Starting phenix.real_space_refine on Wed Feb 14 20:41:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8r_35250/02_2024/8i8r_35250_updated.pdb" } resolution = 2.93 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= 0.005 sd= 0.019 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 6 5.49 5 S 17 5.16 5 C 6433 2.51 5 N 1638 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10151 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2709 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "B" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2709 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "C" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2709 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1565 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 182} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 153 Unusual residues: {'KDL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 153 Unusual residues: {'KDL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 153 Unusual residues: {'KDL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.54 Number of scatterers: 10151 At special positions: 0 Unit cell: (76.728, 93.408, 136.776, 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 17 16.00 P 6 15.00 O 2057 8.00 N 1638 7.00 C 6433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 1.9 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 7 sheets defined 14.7% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 156 through 159 No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 225 through 228 Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.557A pdb=" N ASP A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 5.190A pdb=" N TRP B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 225 through 228 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 117 through 125 removed outlier: 4.034A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 159 No H-bonds generated for 'chain 'C' and resid 156 through 159' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'D' and resid 21 through 28 Processing helix chain 'D' and resid 30 through 33 No H-bonds generated for 'chain 'D' and resid 30 through 33' Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.719A pdb=" N ALA D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 63 through 73 removed outlier: 4.019A pdb=" N MET D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.658A pdb=" N HIS D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 86 " --> pdb=" O HIS D 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 87 " --> pdb=" O PHE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 116 through 123 removed outlier: 4.298A pdb=" N TYR D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 161 through 178 removed outlier: 3.619A pdb=" N VAL D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'D' and resid 192 through 204 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 4.499A pdb=" N TYR A 25 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 96 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN A 80 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR A 94 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN A 82 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER A 92 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 99 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 166 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 200 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 220 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 240 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 278 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 302 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 332 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 334 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 362 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 360 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 358 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.579A pdb=" N TYR B 25 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 109 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 150 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER B 220 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 302 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 286 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 316 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY B 303 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP B 314 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 332 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 364 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 334 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 362 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 363 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 40 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 79 through 81 Processing sheet with id= D, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.691A pdb=" N TYR B 286 " --> pdb=" O PRO B 294 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.621A pdb=" N LEU B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.529A pdb=" N TYR C 25 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 27 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 30 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 