ARG C 244 " model vdw 2.325 3.120 nonbonded pdb=" N SER B 33 " pdb=" OE2 GLU B 36 " model vdw 2.327 3.120 ... (remaining 48749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 288) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.480 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.008 0.135 6840 Z= 0.524 Angle : 0.819 15.522 9259 Z= 0.358 Chirality : 0.041 0.205 1071 Planarity : 0.005 0.113 1110 Dihedral : 22.667 123.128 2669 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.00 % Favored : 93.75 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.48 (0.31), residues: 800 helix: 1.45 (0.24), residues: 536 sheet: 0.08 (1.12), residues: 28 loop : -2.39 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 4 HIS 0.007 0.001 HIS C 203 PHE 0.009 0.001 PHE C 272 TYR 0.015 0.001 TYR C 271 ARG 0.009 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8565 (t80) cc_final: 0.8120 (t80) REVERT: B 62 LEU cc_start: 0.9024 (mt) cc_final: 0.8777 (tt) REVERT: B 79 ASP cc_start: 0.7558 (m-30) cc_final: 0.7189 (m-30) REVERT: B 96 SER cc_start: 0.9055 (t) cc_final: 0.8796 (p) REVERT: D 43 LEU cc_start: 0.8833 (tp) cc_final: 0.8456 (tp) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.1925 time to fit residues: 46.2209 Evaluate side-chains 140 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 6840 Z= 0.428 Angle : 0.839 11.213 9259 Z= 0.393 Chirality : 0.050 0.327 1071 Planarity : 0.006 0.076 1110 Dihedral : 18.497 97.539 1153 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 2.65 % Allowed : 16.22 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 800 helix: 0.98 (0.23), residues: 546 sheet: -0.07 (0.92), residues: 38 loop : -2.58 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 96 HIS 0.006 0.001 HIS A 206 PHE 0.028 0.002 PHE C 118 TYR 0.022 0.002 TYR A 271 ARG 0.004 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.806 Fit side-chains REVERT: A 44 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8555 (mm-40) REVERT: A 84 PHE cc_start: 0.8620 (t80) cc_final: 0.8223 (t80) REVERT: A 236 TYR cc_start: 0.9179 (t80) cc_final: 0.8978 (t80) REVERT: B 79 ASP cc_start: 0.7738 (m-30) cc_final: 0.7506 (m-30) REVERT: B 96 SER cc_start: 0.8999 (t) cc_final: 0.8725 (p) REVERT: C 282 GLU cc_start: 0.8097 (mp0) cc_final: 0.7666 (mp0) REVERT: D 66 ILE cc_start: 0.8655 (mp) cc_final: 0.8441 (mp) outliers start: 18 outliers final: 13 residues processed: 149 average time/residue: 0.1904 time to fit residues: 37.9423 Evaluate side-chains 149 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6840 Z= 0.172 Angle : 0.647 8.521 9259 Z= 0.301 Chirality : 0.043 0.386 1071 Planarity : 0.005 0.061 1110 Dihedral : 14.127 86.733 1153 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 2.21 % Allowed : 18.58 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.41 (0.31), residues: 800 helix: 1.31 (0.23), residues: 530 sheet: -0.10 (0.88), residues: 38 loop : -2.15 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 96 HIS 0.006 0.001 HIS B 118 PHE 0.010 0.001 PHE A 66 TYR 0.022 0.001 TYR A 199 ARG 0.003 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8613 (t80) cc_final: 0.8159 (t80) REVERT: B 62 LEU cc_start: 0.9094 (mp) cc_final: 0.8692 (tt) REVERT: B 79 ASP cc_start: 0.7624 (m-30) cc_final: 0.7388 (m-30) REVERT: B 96 SER cc_start: 0.9013 (t) cc_final: 0.8754 (p) REVERT: C 236 TYR cc_start: 0.8413 (t80) cc_final: 0.8131 (t80) REVERT: C 282 GLU cc_start: 0.8190 (mp0) cc_final: 0.7773 (mp0) REVERT: