Starting phenix.real_space_refine on Tue Feb 13 20:19:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yub_34103/02_2024/7yub_34103_neut_updated.pdb" } resolution = 3.22 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= 0.002 sd= 0.140 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 37 5.16 5 C 4873 2.51 5 N 1271 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7610 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1732 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1619 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "N" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3275 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 13, 'TRANS': 415} Chain breaks: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.52, per 1000 atoms: 0.59 Number of scatterers: 7610 At special positions: 0 Unit cell: (78.1, 88, 154, 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 37 16.00 P 1 15.00 O 1428 8.00 N 1271 7.00 C 4873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 38.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 107 through 110 No H-bonds generated for 'chain 'H' and resid 107 through 110' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.800A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'R' and resid 94 through 118 removed outlier: 5.547A pdb=" N ARG R 99 " --> pdb=" O ALA R 95 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 124 No H-bonds generated for 'chain 'R' and resid 121 through 124' Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 139 through 163 removed outlier: 3.616A pdb=" N LEU R 142 " --> pdb=" O GLY R 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU R 143 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN R 144 " --> pdb=" O GLY R 141 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL R 146 " --> pdb=" O LEU R 143 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA R 155 " --> pdb=" O MET R 152 " (cutoff:3.500A) Proline residue: R 156 - end of helix removed outlier: 4.201A pdb=" N GLY R 162 " --> pdb=" O GLY R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 187 removed outlier: 3.644A pdb=" N VAL R 181 " --> pdb=" O PHE R 177 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 220 removed outlier: 3.587A pdb=" N VAL R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 227 through 235 Processing helix chain 'R' and resid 238 through 256 removed outlier: 3.867A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 263 Processing helix chain 'R' and resid 266 through 280 removed outlier: 3.558A pdb=" N ILE R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR R 275 " --> pdb=" O MET R 271 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 311 removed outlier: 4.370A pdb=" N ARG R 311 " --> pdb=" O LYS R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 346 Proline residue: R 337 - end of helix Processing helix chain 'R' and resid 361 through 390 removed outlier: 3.814A pdb=" N PHE R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL R 378 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU R 390 " --> pdb=" O ARG R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 412 removed outlier: 4.272A pdb=" N ILE R 409 " --> pdb=" O LEU R 405 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE R 410 " --> pdb=" O GLY R 406 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 417 No H-bonds generated for 'chain 'R' and resid 414 through 417' Processing helix chain 'R' and resid 422 through 436 Processing helix chain 'R' and resid 443 through 449 Processing helix chain 'R' and resid 453 through 469 removed outlier: 3.930A pdb=" N ARG R 456 " --> pdb=" O PRO R 453 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA R 457 " --> pdb=" O THR R 454 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR R 458 " --> pdb=" O ARG R 455 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL R 460 " --> pdb=" O ALA R 457 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU R 462 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER R 464 " --> pdb=" O ALA R 461 " (cutoff:3.500A) Processing helix chain 'R' and resid 475 through 489 removed outlier: 4.006A pdb=" N SER R 489 " --> pdb=" O LEU R 485 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 540 removed outlier: 3.820A pdb=" N MET R 506 " --> pdb=" O GLY R 502 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU R 507 " --> pdb=" O TYR R 503 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N CYS R 508 " --> pdb=" O ALA R 504 " (cutoff:3.500A) Proline residue: R 509 - end of helix removed outlier: 3.752A pdb=" N PHE R 525 " --> pdb=" O ALA R 521 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL R 527 " --> pdb=" O ALA R 523 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER R 528 " --> pdb=" O LEU R 524 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 7 through 11 removed outlier: 3.675A pdb=" N ALA H 83 " --> pdb=" O CYS H 26 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR H 82 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 14 through 16 removed outlier: 3.534A pdb=" N ALA H 96 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP H 40 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA H 53 " --> pdb=" O TRP H 40 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG H 42 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TRP H 51 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA H 44 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU H 49 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 