60 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 96 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN C 80 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR C 94 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN C 82 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER C 92 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE C 166 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 216 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 256 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 279 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 262 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 280 " --> pdb=" O GLN C 300 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 300 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 359 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 361 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS C 42 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 363 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 217 through 222 removed outlier: 3.952A pdb=" N SER C 221 " --> pdb=" O ALA C 239 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1185 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: 3.31 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1732 1.30 - 1.43: 2948 1.43 - 1.56: 5550 1.56 - 1.68: 125 1.68 - 1.81: 34 Bond restraints: 10389 Sorted by residual: bond pdb=" CFK KDL B 401 " pdb=" O3 KDL B 401 " ideal model delta sigma weight residual 1.493 1.401 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CFK KDL A 401 " pdb=" O3 KDL A 401 " ideal model delta sigma weight residual 1.493 1.404 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CFK KDL C 401 " pdb=" O3 KDL C 401 " ideal model delta sigma weight residual 1.493 1.406 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CDO KDL C 401 " pdb=" NAO KDL C 401 " ideal model delta sigma weight residual 1.524 1.446 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" CBV KDL A 401 " pdb=" CBX KDL A 401 " ideal model delta sigma weight residual 1.453 1.529 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 10384 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 214 107.47 - 114.09: 5515 114.09 - 120.72: 4213 120.72 - 127.34: 4042 127.34 - 133.97: 67 Bond angle restraints: 14051 Sorted by residual: angle pdb=" CAN KDL A 401 " pdb=" NAO KDL A 401 " pdb=" CDO KDL A 401 " ideal model delta sigma weight residual 119.99 130.51 -10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C7 KDL B 401 " pdb=" C8 KDL B 401 " pdb=" CEW KDL B 401 " ideal model delta sigma weight residual 109.69 120.15 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CAN KDL B 401 " pdb=" NAO KDL B 401 " pdb=" CDO KDL B 401 " ideal model delta sigma weight residual 119.99 130.24 -10.25 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C1 KDL A 401 " pdb=" O5 KDL A 401 " pdb=" C5 KDL A 401 " ideal model delta sigma weight residual 112.16 122.12 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CAN KDL C 401 " pdb=" CAP KDL C 401 " pdb=" CAR KDL C 401 " ideal model delta sigma weight residual 112.46 120.87 -8.41 3.00e+00 1.11e-01 7.85e+00 ... (remaining 14046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.47: 5321 25.47 - 50.94: 492 50.94 - 76.41: 92 76.41 - 101.88: 19 101.88 - 127.35: 13 Dihedral angle restraints: 5937 sinusoidal: 2470 harmonic: 3467 Sorted by residual: dihedral pdb=" CBV KDL B 401 " pdb=" CBX KDL B 401 " pdb=" CBZ KDL B 401 " pdb=" OCA KDL B 401 " ideal model delta sinusoidal sigma weight residual 174.37 -58.28 -127.35 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" CBV KDL C 401 " pdb=" CBX KDL C 401 " pdb=" CBZ KDL C 401 " pdb=" OCA KDL C 401 " ideal model delta sinusoidal sigma weight residual 174.37 -65.51 -120.12 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CBV KDL A 401 " pdb=" CBX KDL A 401 " pdb=" CBZ KDL A 401 " pdb=" OCA KDL A 401 " ideal model delta sinusoidal sigma weight residual 174.37 -66.34 -119.29 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 5934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1335 0.096 - 0.192: 73 0.192 - 0.288: 10 0.288 - 0.384: 1 0.384 - 0.480: 2 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CAT KDL B 401 " pdb=" CAR KDL B 401 " pdb=" CAV KDL B 401 " pdb=" OAU KDL B 401 " both_signs ideal model delta sigma weight residual False -2.66 -2.18 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CAT KDL A 401 " pdb=" CAR KDL A 401 " pdb=" CAV KDL A 401 " pdb=" OAU KDL A 401 " both_signs ideal model delta sigma weight residual False -2.66 -2.23 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CAT KDL C 401 " pdb=" CAR KDL C 401 " pdb=" CAV KDL C 401 " pdb=" OAU KDL C 401 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 1418 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 153 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.26e-01 pdb=" N PRO D 154 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 154 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO D 154 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 63 " -0.013 5.00e-02 4.00e+02 1.89e-02 5.69e-01 pdb=" N PRO D 64 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 48 " -0.012 5.00e-02 4.00e+02 1.82e-02 5.31e-01 pdb=" N PRO D 49 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.010 5.00e-02 4.00e+02 