Starting phenix.real_space_refine on Wed Sep 25 12:12:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/09_2024/5fn2_3237.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/09_2024/5fn2_3237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/09_2024/5fn2_3237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/09_2024/5fn2_3237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/09_2024/5fn2_3237.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/09_2024/5fn2_3237.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6733 2.51 5 N 1674 2.21 5 O 1829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10276 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2339 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 6, 'PTRANS': 10, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 235} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.98, per 1000 atoms: 0.58 Number of scatterers: 10276 At special positions: 0 Unit cell: (89.6, 144.2, 105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1829 8.00 N 1674 7.00 C 6733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.02 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 58.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.773A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.631A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.821A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.825A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.742A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.776A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.616A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 79 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.557A pdb=" N ILE B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 190 removed outlier: 3.869A pdb=" N HIS B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.535A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 429 Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.610A pdb=" N ALA B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.398A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 64 through 105 removed outlier: 3.810A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 143 removed outlier: 4.844A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.523A pdb=" N THR C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 206 Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.783A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 removed outlier: 3.710A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 37 through 43 Processing helix chain 'D' and resid 49 through 82 Processing helix chain 'D' and resid 86 through 92 Processing sheet with id=AA, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.654A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A 96 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU A 121 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 98 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 123 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.523A pdb=" N LEU A 53 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 275 through 278 Processing sheet with id=AD, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AE, first strand: chain 'A' and resid 375 through 377 removed outlier: 3.950A pdb=" N ARG A 414 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.531A pdb=" N THR A 577 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 622 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.604A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1797 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: 3.30 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1689 1.32 - 1.45: 2961 1.45 - 1.58: 5831 1.58 - 1.70: 2 1.70 - 1.83: 61 Bond restraints: 10544 Sorted by residual: bond pdb=" CA ASP A 458 " pdb=" C ASP A 458 " ideal model delta sigma weight residual 1.523 1.586 -0.062 1.34e-02 5.57e+03 2.17e+01 bond pdb=" C THR B 116 " pdb=" N