139 through 143 removed outlier: 3.742A pdb=" N GLY H 158 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.918A pdb=" N TYR H 213 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 7 through 9 removed outlier: 3.598A pdb=" N THR L 7 " --> pdb=" O ARG L 26 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR L 24 " --> pdb=" O SER L 9 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 12 through 14 removed outlier: 5.995A pdb=" N LYS L 105 " --> pdb=" O LEU L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 87 through 91 removed outlier: 3.790A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.691A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER L 178 " --> pdb=" O SER L 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER L 164 " --> pdb=" O SER L 178 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 146 through 152 removed outlier: 3.538A pdb=" N VAL L 198 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL L 207 " --> pdb=" O VAL L 198 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 4 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.515A pdb=" N TYR N 95 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG N 39 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLY N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 98 through 100 361 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2382 1.34 - 1.46: 1906 1.46 - 1.58: 3445 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 7787 Sorted by residual: bond pdb=" O1 S1P R 601 " pdb=" P22 S1P R 601 " ideal model delta sigma weight residual 1.661 1.816 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C5 S1P R 601 " pdb=" C6 S1P R 601 " ideal model delta sigma weight residual 1.550 1.485 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 S1P R 601 " pdb=" O1 S1P R 601 " ideal model delta sigma weight residual 1.405 1.342 0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" N ILE R 175 " pdb=" CA ILE R 175 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.69e+00 bond pdb=" C11 S1P R 601 " pdb=" C12 S1P R 601 " ideal model delta sigma weight residual 1.573 1.519 0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 7782 not shown) Histogram of bond angle deviations from ideal: 95.12 - 102.95: 50 102.95 - 110.78: 2650 110.78 - 118.61: 3431 118.61 - 126.44: 4318 126.44 - 134.27: 128 Bond angle restraints: 10577 Sorted by residual: angle pdb=" O1 S1P R 601 " pdb=" P22 S1P R 601 " pdb=" O25 S1P R 601 " ideal model delta sigma weight residual 109.48 95.12 14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" C TYR H 114 " pdb=" N TRP H 115 " pdb=" CA TRP H 115 " ideal model delta sigma weight residual 122.17 115.00 7.17 1.54e+00 4.22e-01 2.17e+01 angle pdb=" N THR N 34 " pdb=" CA THR N 34 " pdb=" C THR N 34 " ideal model delta sigma weight residual 112.03 117.86 -5.83 1.31e+00 5.83e-01 1.98e+01 angle pdb=" C THR H 184 " pdb=" N PHE H 185 " pdb=" CA PHE H 185 " ideal model delta sigma weight residual 120.68 127.41 -6.73 1.52e+00 4.33e-01 1.96e+01 angle pdb=" N SER L 32 " pdb=" CA SER L 32 " pdb=" CB SER L 32 " ideal model delta sigma weight residual 114.17 109.35 4.82 1.14e+00 7.69e-01 1.79e+01 ... (remaining 10572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4233 17.92 - 35.85: 263 35.85 - 53.77: 49 53.77 - 71.69: 12 71.69 - 89.62: 8 Dihedral angle restraints: 4565 sinusoidal: 1711 harmonic: 2854 Sorted by residual: dihedral pdb=" CA VAL L 31 " pdb=" C VAL L 31 " pdb=" N SER L 32 " pdb=" CA SER L 32 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA HIS H 110 " pdb=" C HIS H 110 " pdb=" N ALA H 111 " pdb=" CA ALA H 111 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TRP H 113 " pdb=" C TRP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 4562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1011 0.058 - 0.117: 156 0.117 - 0.175: 25 0.175 - 0.234: 6 0.234 - 0.292: 1 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA SER H 112 " pdb=" N SER H 112 " pdb=" C SER H 112 " pdb=" CB SER H 112 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA PHE R 236 " pdb=" N PHE R 236 " pdb=" C PHE R 236 " pdb=" CB PHE R 236 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA HIS H 110 " pdb=" N HIS H 110 " pdb=" C HIS H 110 " pdb=" CB HIS H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1196 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 214 " 0.054 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO R 215 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 41 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO N 42 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO N 42 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 42 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 526 " 0.019 2.00e-02 2.50e+03 1.47e-02 3.76e+00 pdb=" CG PHE R 526 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE R 526 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE R 526 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 526 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 526 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 526 " 0.006 2.00e-02 2.50e+03 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 106 2.68 - 3.24: 6883 3.24 - 3.79: 10655 3.79 - 4.35: 14360 4.35 - 4.90: 24943 Nonbonded interactions: 56947 Sorted by model distance: nonbonded pdb=" O TRP H 113 " pdb=" OG SER L 33 " model vdw 2.127 2.440 nonbonded pdb=" OH TYR R 116 " pdb=" O3 S1P R 601 " model vdw 2.199 2.440 nonbonded pdb=" OG SER R 314 " pdb=" OD2 ASP