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3349 2.82 - 3.34: 7991 3.34 - 3.86: 16682 3.86 - 4.38: 18672 4.38 - 4.90: 34068 Nonbonded interactions: 80762 Sorted by model distance: nonbonded pdb=" O PHE D 86 " pdb=" OG1 THR D 90 " model vdw 2.303 2.440 nonbonded pdb=" NZ LYS B 173 " pdb=" CBK KDL B 401 " model vdw 2.303 3.520 nonbonded pdb=" OE1 GLN C 66 " pdb=" OG1 THR C 72 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR A 111 " pdb=" OD1 ASP C 53 " model vdw 2.323 2.440 nonbonded pdb=" OE1 GLN A 261 " pdb=" OH TYR A 263 " model vdw 2.326 2.440 ... (remaining 80757 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' selection = chain 'B' selection = chain 'C' } 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: 2.100 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: 7.130 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 31.680 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.006 0.092 10389 Z= 0.406 Angle : 0.707 10.520 14051 Z= 0.273 Chirality : 0.049 0.480 1421 Planarity : 0.002 0.021 1842 Dihedral : 20.492 127.352 3797 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.47 % Rotamer: Outliers : 1.82 % Allowed : 25.53 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1224 helix: -0.17 (0.41), residues: 143 sheet: 0.57 (0.25), residues: 534 loop : -1.48 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP D 161 HIS 0.000 0.000 HIS C 42 PHE 0.009 0.000 PHE A 290 TYR 0.004 0.000 TYR C 209 ARG 0.001 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.163 Fit side-chains REVERT: C 23 GLU cc_start: 0.6954 (tp30) cc_final: 0.6562 (tp30) REVERT: C 26 ASN cc_start: 0.7881 (t0) cc_final: 0.7554 (m-40) REVERT: C 64 GLU cc_start: 0.8219 (tt0) cc_final: 0.7938 (tt0) REVERT: C 103 PHE cc_start: 0.7644 (m-80) cc_final: 0.7251 (t80) REVERT: C 313 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7131 (mp0) REVERT: D 56 ASN cc_start: 0.8877 (m110) cc_final: 0.8578 (m-40) REVERT: D 105 ASN cc_start: 0.8480 (t0) cc_final: 0.8063 (m-40) REVERT: D 109 GLN cc_start: 0.8430 (mm110) cc_final: 0.8103 (mm110) outliers start: 18 outliers final: 5 residues processed: 170 average time/residue: 0.8007 time to fit residues: 151.8926 Evaluate side-chains 78 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 GLN A 354 ASN B 42 HIS B 171 GLN B 174 ASN B 227 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 197 ASN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 69 ASN D 73 GLN D 204 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10389 Z= 0.289 Angle : 0.650 8.465 14051 Z= 0.330 Chirality : 0.045 0.173 1421 Planarity : 0.004 0.049 1842 Dihedral : 17.976 117.384 1705 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 5.37 % Allowed : 25.43 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1224 helix: 0.17 (0.41), residues: 152 sheet: 0.38 (0.24), residues: 513 loop : -1.53 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 161 HIS 0.006 0.001 HIS B 42 PHE 0.018 0.002 PHE B 149 TYR 0.020 0.002 TYR B 365 ARG 0.004 0.001 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 80 time to evaluate : 1.154 Fit side-chains REVERT: C 64 GLU cc_start: 0.8461 (tt0) cc_final: 0.8206 (tt0) REVERT: C 103 PHE cc_start: 0.8050 (m-80) cc_final: 0.7239 (t80) REVERT: C 313 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7815 (mp0) REVERT: D 56 ASN cc_start: 0.8741 (m-40) cc_final: 0.8475 (m-40) REVERT: D 105 ASN cc_start: 0.8784 (t0) cc_final: 0.8290 (t0) REVERT: D 109 GLN cc_start: 0.8536 (mm110) cc_final: 0.8184 (mm110) REVERT: D 174 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8648 (mm-30) REVERT: D 202 GLN cc_start: 0.8996 (tt0) cc_final: 0.8475 (tm-30) outliers start: 53 outliers final: 19 residues processed: 124 average time/residue: 0.8589 time to fit residues: 118.3632 Evaluate side-chains 75 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 264 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10389 Z= 0.253 Angle : 0.599 8.221 14051 Z= 0.302 Chirality : 0.043 0.166 1421 Planarity : 0.003 0.042 1842 Dihedral : 16.790 115.980 1701 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 5.37 % Allowed : 24.11 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1224 helix: 0.76 (0.44), residues: 152 sheet: 0.22 (0.23), residues: 516 loop : -1.67 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 161 HIS 0.002 0.001 HIS A 42 PHE 0.012 0.001 PHE A 103 TYR 0.013 0.001 TYR B 209 ARG 0.004 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 61 time to evaluate : 1.161 Fit side-chains REVERT: C 47 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8490 (t0) REVERT: D 56 ASN cc_start: 0.8759 (m-40) cc_final: 0.8512 (m-40) REVERT: D 109 GLN cc_start: 0.8560 (mm110) cc_final: 0.8326 (mm-40) REVERT: D 202 GLN cc_start: 0.9021 (tt0) cc_final: 0.8501 (tm-30) outliers start: 53 outliers final: 21 residues processed: 102 average time/residue: 0.7911 time to fit residues: 91.1040 Evaluate side-chains 76 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 25 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 0.0010 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 300 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10389 Z= 0.245 Angle : 0.585 8.067 14051 Z= 0.293 Chirality : 0.043 0.165 1421 Planarity : 0.003 0.040 1842 Dihedral : 16.348 116.168 1701 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 