PRO B 117 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.30e-02 5.92e+03 1.93e+01 bond pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 1.539 1.563 -0.024 5.40e-03 3.43e+04 1.90e+01 bond pdb=" N PRO B 117 " pdb=" CD PRO B 117 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO B 264 " pdb=" CD PRO B 264 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13247 2.93 - 5.87: 1034 5.87 - 8.80: 86 8.80 - 11.74: 12 11.74 - 14.67: 4 Bond angle restraints: 14383 Sorted by residual: angle pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 120.38 132.33 -11.95 1.03e+00 9.43e-01 1.35e+02 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 122.17 -11.47 1.22e+00 6.72e-01 8.84e+01 angle pdb=" CA VAL B 87 " pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 120.83 115.48 5.35 6.10e-01 2.69e+00 7.69e+01 angle pdb=" N ARG B 108 " pdb=" CA ARG B 108 " pdb=" C ARG B 108 " ideal model delta sigma weight residual 109.52 122.31 -12.79 1.55e+00 4.16e-01 6.81e+01 angle pdb=" N ILE B 227 " pdb=" CA ILE B 227 " pdb=" CB ILE B 227 " ideal model delta sigma weight residual 110.55 119.16 -8.61 1.17e+00 7.31e-01 5.41e+01 ... (remaining 14378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 5154 17.08 - 34.15: 725 34.15 - 51.22: 207 51.22 - 68.30: 65 68.30 - 85.37: 10 Dihedral angle restraints: 6161 sinusoidal: 2343 harmonic: 3818 Sorted by residual: dihedral pdb=" CA CYS B 263 " pdb=" C CYS B 263 " pdb=" N PRO B 264 " pdb=" CA PRO B 264 " ideal model delta harmonic sigma weight residual -180.00 -123.15 -56.85 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -171.37 85.37 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -155.64 69.64 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 6158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1331 0.118 - 0.236: 285 0.236 - 0.353: 43 0.353 - 0.471: 12 0.471 - 0.589: 1 Chirality restraints: 1672 Sorted by residual: chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA PHE B 388 " pdb=" N PHE B 388 " pdb=" C PHE B 388 " pdb=" CB PHE B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA PHE A 525 " pdb=" N PHE A 525 " pdb=" C PHE A 525 " pdb=" CB PHE A 525 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1669 not shown) Planarity restraints: 1789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 178 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 179 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 215 " -0.058 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO C 216 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 267 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " -0.043 5.00e-02 4.00e+02 ... (remaining 1786 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 55 2.49 - 3.09: 7753 3.09 - 3.70: 16942 3.70 - 4.30: 22833 4.30 - 4.90: 38468 Nonbonded interactions: 86051 Sorted by model distance: nonbonded pdb=" O CYS B 263 " pdb=" N GLY B 266 " model vdw 1.890 3.120 nonbonded pdb=" CD2 LEU B 113 " pdb=" O TYR B 240 " model vdw 2.001 3.460 nonbonded pdb=" O ILE B 114 " pdb=" CD PRO B 117 " model vdw 2.060 3.440 nonbonded pdb=" ND1 HIS B 163 " pdb=" OE1 GLU B 280 " model vdw 2.106 3.120 nonbonded pdb=" O CYS B 263 " pdb=" CD PRO B 267 " model vdw 2.152 3.440 ... (remaining 86046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 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 : 0.009 0.066 10544 Z= 0.625 Angle : 1.735 14.672 14383 Z= 1.240 Chirality : 0.101 0.589 1672 Planarity : 0.008 0.088 1789 Dihedral : 17.975 83.353 3684 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 3.93 % Allowed : 11.93 % Favored : 84.14 % Rotamer: Outliers : 11.69 % Allowed : 14.66 % Favored : 73.65 % Cbeta Deviations : 1.87 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 3.39 % Twisted General : 0.40 % 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: -1.77 (0.20), residues: 1299 helix: 0.96 (0.15), residues: 745 sheet: -3.87 (0.50), residues: 57 loop : -4.43 (0.20), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 58 HIS 0.011 0.003 HIS A 553 PHE 0.052 0.004 PHE A 302 TYR 0.042 0.004 TYR C 119 ARG 0.006 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 457 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 86 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6137 (mp) REVERT: A 87 THR cc_start: 0.7955 (t) cc_final: 0.7657 (t) REVERT: A 95 MET cc_start: 0.7656 (mmt) cc_final: 0.7334 (mmm) REVERT: A 156 PHE cc_start: 0.7993 (m-80) cc_final: 0.7391 (m-80) REVERT: A 221 MET cc_start: 0.8672 (mmp) cc_final: 0.8414 (mmp) REVERT: A 243 ASN cc_start: 0.7305 (m-40) cc_final: 0.7079 (p0) REVERT: A 326 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6681 (tmm) REVERT: A 426 SER cc_start: 0.8703 (t) cc_final: 0.8398 (m) REVERT: A 443 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5693 (t70) REVERT: A 444 HIS cc_start: 0.8256 (p-80) cc_final: 0.7908 (p90) REVERT: A 454 GLN cc_start: 0.7887 (pt0) cc_final: 0.7630 (mp10) REVERT: A 561 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6619 (p) REVERT: A 575 THR cc_start: 0.8077 (p) cc_final: 0.7794 (p) REVERT: A 622 ARG cc_start: 0.8137 (ptt90) cc_final: 0.7920 (ptp90) REVERT: B 174 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8555 (tt) REVERT: B 203 TRP cc_start: 0.6969 (t-100) cc_final: 0.6732 (t-100) REVERT: B 222 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8709 (tm-30) REVERT: C 62 ARG cc_start: 0.6636 (tpt-90) cc_final: 0.6088 (ptp-110) REVERT: C 174 TRP cc_start: 0.8117 (m-10) cc_final: 0.7534 (m-90) REVERT: C 206 LEU cc_start: 0.8303 (mp) cc_final: 0.8012 (tp) REVERT: C 207 ASN cc_start: 0.7250 (t0) cc_final: 0.6270 (t0) REVERT: C 214 LEU cc_start: 0.8046 (tp) cc_final: 0.7738 (tp) REVERT: C 218 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: C 231 THR cc_start: 0.6993 (p) cc_final: 0.6654 (p) REVERT: C 236 LEU cc_start: 0.7549 (mt) cc_final: 0.7116 (tp) REVERT: C 243 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5244 (mt) REVERT: D 6 VAL cc_start: 0.4617 (t) cc_final: 0.3878 (t) REVERT: D 34 ILE cc_start: 0.8012 (mt) cc_final: 0.7731 (mt) REVERT: D 40 GLU cc_start: 0.8278 (mp0) cc_final: 0.7769 (mp0) REVERT: D 64 PHE cc_start: 0.7213 (t80) cc_final: 0.6985 (t80) REVERT: D 84 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7618 (ttp-170) REVERT: D 94 PHE cc_start: 0.7342 (t80) cc_final: 0.6925 (t80) REVERT: D 95 THR cc_start: 0.7508 (m) cc_final: 0.6675 (t) outliers start: 130 outliers final: 49 residues processed: 525 average time/residue: 0.2081 time to fit residues: 154.8871 Evaluate side-chains 383 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 325 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN A 199 HIS A 313 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 405 ASN B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 171 HIS D 8 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10544 Z= 0.314 Angle : 0.941 13.681 14383 Z= 0.492 Chirality : 0.050 0.217 1672 Planarity : 0.007 0.064 1789 Dihedral : 7.108 43.432 1410 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 1.15 % Allowed : 9.16 % Favored : 89.68 % Rotamer: Outliers : 0.81 % Allowed : 5.22 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 1.69 % Twisted General : 0.40 % 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: -0.62 (0.24), residues: 1299 helix: 1.86 (0.19), residues: 751 sheet: -3.60 (0.38), residues: 98 loop : -3.86 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 247 HIS 0.007 0.002 HIS A 199 PHE 0.054 0.003 PHE C 162 TYR 0.030 0.002 TYR B 466 ARG 0.009 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 439 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8291 (mp0) cc_final: 0.7988 (tm-30) REVERT: A 108 MET cc_start: 0.7984 (tmm) cc_final: 0.7587 (tmm) REVERT: A 184 GLU cc_start: 0.8251 (pp20) cc_final: 0.7834 (pm20) REVERT: A 221 MET cc_start: 0.8491 (mmp) cc_final: 0.8232 (mmp) REVERT: A 333 GLU