R 529 " model vdw 2.295 2.440 nonbonded pdb=" O TRP R 496 " pdb=" OG SER R 500 " model vdw 2.339 2.440 nonbonded pdb=" O PHE R 236 " pdb=" CG PHE R 236 " model vdw 2.371 3.260 ... (remaining 56942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.120 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.005 0.155 7787 Z= 0.321 Angle : 0.767 14.355 10577 Z= 0.449 Chirality : 0.047 0.292 1199 Planarity : 0.005 0.080 1325 Dihedral : 12.952 89.616 2734 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.27), residues: 985 helix: 0.49 (0.28), residues: 376 sheet: 0.76 (0.35), residues: 225 loop : -1.30 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 496 HIS 0.007 0.001 HIS H 110 PHE 0.033 0.002 PHE R 526 TYR 0.017 0.001 TYR H 54 ARG 0.004 0.000 ARG R 530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.881 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2598 time to fit residues: 27.8190 Evaluate side-chains 70 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 0.0020 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7787 Z= 0.159 Angle : 0.558 7.359 10577 Z= 0.297 Chirality : 0.042 0.158 1199 Planarity : 0.005 0.050 1325 Dihedral : 6.645 73.960 1099 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.85 % Allowed : 4.74 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 985 helix: 0.80 (0.28), residues: 381 sheet: 1.14 (0.36), residues: 225 loop : -1.02 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 113 HIS 0.003 0.001 HIS H 110 PHE 0.023 0.002 PHE R 236 TYR 0.015 0.001 TYR R 160 ARG 0.003 0.000 ARG R 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.868 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.2345 time to fit residues: 25.1564 Evaluate side-chains 76 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN N 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7787 Z= 0.153 Angle : 0.525 7.340 10577 Z= 0.278 Chirality : 0.041 0.154 1199 Planarity : 0.004 0.039 1325 Dihedral : 6.254 75.424 1099 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.58 % Allowed : 5.96 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 985 helix: 1.06 (0.29), residues: 380 sheet: 1.34 (0.36), residues: 225 loop : -0.91 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.019 0.001 PHE R 236 TYR 0.014 0.001 TYR N 32 ARG 0.002 0.000 ARG R 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.840 Fit side-chains REVERT: H 104 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: R 396 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7091 (m-30) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.2356 time to fit residues: 25.8064 Evaluate side-chains 76 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.0270 chunk 88 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7787 Z= 0.129 Angle : 0.502 8.164 10577 Z= 0.262 Chirality : 0.040 0.138 1199 Planarity : 0.004 0.034 1325 Dihedral : 5.987 72.733 1099 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.09 % Allowed : 7.06 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 985 helix: 1.24 (0.29), residues: 379 sheet: 1.59 (0.36), residues: 220 loop : -0.90 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.030 0.001 PHE R 236 TYR 0.011 0.001 TYR N 32 ARG 0.001 0.000 ARG R 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.872 Fit side-chains REVERT: H 54 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8085 (t80) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.2381 time to fit residues: 24.3183 Evaluate side-chains 74 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 0.0000 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7787 Z= 0.148 Angle : 0.511 7.717 10577 Z= 0.266 Chirality : 0.040 0.151 1199 Planarity : 0.004 0.034 1325 Dihedral : 5.880 69.941 1099 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.22 % Allowed : 8.15 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.28), residues: 985 helix: 1.28 (0.29), residues: 380 sheet: 1.63 (0.36), residues: 226 loop : -0.85 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.030 0.001 PHE R 236 TYR 0.014 0.001 TYR N 32 ARG 0.005 0.000 ARG R 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.801 Fit side-chains REVERT: H 54 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8149 (t80) REVERT: R 396 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7135 (m-30) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.2337 time to fit residues: 24.5851 Evaluate side-chains 77 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7787 Z= 0.400 Angle : 0.681 8.638 10577 Z= 0.360 Chirality : 0.046 0.210 1199 Planarity : 0.005 0.043 1325 Dihedral : 6.333 71.332 1099 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.58 % Allowed : 9.49 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 985 helix: 0.79 (0.28), residues: 379 sheet: 1.36 (0.36), residues: 222 loop : -1.05 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 178 HIS 0.008 0.002 HIS H 110 PHE 0.022 0.002 PHE R 236 TYR 0.023 0.002 TYR H 54 ARG 0.006 0.001 ARG N 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.733 Fit side-chains REVERT: H 54 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7857 (t80) REVERT: R 164 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6762 (mmt90) REVERT: R 396 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (m-30) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.2242 time to fit residues: 23.6401 Evaluate side-chains 79 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7787 Z= 0.184 Angle : 0.543 7.993 