D 43 LEU cc_start: 0.8912 (tp) cc_final: 0.8534 (tp) REVERT: D 66 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8393 (mp) outliers start: 15 outliers final: 8 residues processed: 161 average time/residue: 0.2229 time to fit residues: 48.8209 Evaluate side-chains 155 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6840 Z= 0.215 Angle : 0.664 13.795 9259 Z= 0.309 Chirality : 0.042 0.308 1071 Planarity : 0.005 0.059 1110 Dihedral : 10.732 86.960 1153 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.62 % Favored : 93.25 % Rotamer: Outliers : 3.39 % Allowed : 20.35 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.44 (0.31), residues: 800 helix: 1.31 (0.23), residues: 530 sheet: -0.00 (0.88), residues: 38 loop : -2.09 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 96 HIS 0.005 0.001 HIS C 113 PHE 0.014 0.001 PHE C 118 TYR 0.023 0.001 TYR A 271 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8656 (t80) cc_final: 0.8208 (t80) REVERT: A 281 MET cc_start: 0.7167 (ptt) cc_final: 0.6742 (ptt) REVERT: B 37 GLU cc_start: 0.7939 (pp20) cc_final: 0.7562 (tt0) REVERT: B 62 LEU cc_start: 0.9117 (mp) cc_final: 0.8673 (tt) REVERT: B 79 ASP cc_start: 0.7643 (m-30) cc_final: 0.7434 (m-30) REVERT: B 96 SER cc_start: 0.9025 (t) cc_final: 0.8753 (p) REVERT: C 282 GLU cc_start: 0.8208 (mp0) cc_final: 0.7851 (mp0) REVERT: D 43 LEU cc_start: 0.8788 (tp) cc_final: 0.8488 (tp) REVERT: D 66 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8403 (mp) outliers start: 23 outliers final: 15 residues processed: 166 average time/residue: 0.1834 time to fit residues: 40.3717 Evaluate side-chains 162 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6840 Z= 0.213 Angle : 0.629 12.543 9259 Z= 0.302 Chirality : 0.040 0.261 1071 Planarity : 0.005 0.057 1110 Dihedral : 10.138 86.764 1153 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 3.83 % Allowed : 21.39 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.49 (0.31), residues: 800 helix: 1.35 (0.23), residues: 530 sheet: -0.02 (0.88), residues: 38 loop : -2.08 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 96 HIS 0.005 0.001 HIS B 118 PHE 0.014 0.001 PHE C 118 TYR 0.008 0.001 TYR C 204 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8654 (t80) cc_final: 0.8171 (t80) REVERT: A 281 MET cc_start: 0.7181 (ptt) cc_final: 0.6694 (ptt) REVERT: B 62 LEU cc_start: 0.9123 (mp) cc_final: 0.8673 (tt) REVERT: B 79 ASP cc_start: 0.7659 (m-30) cc_final: 0.7433 (m-30) REVERT: B 96 SER cc_start: 0.8993 (t) cc_final: 0.8744 (p) REVERT: C 282 GLU cc_start: 0.8160 (mp0) cc_final: 0.7770 (mp0) REVERT: D 43 LEU cc_start: 0.8798 (tp) cc_final: 0.8471 (tp) REVERT: D 66 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8414 (mp) outliers start: 26 outliers final: 20 residues processed: 170 average time/residue: 0.1851 time to fit residues: 41.9165 Evaluate side-chains 169 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 39 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6840 Z= 0.206 Angle : 0.650 15.832 9259 Z= 0.307 Chirality : 0.040 0.224 1071 Planarity : 0.005 0.054 1110 Dihedral : 9.798 86.406 1153 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.38 % Rotamer: Outliers : 4.42 % Allowed : 23.60 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.54 (0.31), residues: 800 helix: 1.39 (0.23), residues: 530 sheet: 0.02 (0.86), residues: 38 loop : -2.07 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 96 HIS 0.005 0.001 HIS C 237 PHE 