cc_start: 0.7017 (mp0) cc_final: 0.6512 (mp0) REVERT: A 335 PHE cc_start: 0.8236 (m-80) cc_final: 0.7772 (m-10) REVERT: A 355 GLN cc_start: 0.7738 (mm110) cc_final: 0.7527 (mm-40) REVERT: A 500 GLU cc_start: 0.8612 (tt0) cc_final: 0.8264 (pt0) REVERT: A 501 LEU cc_start: 0.9549 (mm) cc_final: 0.9173 (mm) REVERT: A 555 ILE cc_start: 0.6632 (mp) cc_final: 0.6078 (mt) REVERT: A 574 LEU cc_start: 0.8911 (mp) cc_final: 0.8652 (mp) REVERT: A 595 GLU cc_start: 0.6378 (mm-30) cc_final: 0.6084 (mm-30) REVERT: B 93 MET cc_start: 0.8708 (mmt) cc_final: 0.8484 (mmt) REVERT: B 416 ILE cc_start: 0.8494 (mm) cc_final: 0.8206 (mm) REVERT: B 423 LEU cc_start: 0.7929 (mt) cc_final: 0.7573 (pp) REVERT: C 135 ILE cc_start: 0.7979 (tp) cc_final: 0.7775 (tp) REVERT: C 136 ASN cc_start: 0.7975 (p0) cc_final: 0.7508 (m-40) REVERT: C 137 ILE cc_start: 0.7588 (pt) cc_final: 0.7122 (tt) REVERT: C 140 ASP cc_start: 0.8716 (m-30) cc_final: 0.8166 (m-30) REVERT: C 206 LEU cc_start: 0.8419 (mp) cc_final: 0.8191 (tp) REVERT: D 64 PHE cc_start: 0.7238 (t80) cc_final: 0.6921 (t80) REVERT: D 84 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7511 (ttp-170) REVERT: D 92 LEU cc_start: 0.7753 (pp) cc_final: 0.7307 (pp) REVERT: D 95 THR cc_start: 0.7957 (m) cc_final: 0.7457 (t) outliers start: 9 outliers final: 0 residues processed: 442 average time/residue: 0.1961 time to fit residues: 124.7559 Evaluate side-chains 304 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 606 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 405 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10544 Z= 0.291 Angle : 0.885 13.612 14383 Z= 0.461 Chirality : 0.048 0.221 1672 Planarity : 0.007 0.088 1789 Dihedral : 6.614 38.242 1410 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 1.08 % Allowed : 9.16 % Favored : 89.76 % Rotamer: Outliers : 0.72 % Allowed : 4.41 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.23), residues: 1299 helix: 1.28 (0.19), residues: 750 sheet: -3.05 (0.41), residues: 101 loop : -3.57 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 36 HIS 0.007 0.001 HIS C 171 PHE 0.041 0.003 PHE B 86 TYR 0.040 0.002 TYR B 389 ARG 0.008 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 369 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8486 (mp0) cc_final: 0.8233 (tm-30) REVERT: A 108 MET cc_start: 0.8043 (tmm) cc_final: 0.7738 (tmm) REVERT: A 184 GLU cc_start: 0.8254 (pp20) cc_final: 0.8019 (pm20) REVERT: A 221 MET cc_start: 0.8613 (mmp) cc_final: 0.8380 (mmp) REVERT: A 355 GLN cc_start: 0.7935 (mm110) cc_final: 0.7536 (mm-40) REVERT: A 444 HIS cc_start: 0.8035 (p90) cc_final: 0.7785 (p90) REVERT: A 500 GLU cc_start: 0.8746 (tt0) cc_final: 0.8403 (pt0) REVERT: A 501 LEU cc_start: 0.9517 (mm) cc_final: 0.8992 (mm) REVERT: A 561 THR cc_start: 0.7570 (t) cc_final: 0.7260 (p) REVERT: B 93 MET cc_start: 0.8793 (mmt) cc_final: 0.8589 (mmt) REVERT: B 189 TYR cc_start: 0.8844 (m-10) cc_final: 0.8105 (t80) REVERT: B 222 GLN cc_start: 0.8899 (tm130) cc_final: 0.8605 (tm-30) REVERT: B 399 THR cc_start: 0.7722 (m) cc_final: 0.7464 (p) REVERT: B 423 LEU cc_start: 0.7872 (mt) cc_final: 0.7585 (pp) REVERT: C 87 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8060 (mtp85) REVERT: C 125 PHE cc_start: 0.8400 (m-80) cc_final: 0.8141 (t80) REVERT: C 128 ILE cc_start: 0.8395 (tp) cc_final: 0.8118 (tp) REVERT: C 133 SER cc_start: 0.9266 (t) cc_final: 0.8765 (p) REVERT: C 136 ASN cc_start: 0.7763 (p0) cc_final: 0.7302 (t0) REVERT: C 137 ILE cc_start: 0.7618 (pt) cc_final: 0.7042 (tt) REVERT: C 140 ASP cc_start: 0.8608 (m-30) cc_final: 0.8297 (m-30) REVERT: C 206 LEU cc_start: 0.8469 (mp) cc_final: 0.8254 (tp) REVERT: D 95 THR cc_start: 0.7794 (m) cc_final: 0.7276 (p) outliers start: 8 outliers final: 3 residues processed: 373 average time/residue: 0.1785 time to fit residues: 99.2062 Evaluate side-chains 284 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 281 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 