10577 Z= 0.286 Chirality : 0.041 0.172 1199 Planarity : 0.004 0.037 1325 Dihedral : 6.040 68.805 1099 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.82 % Allowed : 10.10 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 985 helix: 1.04 (0.28), residues: 381 sheet: 1.38 (0.36), residues: 226 loop : -0.91 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.031 0.001 PHE R 236 TYR 0.012 0.001 TYR R 160 ARG 0.005 0.000 ARG R 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.916 Fit side-chains REVERT: H 54 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8082 (t80) REVERT: R 164 ARG cc_start: 0.7310 (mmt90) cc_final: 0.6841 (mmt90) REVERT: R 334 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6471 (ttt) REVERT: R 396 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7278 (m-30) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.2481 time to fit residues: 25.8067 Evaluate side-chains 87 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 85 optimal weight: 0.0270 chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7787 Z= 0.139 Angle : 0.502 7.594 10577 Z= 0.263 Chirality : 0.040 0.147 1199 Planarity : 0.004 0.035 1325 Dihedral : 5.843 66.184 1099 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.95 % Allowed : 10.10 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 985 helix: 1.25 (0.29), residues: 380 sheet: 1.49 (0.36), residues: 226 loop : -0.82 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.031 0.001 PHE R 236 TYR 0.011 0.001 TYR N 32 ARG 0.006 0.000 ARG R 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.829 Fit side-chains REVERT: H 47 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7593 (mtmt) REVERT: H 54 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8170 (t80) REVERT: H 142 PRO cc_start: 0.7887 (Cg_endo) cc_final: 0.7627 (Cg_exo) REVERT: R 164 ARG cc_start: 0.7231 (mmt90) cc_final: 0.6822 (mmt90) REVERT: R 396 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7143 (m-30) outliers start: 16 outliers final: 12 residues processed: 83 average time/residue: 0.2382 time to fit residues: 26.1799 Evaluate side-chains 87 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7787 Z= 0.214 Angle : 0.555 7.954 10577 Z= 0.290 Chirality : 0.042 0.186 1199 Planarity : 0.004 0.036 1325 Dihedral : 5.921 66.534 1099 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.70 % Allowed : 9.98 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 985 helix: 1.15 (0.28), residues: 381 sheet: 1.41 (0.36), residues: 226 loop : -0.81 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.032 0.002 PHE R 236 TYR 0.016 0.001 TYR N 32 ARG 0.006 0.000 ARG R 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.812 Fit side-chains REVERT: H 47 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7601 (mtmt) REVERT: H 54 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7981 (t80) REVERT: H 142 PRO cc_start: 0.7836 (Cg_endo) cc_final: 0.7545 (Cg_exo) REVERT: R 164 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6904 (mmt90) REVERT: R 334 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6317 (ttt) REVERT: R 396 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7304 (m-30) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.2413 time to fit residues: 25.3502 Evaluate side-chains 89 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 81 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7787 Z= 0.147 Angle : 0.508 7.837 10577 Z= 0.264 Chirality : 0.040 0.154 1199 Planarity : 0.004 0.035 1325 Dihedral : 5.758 64.750 1099 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.70 % Allowed : 9.85 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.28), residues: 985 helix: 1.37 (0.29), residues: 374 sheet: 1.48 (0.36), residues: 226 loop : -0.68 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.032 0.001 PHE R 236 TYR 0.012 0.001 TYR N 32 ARG 0.005 0.000 ARG R 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.816 Fit side-chains REVERT: H 47 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7597 (mtmt) REVERT: H 54 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8073 (t80) REVERT: H 142 PRO cc_start: 0.7875 (Cg_endo) cc_final: 0.7610 (Cg_exo) REVERT: R 164 ARG cc_start: 0.7255 (mmt90) cc_final: 0.6899 (mmt90) REVERT: R 191 GLN cc_start: 0.8441 (mp10) cc_final: 0.8202 (pm20) REVERT: R 396 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7171 (m-30) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.2303 time to fit residues: 24.8015 Evaluate side-chains 87 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain R residue 236 PHE Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.191022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136275 restraints weight = 8172.828| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.79 r_work: 0.3146 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7787 Z= 0.278 Angle : 0.596 8.167 10577 Z= 0.312 Chirality : 0.043 0.199 1199 Planarity : 0.004 0.037 1325 Dihedral : 5.981 67.157 1099 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.58 % Allowed : 9.98 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 985 helix: 1.15 (0.28), residues: 375 sheet: 1.30 (0.36), residues: 226 loop : -0.79 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 178 HIS 0.006 0.001 HIS H 110 PHE 0.032 0.002 PHE R 236 TYR 0.021 0.002 TYR N 32 ARG 0.006 0.000 ARG R 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.89 seconds wall clock time: 33 minutes 43.72 seconds (2023.72 seconds total)