0.013 0.001 PHE A 146 TYR 0.025 0.001 TYR C 199 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8636 (t80) cc_final: 0.8140 (t80) REVERT: A 281 MET cc_start: 0.7040 (ptt) cc_final: 0.6424 (ptt) REVERT: B 62 LEU cc_start: 0.9110 (mp) cc_final: 0.8674 (tt) REVERT: B 79 ASP cc_start: 0.7634 (m-30) cc_final: 0.7430 (m-30) REVERT: B 96 SER cc_start: 0.8965 (t) cc_final: 0.8717 (p) REVERT: C 282 GLU cc_start: 0.8075 (mp0) cc_final: 0.7633 (mp0) REVERT: D 43 LEU cc_start: 0.8761 (tp) cc_final: 0.8422 (tp) REVERT: D 66 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8421 (mp) outliers start: 30 outliers final: 20 residues processed: 173 average time/residue: 0.1811 time to fit residues: 41.6917 Evaluate side-chains 168 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6840 Z= 0.201 Angle : 0.645 12.097 9259 Z= 0.309 Chirality : 0.039 0.201 1071 Planarity : 0.005 0.051 1110 Dihedral : 9.634 86.372 1153 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.62 % Favored : 93.25 % Rotamer: Outliers : 3.69 % Allowed : 25.22 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.50 (0.31), residues: 800 helix: 1.35 (0.23), residues: 544 sheet: 0.10 (0.87), residues: 38 loop : -2.28 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 96 HIS 0.006 0.001 HIS C 113 PHE 0.011 0.001 PHE A 146 TYR 0.027 0.001 TYR A 199 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8648 (t80) cc_final: 0.8273 (t80) REVERT: A 281 MET cc_start: 0.7088 (ptt) cc_final: 0.6256 (ptt) REVERT: B 79 ASP cc_start: 0.7621 (m-30) cc_final: 0.7407 (m-30) REVERT: B 96 SER cc_start: 0.8970 (t) cc_final: 0.8706 (p) REVERT: C 282 GLU cc_start: 0.8007 (mp0) cc_final: 0.7546 (mp0) REVERT: D 43 LEU cc_start: 0.8706 (tp) cc_final: 0.8428 (tp) REVERT: D 66 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8415 (mp) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 0.1571 time to fit residues: 33.9593 Evaluate side-chains 162 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 0.0370 chunk 59 optimal weight: 0.0870 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6840 Z= 0.167 Angle : 0.626 13.305 9259 Z= 0.300 Chirality : 0.038 0.166 1071 Planarity : 0.004 0.050 1110 Dihedral : 9.399 87.941 1153 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.50 % Rotamer: Outliers : 2.95 % Allowed : 26.11 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.32), residues: 800 helix: 1.48 (0.24), residues: 532 sheet: 0.18 (0.86), residues: 38 loop : -1.98 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.005 0.001 HIS C 237 PHE 0.013 0.001 PHE A 66 TYR 0.011 0.001 TYR C 199 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8600 (t80) cc_final: 0.8193 (t80) REVERT: A 281 MET cc_start: 0.7077 (ptt) cc_final: 0.6306 (ptt) REVERT: B 37 GLU cc_start: 0.8104 (pp20) cc_final: 0.7551 (tt0) REVERT: B 79 ASP cc_start: 0.7543 (m-30) cc_final: 0.7309 (m-30) REVERT: B 96 SER cc_start: 0.8908 (t) cc_final: 0.8667 (p) REVERT: C 282 GLU cc_start: 0.7931 (mp0) cc_final: 0.7365 (mp0) REVERT: D 43 LEU cc_start: 0.8713 (tp) cc_final: 0.8427 (tp) REVERT: D 66 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (mp) outliers start: 20 outliers final: 15 residues processed: 171 average time/residue: 0.1925 time to fit residues: 43.7702 Evaluate side-chains 168 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6840 Z= 0.188 Angle : 0.647 14.873 9259 Z= 0.311 Chirality : 0.038 0.169 1071 Planarity : 0.004 0.049 1110 Dihedral : 9.376 87.940 1153 