428 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10544 Z= 0.323 Angle : 0.847 13.504 14383 Z= 0.446 Chirality : 0.047 0.246 1672 Planarity : 0.006 0.073 1789 Dihedral : 6.359 35.796 1410 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 1.08 % Allowed : 9.55 % Favored : 89.38 % Rotamer: Outliers : 0.45 % Allowed : 4.41 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.11 (0.23), residues: 1299 helix: 1.00 (0.18), residues: 746 sheet: -2.66 (0.46), residues: 89 loop : -3.38 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 36 HIS 0.009 0.002 HIS C 197 PHE 0.042 0.003 PHE B 86 TYR 0.033 0.002 TYR A 345 ARG 0.009 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 344 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8407 (mp0) cc_final: 0.8153 (tm-30) REVERT: A 83 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8608 (tp-100) REVERT: A 108 MET cc_start: 0.8023 (tmm) cc_final: 0.7710 (tmm) REVERT: A 156 PHE cc_start: 0.7886 (m-80) cc_final: 0.7477 (m-80) REVERT: A 184 GLU cc_start: 0.8274 (pp20) cc_final: 0.8059 (pm20) REVERT: A 221 MET cc_start: 0.8378 (mmp) cc_final: 0.8077 (mmp) REVERT: A 326 MET cc_start: 0.7869 (tmm) cc_final: 0.7618 (tmm) REVERT: A 333 GLU cc_start: 0.7140 (mp0) cc_final: 0.6775 (mp0) REVERT: A 355 GLN cc_start: 0.7789 (mm110) cc_final: 0.7489 (mm-40) REVERT: A 500 GLU cc_start: 0.8723 (tt0) cc_final: 0.8392 (pt0) REVERT: A 501 LEU cc_start: 0.9464 (mm) cc_final: 0.9023 (mm) REVERT: A 555 ILE cc_start: 0.6859 (mt) cc_final: 0.6336 (mp) REVERT: A 616 ARG cc_start: 0.7454 (mpt-90) cc_final: 0.7238 (mmt90) REVERT: B 189 TYR cc_start: 0.8693 (m-10) cc_final: 0.7900 (t80) REVERT: B 222 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8595 (tm-30) REVERT: B 397 SER cc_start: 0.8133 (t) cc_final: 0.7786 (p) REVERT: B 419 CYS cc_start: 0.8885 (p) cc_final: 0.8505 (p) REVERT: B 423 LEU cc_start: 0.7790 (mt) cc_final: 0.7503 (pp) REVERT: C 87 ARG cc_start: 0.8903 (mtp85) cc_final: 0.8663 (mtp85) REVERT: C 133 SER cc_start: 0.9399 (t) cc_final: 0.9167 (p) REVERT: C 140 ASP cc_start: 0.8719 (m-30) cc_final: 0.8456 (m-30) REVERT: C 206 LEU cc_start: 0.8514 (mp) cc_final: 0.8259 (tp) REVERT: D 26 LEU cc_start: 0.7956 (mp) cc_final: 0.7623 (mp) REVERT: D 95 THR cc_start: 0.7459 (m) cc_final: 0.6750 (p) outliers start: 5 outliers final: 0 residues processed: 347 average time/residue: 0.2004 time to fit residues: 107.0431 Evaluate side-chains 270 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 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 63 GLN A 305 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10544 Z= 0.301 Angle : 0.817 12.119 14383 Z= 0.430 Chirality : 0.046 0.283 1672 Planarity : 0.006 0.068 1789 Dihedral : 6.221 33.145 1410 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.85 % Favored : 90.15 % Rotamer: Outliers : 0.36 % Allowed : 3.87 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.09 (0.23), residues: 1299 helix: 0.94 (0.18), residues: 745 sheet: -2.37 (0.47), residues: 90 loop : -3.26 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 247 HIS 0.018 0.002 HIS C 197 PHE 0.040 0.003 PHE B 86 TYR 0.042 0.002 TYR B 389 ARG 0.010 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 338 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8159 (mp0) cc_final: 0.7947 (tm-30) REVERT: A 108 MET cc_start: 0.7974 (tmm) cc_final: 0.7588 (tmm) REVERT: A 156 PHE cc_start: 0.7894 (m-80) cc_final: 0.7477 (m-80) REVERT: A 184 GLU cc_start: 0.8227 (pp20) cc_final: 0.7976 (pm20) REVERT: A 333 GLU cc_start: 0.6860 (mp0) cc_final: 0.6436 (mp0) REVERT: A 355 GLN cc_start: 0.7752 (mm110) cc_final: 0.7500 (mm-40) REVERT: A 444 HIS cc_start: 0.7955 (p90) cc_final: 0.7720 (p90) REVERT: A 500 GLU cc_start: 0.8697 (tt0) cc_final: 0.8379 (pt0) REVERT: A 501 LEU cc_start: 0.9422 (mm) cc_final: 0.8941 (mm) REVERT: A 555 ILE cc_start: 0.6822 (mt) cc_final: 0.6414 (mm) REVERT: B 222 