4.86 % Allowed : 24.62 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.24), residues: 1224 helix: 0.86 (0.43), residues: 152 sheet: 0.12 (0.23), residues: 525 loop : -1.71 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 161 HIS 0.001 0.001 HIS D 114 PHE 0.011 0.001 PHE D 87 TYR 0.011 0.001 TYR A 318 ARG 0.003 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 51 time to evaluate : 1.122 Fit side-chains REVERT: B 308 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7110 (mmt90) REVERT: C 47 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8549 (t0) REVERT: D 56 ASN cc_start: 0.8717 (m-40) cc_final: 0.8457 (m-40) REVERT: D 202 GLN cc_start: 0.9019 (tt0) cc_final: 0.8538 (tm-30) outliers start: 48 outliers final: 28 residues processed: 91 average time/residue: 0.8283 time to fit residues: 84.8063 Evaluate side-chains 79 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 49 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 25 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN B 82 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN C 264 ASN D 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 10389 Z= 0.484 Angle : 0.701 8.891 14051 Z= 0.353 Chirality : 0.047 0.197 1421 Planarity : 0.004 0.060 1842 Dihedral : 16.466 119.592 1701 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer: Outliers : 6.69 % Allowed : 22.70 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1224 helix: 0.29 (0.42), residues: 172 sheet: -0.10 (0.23), residues: 534 loop : -1.92 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 161 HIS 0.005 0.001 HIS D 82 PHE 0.019 0.002 PHE D 87 TYR 0.014 0.002 TYR A 318 ARG 0.003 0.001 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 52 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: B 308 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7329 (mmt90) REVERT: C 103 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7374 (t80) REVERT: D 18 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7311 (t80) REVERT: D 109 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8458 (mm-40) REVERT: D 202 GLN cc_start: 0.9042 (tt0) cc_final: 0.8616 (tm-30) outliers start: 66 outliers final: 42 residues processed: 110 average time/residue: 0.7824 time to fit residues: 96.9711 Evaluate side-chains 85 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 40 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN B 174 ASN B 279 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10389 Z= 0.234 Angle : 0.600 8.688 14051 Z= 0.299 Chirality : 0.043 0.165 1421 Planarity : 0.003 0.044 1842 Dihedral : 15.981 117.635 1701 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 5.37 % Allowed : 24.21 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1224 helix: 0.95 (0.44), residues: 154 sheet: 0.01 (0.23), residues: 525 loop : -1.79 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 161 HIS 0.001 0.001 HIS D 114 PHE 0.013 0.001 PHE A 367 TYR 0.015 0.001 TYR C 136 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 44 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: B 308 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7396 (mmt90) REVERT: B 357 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8706 (m110) REVERT: C 103 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7360 (t80) REVERT: D 18 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7352 (t80) REVERT: D 109 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8438 (mm-40) REVERT: D 202 GLN cc_start: 0.9040 (tt0) cc_final: 0.8621 (tm-30) outliers start: 53 outliers final: 36 residues processed: 91 average time/residue: 0.7849 time to fit residues: 80.3501 Evaluate side-chains 83 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 43 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 25 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 116 optimal weight: 0.0030 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN C 30 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 10389 Z= 0.360 Angle : 0.637 8.898 14051 Z= 0.320 Chirality : 0.045 0.169 1421 Planarity : 0.003 0.048 1842 Dihedral : 15.941 118.412 1701 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer: Outliers : 5.98 % Allowed : 23.71 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1224 helix: 0.40 (0.42), residues: 172 sheet: -0.08 (0.23), residues: 531 loop : -1.90 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 161 HIS 0.003 0.001 HIS D 82 PHE 0.015 0.001 PHE D 87 TYR 0.015 0.001 TYR A 298 ARG 0.003 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 40 time to evaluate : 1.203 Fit side-chains REVERT: B 308 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7213 (mmt90) REVERT: B 357 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8757 (m110) REVERT: C 103 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7359 (t80) REVERT: D 18 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7536 (t80) REVERT: D 109 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8445 (mm-40) REVERT: D 202 GLN cc_start: 0.9079 (tt0) cc_final: 0.8601 (tm-30) outliers start: 59 outliers final: 41 residues processed: 95 average time/residue: 0.7832 time to fit residues: 84.0622 Evaluate side-chains 83 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 38 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 194 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN C 30 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10389 Z= 0.162 Angle : 0.564 8.843 14051 Z= 0.281 Chirality : 0.042 0.160 1421 Planarity : 0.003 0.043 1842 Dihedral : 15.465 115.975 1701 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 4.96 % Allowed : 24.82 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1224 helix: 1.09 (0.44), residues: 154 sheet: 0.04 (0.23), residues: 522 loop : -1.80 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 168 HIS 0.001 0.001 HIS D 82 PHE 0.009 0.001 PHE B 61 TYR 0.013 0.001 TYR A 318 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 46 time to evaluate : 1.173 Fit side-chains REVERT: B 308 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7279 (mmt90) REVERT: B 357 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8632 (m110) REVERT: C 30 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7864 (t0) REVERT: C 103 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7364 (t80) REVERT: D 18 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7539 (t80) REVERT: D 109 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8417 (mm-40) REVERT: D 178 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8735 (mt0) REVERT: D 202 GLN cc_start: 0.9050 (tt0) cc_final: 0.8592 (tm-30) outliers start: 49 outliers final: 30 residues processed: 90 average time/residue: 0.7701 time to fit residues: 78.5432 Evaluate side-chains 79 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 43 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 178 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN C 30 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 10389 Z= 0.367 Angle : 0.643 10.457 14051 Z= 0.322 Chirality : 0.045 0.166 1421 Planarity : 0.003 0.048 1842 Dihedral : 15.637 117.453 1700 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.29 % Favored : 93.55 % Rotamer: Outliers : 4.15 % Allowed : 25.94 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1224 helix: 0.61 (0.43), residues: 172 sheet: -0.11 (0.23), residues: 531 loop : -1.88 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 158 HIS 0.003 0.001 HIS D 82 PHE 0.015 0.001 PHE D 87 TYR 0.015 0.001 TYR A 298 ARG 0.002 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 39 time to evaluate : 1.115 Fit side-chains REVERT: B 308 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7216 (mmt90) REVERT: B 357 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8707 (m110) REVERT: C 103 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7368 (t80) REVERT: D 18 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7631 (t80) REVERT: D 56 ASN cc_start: 0.8682 (m110) cc_final: 0.8459 (m-40) REVERT: D 109 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8467 (mm-40) REVERT: D 202 GLN cc_start: 0.9085 (tt0) cc_final: 0.8618 (tm-30) outliers start: 41 outliers final: 32 residues processed: 77 average time/residue: 0.8125 time to fit residues: 70.3397 Evaluate side-chains 75 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 39 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 194 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN C 30 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10389 Z= 0.334 Angle : 0.634 10.254 14051 Z= 0.317 Chirality : 0.044 0.164 1421 Planarity : 0.003 0.046 1842 Dihedral : 15.616 117.433 1700 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.88 % Favored : 93.95 % Rotamer: Outliers : 3.95 % Allowed : 26.34 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1224 helix: 0.60 (0.43), residues: 172 sheet: -0.00 (0.23), residues: 522 loop : -1.92 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.001 HIS D 82 PHE 0.013 0.001 PHE D 87 TYR 0.013 0.001 TYR A 298 ARG 0.002 0.000 ARG A 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 40 time to evaluate : 1.209 Fit side-chains REVERT: B 308 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7336 (mmt90) REVERT: B 357 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8701 (m110) REVERT: C 103 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7380 (t80) REVERT: D 56 ASN cc_start: 0.8682 (m110) cc_final: 0.8449 (m-40) REVERT: D 109 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8477 (mm-40) REVERT: D 202 GLN cc_start: 0.9081 (tt0) cc_final: 0.8623 (tm-30) outliers start: 39 outliers final: 29 residues processed: 76 average time/residue: 0.9161 time to fit residues: 77.7648 Evaluate side-chains 71 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 39 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.064174 restraints weight = 18995.793| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.32 r_work: 0.2814 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10389 Z= 0.190 Angle : 0.580 9.955 14051 Z= 0.290 Chirality : 0.042 0.162 1421 Planarity : 0.003 0.044 1842 Dihedral : 15.250 115.496 1700 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.20 % Rotamer: Outliers : 3.44 % Allowed : 26.95 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1224 helix: 1.27 (0.45), residues: 153 sheet: -0.01 (0.23), residues: 522 loop : -1.82 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.002 0.001 HIS D 82 PHE 0.009 0.001 PHE B 61 TYR 0.013 0.001 TYR B 318 ARG 0.007 0.000 ARG D 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.94 seconds wall clock time: 50 minutes 13.20 seconds (3013.20 seconds total)