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.38 % Rotamer: Outliers : 2.95 % Allowed : 27.73 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.71 (0.31), residues: 800 helix: 1.49 (0.23), residues: 532 sheet: 0.23 (0.86), residues: 38 loop : -1.98 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 4 HIS 0.006 0.001 HIS B 118 PHE 0.011 0.001 PHE C 118 TYR 0.013 0.001 TYR C 199 ARG 0.005 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8611 (t80) cc_final: 0.8219 (t80) REVERT: A 281 MET cc_start: 0.7209 (ptt) cc_final: 0.6434 (ptt) REVERT: B 37 GLU cc_start: 0.8000 (pp20) cc_final: 0.7686 (tt0) REVERT: B 79 ASP cc_start: 0.7581 (m-30) cc_final: 0.7342 (m-30) REVERT: B 96 SER cc_start: 0.8932 (t) cc_final: 0.8663 (p) REVERT: C 282 GLU cc_start: 0.7977 (mp0) cc_final: 0.7416 (mp0) REVERT: D 43 LEU cc_start: 0.8723 (tp) cc_final: 0.8459 (tp) REVERT: D 66 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8418 (mp) outliers start: 20 outliers final: 16 residues processed: 165 average time/residue: 0.1908 time to fit residues: 41.9045 Evaluate side-chains 165 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6840 Z= 0.199 Angle : 0.665 12.969 9259 Z= 0.317 Chirality : 0.038 0.171 1071 Planarity : 0.004 0.049 1110 Dihedral : 9.382 87.734 1153 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.62 % Favored : 93.25 % Rotamer: Outliers : 3.10 % Allowed : 27.14 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.31), residues: 800 helix: 1.51 (0.23), residues: 530 sheet: 0.25 (0.86), residues: 38 loop : -2.06 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 4 HIS 0.006 0.001 HIS C 237 PHE 0.010 0.001 PHE C 118 TYR 0.013 0.001 TYR C 199 ARG 0.005 0.000 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8609 (t80) cc_final: 0.8220 (t80) REVERT: A 281 MET cc_start: 0.7248 (ptt) cc_final: 0.6598 (ptt) REVERT: B 37 GLU cc_start: 0.7998 (pp20) cc_final: 0.7724 (tt0) REVERT: B 79 ASP cc_start: 0.7532 (m-30) cc_final: 0.7314 (m-30) REVERT: B 96 SER cc_start: 0.8922 (t) cc_final: 0.8658 (p) REVERT: C 282 GLU cc_start: 0.7989 (mp0) cc_final: 0.7383 (mp0) REVERT: D 43 LEU cc_start: 0.8722 (tp) cc_final: 0.8461 (tp) REVERT: D 66 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8431 (mp) outliers start: 21 outliers final: 16 residues processed: 162 average time/residue: 0.1880 time to fit residues: 40.6291 Evaluate side-chains 164 residues out of total 712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 chunk 3 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112298 restraints weight = 11568.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115223 restraints weight = 6686.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117146 restraints weight = 4755.503| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6840 Z= 0.236 Angle : 0.692 15.199 9259 Z= 0.330 Chirality : 0.040 0.180 1071 Planarity : 0.005 0.049 1110 Dihedral : 9.511 86.351 1153 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.88 % Favored : 93.00 % Rotamer: Outliers : 2.95 % Allowed : 27.43 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.58 (0.31), residues: 800 helix: 1.44 (0.23), residues: 530 sheet: 0.24 (0.85), residues: 38 loop : -2.13 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 4 HIS 0.006 0.001 HIS B 118 PHE 0.015 0.001 PHE C 118 TYR 0.015 0.001 TYR C 199 ARG 0.005 0.000 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.14 seconds wall clock time: 35 minutes 15.76 seconds (2115.76 seconds total)