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 397 SER cc_start: 0.8110 (t) cc_final: 0.7764 (p) REVERT: C 87 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8606 (mtp85) REVERT: C 109 ARG cc_start: 0.7304 (tpp-160) cc_final: 0.7005 (mmm160) REVERT: C 140 ASP cc_start: 0.8803 (m-30) cc_final: 0.8565 (m-30) REVERT: C 206 LEU cc_start: 0.8442 (mp) cc_final: 0.8194 (tp) REVERT: D 64 PHE cc_start: 0.7220 (t80) cc_final: 0.6919 (t80) REVERT: D 95 THR cc_start: 0.7026 (m) cc_final: 0.6533 (p) outliers start: 4 outliers final: 0 residues processed: 339 average time/residue: 0.1788 time to fit residues: 90.9108 Evaluate side-chains 270 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 10544 Z= 0.420 Angle : 0.893 13.492 14383 Z= 0.473 Chirality : 0.050 0.271 1672 Planarity : 0.006 0.065 1789 Dihedral : 6.411 32.260 1410 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.70 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.42 (0.22), residues: 1299 helix: 0.67 (0.18), residues: 739 sheet: -2.50 (0.47), residues: 88 loop : -3.35 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 74 HIS 0.014 0.002 HIS C 197 PHE 0.041 0.003 PHE A 218 TYR 0.043 0.003 TYR D 56 ARG 0.009 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8263 (mp0) cc_final: 0.7933 (tm-30) REVERT: A 108 MET cc_start: 0.7880 (tmm) cc_final: 0.7517 (tmm) REVERT: A 213 CYS cc_start: 0.8606 (t) cc_final: 0.8385 (t) REVERT: A 305 GLN cc_start: 0.8820 (tp40) cc_final: 0.8577 (tm-30) REVERT: A 347 MET cc_start: 0.8107 (mmm) cc_final: 0.7603 (tpp) REVERT: A 500 GLU cc_start: 0.8454 (tt0) cc_final: 0.8244 (mt-10) REVERT: B 93 MET cc_start: 0.9354 (mpp) cc_final: 0.9046 (mpp) REVERT: B 135 ASN cc_start: 0.8400 (p0) cc_final: 0.8179 (p0) REVERT: B 222 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8722 (tm-30) REVERT: B 397 SER cc_start: 0.8360 (t) cc_final: 0.7995 (p) REVERT: C 87 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8317 (mtm180) REVERT: C 109 ARG cc_start: 0.7398 (tpp-160) cc_final: 0.7075 (mmm160) REVERT: C 140 ASP cc_start: 0.8761 (m-30) cc_final: 0.8525 (m-30) REVERT: C 180 ASP cc_start: 0.7985 (t0) cc_final: 0.7617 (t0) REVERT: C 206 LEU cc_start: 0.8395 (mp) cc_final: 0.8158 (tp) REVERT: C 231 THR cc_start: 0.7326 (p) cc_final: 0.7023 (p) REVERT: D 26 LEU cc_start: 0.7826 (mp) cc_final: 0.7535 (mp) REVERT: D 74 TRP cc_start: 0.8797 (t-100) cc_final: 0.8541 (t-100) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1712 time to fit residues: 82.6317 Evaluate side-chains 245 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 305 GLN A 428 GLN A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS B 464 GLN C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10544 Z= 0.272 Angle : 0.841 12.782 14383 Z= 0.437 Chirality : 0.048 0.362 1672 Planarity : 0.006 0.089 1789 Dihedral : 6.068 30.963 1410 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.70 % Favored : 90.38 % Rotamer: Outliers : 0.27 % Allowed : 2.34 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.17 (0.23), residues: 1299 helix: 0.76 (0.18), residues: 742 sheet: -2.13 (0.53), residues: 83 loop : -3.14 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 247 HIS 0.007 0.001 HIS C 197 PHE 0.037 0.002 PHE B 86 TYR 0.039 0.002 TYR D 56 ARG 0.010 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 330 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8374 (mp0) cc_final: 0.8033 (tm-30) REVERT: A 108 MET cc_start: 0.7836 (tmm) cc_final: 0.7367 (tmm) REVERT: A 305 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: A 330 PHE cc_start: 0.7496 (m-80) cc_final: 0.7166 (m-80) REVERT: A 347 MET cc_start: 0.8357 (mmm) cc_final: 0.7760 (tpp) REVERT: A 428 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: A 500 GLU cc_start: 0.8527 (tt0) cc_final: 0.8237 (pt0) REVERT: A 501 LEU cc_start: 0.9380 (mt) cc_final: 0.9021 (mt) REVERT: B 135 ASN cc_start: 0.8384 (p0) cc_final: 0.8149 (p0) REVERT: B 222 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8697 (tm-30) REVERT: B 397 SER cc_start: 0.8123 (t) cc_final: 0.7688 (p) REVERT: B 464 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7767 (tp-100) REVERT: C 109 ARG cc_start: 0.7381 (tpp-160) cc_final: 0.7124 (mmm160) REVERT: C 140 ASP cc_start: 0.8763 (m-30) cc_final: 0.8529 (m-30) REVERT: C 156 TYR cc_start: 0.8539 (t80) cc_final: 0.8317 (t80) REVERT: C 206 LEU cc_start: 0.8386 (mp) cc_final: 0.8167 (tp) REVERT: D 74 TRP cc_start: 0.8841 (t-100) cc_final: 0.8570 (t-100) REVERT: D 95 THR cc_start: 0.6299 (p) cc_final: 0.5818 (p) outliers start: 3 outliers final: 0 residues processed: 331 average time/residue: 0.1770 time to fit residues: 86.7678 Evaluate side-chains 271 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 268 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10544 Z= 0.439 Angle : 0.898 12.153 14383 Z= 0.477 Chirality : 0.051 0.282 1672 Planarity : 0.006 0.064 1789 Dihedral : 6.267 33.002 1410 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.39 % Favored : 88.68 % Rotamer: Outliers : 0.09 % Allowed : 1.35 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.37 (0.23), residues: 1299 helix: 0.57 (0.18), residues: 737 sheet: -2.02 (0.49), residues: 94 loop : -3.17 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 36 HIS 0.016 0.002 HIS C 197 PHE 0.042 0.003 PHE A 430 TYR 0.036 0.003 TYR D 56 ARG 0.010 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8400 (mp0) cc_final: 0.8033 (tm-30) REVERT: A 108 MET cc_start: 0.7641 (tmm) cc_final: 0.7400 (tmm) REVERT: A 215 MET cc_start: 0.8021 (ttp) cc_final: 0.7818 (ttp) REVERT: A 257 TRP cc_start: 0.7620 (t60) cc_final: 0.7408 (t60) REVERT: A 500 GLU cc_start: 0.8484 (tt0) cc_final: 0.8244 (mt-10) REVERT: B 93 MET cc_start: 0.9279 (mmp) cc_final: 0.8773 (mmm) REVERT: B 105 PHE cc_start: 0.8163 (t80) cc_final: 0.7945 (t80) REVERT: B 222 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8731 (tm-30) REVERT: B 397 SER cc_start: 0.8361 (t) cc_final: 0.7932 (p) REVERT: B 423 LEU cc_start: 0.8081 (mm) cc_final: 0.7843 (pp) REVERT: C 109 ARG cc_start: 0.7503 (tpp-160) cc_final: 0.7299 (mmm160) REVERT: C 206 LEU cc_start: 0.8347 (mp) cc_final: 0.8099 (tp) REVERT: D 26 LEU cc_start: 0.7799 (mp) cc_final: 0.7475 (mp) REVERT: D 58 TRP cc_start: 0.5813 (t60) cc_final: 0.5448 (t60) REVERT: D 95 THR cc_start: 0.6276 (p) cc_final: 0.5978 (p) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.1727 time to fit residues: 83.1037 Evaluate side-chains 254 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 0.0170 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10544 Z= 0.262 Angle : 0.846 12.876 14383 Z= 0.438 Chirality : 0.048 0.242 1672 Planarity : 0.006 0.064 1789 Dihedral : 5.939 33.116 1410 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.19 (0.23), residues: 1299 helix: 0.71 (0.18), residues: 745 sheet: -1.93 (0.47), residues: 111 loop : -3.17 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 36 HIS 0.014 0.002 HIS C 197 PHE 0.043 0.002 PHE B 86 TYR 0.038 0.002 TYR D 56 ARG 0.006 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8302 (mp0) cc_final: 0.7865 (tm-30) REVERT: A 108 MET cc_start: 0.7669 (tmm) cc_final: 0.7420 (tmm) REVERT: A 253 ASP cc_start: 0.8272 (p0) cc_final: 0.8064 (p0) REVERT: A 254 TYR cc_start: 0.7414 (m-80) cc_final: 0.7197 (m-80) REVERT: A 259 MET cc_start: 0.7531 (tpt) cc_final: 0.7190 (mmm) REVERT: A 310 GLU cc_start: 0.8798 (tp30) cc_final: 0.8495 (tm-30) REVERT: A 347 MET cc_start: 0.8207 (mmm) cc_final: 0.7697 (tpp) REVERT: A 400 THR cc_start: 0.9238 (p) cc_final: 0.8804 (p) REVERT: A 500 GLU cc_start: 0.8400 (tt0) cc_final: 0.8107 (pt0) REVERT: A 501 LEU cc_start: 0.9348 (mt) cc_final: 0.8993 (mt) REVERT: B 93 MET cc_start: 0.9262 (mmp) cc_final: 0.8872 (mmt) REVERT: B 116 THR cc_start: 0.6919 (p) cc_final: 0.6550 (p) REVERT: B 210 MET cc_start: 0.8375 (ppp) cc_final: 0.8141 (mmt) REVERT: B 222 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8687 (tm-30) REVERT: B 397 SER cc_start: 0.8311 (t) cc_final: 0.7886 (p) REVERT: B 423 LEU cc_start: 0.8036 (mm) cc_final: 0.7808 (pp) REVERT: C 109 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.7143 (mmm160) REVERT: C 206 LEU cc_start: 0.8494 (mp) cc_final: 0.8249 (tp) REVERT: D 74 TRP cc_start: 0.8630 (t-100) cc_final: 0.8343 (t-100) REVERT: D 95 THR cc_start: 0.6240 (p) cc_final: 0.5477 (p) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1697 time to fit residues: 86.7093 Evaluate side-chains 271 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.7401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10544 Z= 0.256 Angle : 0.841 11.858 14383 Z= 0.437 Chirality : 0.050 0.602 1672 Planarity : 0.006 0.067 1789 Dihedral : 5.813 33.301 1410 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.85 % Favored : 90.22 % Rotamer: Outliers : 0.09 % Allowed : 0.63 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1299 helix: 0.74 (0.18), residues: 745 sheet: -1.91 (0.48), residues: 111 loop : -3.10 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 247 HIS 0.015 0.002 HIS C 197 PHE 0.044 0.002 PHE B 86 TYR 0.038 0.002 TYR D 56 ARG 0.007 0.001 ARG A 626 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.7940 (m) cc_final: 0.7675 (t) REVERT: A 79 GLU cc_start: 0.8314 (mp0) cc_final: 0.7919 (tm-30) REVERT: A 108 MET cc_start: 0.7966 (tmm) cc_final: 0.7512 (tmm) REVERT: A 257 TRP cc_start: 0.7303 (t60) cc_final: 0.6997 (t60) REVERT: A 310 GLU cc_start: 0.8819 (tp30) cc_final: 0.8511 (tm-30) REVERT: A 347 MET cc_start: 0.8185 (mmm) cc_final: 0.7779 (tpp) REVERT: A 400 THR cc_start: 0.9249 (p) cc_final: 0.8805 (p) REVERT: A 500 GLU cc_start: 0.8407 (tt0) cc_final: 0.8119 (pt0) REVERT: A 501 LEU cc_start: 0.9283 (mt) cc_final: 0.8950 (mt) REVERT: B 93 MET cc_start: 0.9292 (mmp) cc_final: 0.8995 (mmt) REVERT: B 116 THR cc_start: 0.7039 (p) cc_final: 0.6368 (t) REVERT: B 210 MET cc_start: 0.8273 (ppp) cc_final: 0.7979 (mmt) REVERT: B 222 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8601 (tm-30) REVERT: B 383 LEU cc_start: 0.7553 (tp) cc_final: 0.7277 (tp) REVERT: B 397 SER cc_start: 0.8262 (t) cc_final: 0.7826 (p) REVERT: B 423 LEU cc_start: 0.8035 (mm) cc_final: 0.7808 (pp) REVERT: C 53 TRP cc_start: 0.8877 (t60) cc_final: 0.8669 (t60) REVERT: C 109 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.7166 (mmm160) REVERT: C 140 ASP cc_start: 0.8779 (m-30) cc_final: 0.8547 (m-30) REVERT: C 173 PHE cc_start: 0.7743 (m-80) cc_final: 0.7387 (m-80) REVERT: C 180 ASP cc_start: 0.7296 (t0) cc_final: 0.7059 (t0) REVERT: C 206 LEU cc_start: 0.8504 (mp) cc_final: 0.8265 (tp) REVERT: D 74 TRP cc_start: 0.8722 (t-100) cc_final: 0.8469 (t-100) REVERT: D 95 THR cc_start: 0.6063 (p) cc_final: 0.5376 (p) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.1750 time to fit residues: 89.7432 Evaluate side-chains 270 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN B 163 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080704 restraints weight = 38095.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082155 restraints weight = 25560.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083256 restraints weight = 18796.584| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10544 Z= 0.416 Angle : 0.890 11.157 14383 Z= 0.470 Chirality : 0.053 0.580 1672 Planarity : 0.006 0.063 1789 Dihedral : 6.049 34.618 1410 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.70 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.20 (0.23), residues: 1299 helix: 0.70 (0.18), residues: 736 sheet: -2.05 (0.49), residues: 105 loop : -3.04 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 174 HIS 0.009 0.002 HIS C 171 PHE 0.042 0.003 PHE B 86 TYR 0.051 0.003 TYR B 389 ARG 0.010 0.001 ARG A 657 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.20 seconds wall clock time: 43 minutes 42.83 seconds (2622.83 seconds total)