Starting phenix.real_space_refine on Fri Mar 15 01:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/03_2024/5fn2_3237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/03_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_3237/03_2024/5fn2_3237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/03_2024/5fn2_3237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/03_2024/5fn2_3237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/03_2024/5fn2_3237.pdb" } 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 Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.56, per 1000 atoms: 0.54 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 - 3.50 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: 4.12 Conformation dependent library (CDL) restraints added in 1.8 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: 0.94 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: 3.04 Time building geometry restraints manager: 4.45 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: 99.79 - 107.76: 551 107.76 - 115.74: 6692 115.74 - 123.72: 5999 123.72 - 131.69: 1109 131.69 - 139.67: 32 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 2.520 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 2.520 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 ========== 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.870 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.830 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- 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 : 1.170 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: 0.2085 time to fit residues: 155.2459 Evaluate side-chains 383 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 325 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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: 0.9980 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN A 313 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS B 405 ASN B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS D 8 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10544 Z= 0.296 Angle : 0.916 12.802 14383 Z= 0.479 Chirality : 0.049 0.214 1672 Planarity : 0.006 0.066 1789 Dihedral : 7.113 38.054 1410 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 1.23 % Allowed : 9.16 % Favored : 89.61 % Rotamer: Outliers : 0.54 % Allowed : 5.40 % Favored : 94.06 % 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: -0.61 (0.24), residues: 1299 helix: 1.90 (0.19), residues: 751 sheet: -3.59 (0.37), residues: 101 loop : -3.92 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 247 HIS 0.007 0.001 HIS A 199 PHE 0.052 0.003 PHE C 162 TYR 0.023 0.002 TYR C 69 ARG 0.008 0.001 ARG A 281 *********************** 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 440 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 434 time to evaluate : 1.182 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: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6203 (ttm170) cc_final: 0.5833 (ttm170) REVERT: A 79 GLU cc_start: 0.8494 (mp0) cc_final: 0.8259 (tm-30) REVERT: A 108 MET cc_start: 0.7921 (tmm) cc_final: 0.7526 (tmm) REVERT: A 156 PHE cc_start: 0.7991 (m-80) cc_final: 0.7477 (m-80) REVERT: A 184 GLU cc_start: 0.8255 (pp20) cc_final: 0.7856 (pm20) REVERT: A 221 MET cc_start: 0.8432 (mmp) cc_final: 0.8149 (mmp) REVERT: A 253 ASP cc_start: 0.7900 (p0) cc_final: 0.7385 (p0) REVERT: A 333 GLU cc_start: 0.7157 (mp0) cc_final: 0.6937 (mp0) REVERT: A 355 GLN cc_start: 0.7945 (mm110) cc_final: 0.7685 (mm-40) REVERT: A 500 GLU cc_start: 0.8621 (tt0) cc_final: 0.8281 (pt0) REVERT: A 501 LEU cc_start: 0.9561 (mm) cc_final: 0.9185 (mm) REVERT: A 554 TYR cc_start: 0.6638 (t80) cc_final: 0.6239 (t80) REVERT: A 561 THR cc_start: 0.7228 (t) cc_final: 0.6998 (p) REVERT: A 574 LEU cc_start: 0.8898 (mp) cc_final: 0.8644 (mp) REVERT: A 622 ARG cc_start: 0.8009 (ptt90) cc_final: 0.7769 (ptp90) REVERT: B 93 MET cc_start: 0.8689 (mmt) cc_final: 0.8463 (mmt) REVERT: B 142 VAL cc_start: 0.9034 (t) cc_final: 0.8570 (t) REVERT: B 416 ILE cc_start: 0.8448 (mm) cc_final: 0.8091 (mm) REVERT: B 423 LEU cc_start: 0.7928 (mt) cc_final: 0.7572 (pp) REVERT: C 206 LEU cc_start: 0.8406 (mp) cc_final: 0.8178 (tp) REVERT: D 64 PHE cc_start: 0.7244 (t80) cc_final: 0.6925 (t80) REVERT: D 84 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7560 (ttp-170) REVERT: D 92 LEU cc_start: 0.7764 (pp) cc_final: 0.7369 (pp) REVERT: D 95 THR cc_start: 0.7944 (m) cc_final: 0.7540 (p) outliers start: 6 outliers final: 0 residues processed: 436 average time/residue: 0.1983 time to fit residues: 124.4106 Evaluate side-chains 296 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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: 0.7980 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 516 GLN A 606 GLN B 204 ASN B 222 GLN B 405 ASN B 464 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10544 Z= 0.252 Angle : 0.842 12.789 14383 Z= 0.439 Chirality : 0.047 0.213 1672 Planarity : 0.006 0.083 1789 Dihedral : 6.471 33.558 1410 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 1.15 % Allowed : 9.01 % Favored : 89.84 % Rotamer: Outliers : 0.36 % Allowed : 4.59 % Favored : 95.05 % 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: -0.82 (0.24), residues: 1299 helix: 1.44 (0.19), residues: 754 sheet: -3.13 (0.40), residues: 100 loop : -3.59 (0.25), residues: 445 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 0.041 0.003 PHE B 86 TYR 0.042 0.002 TYR B 389 ARG 0.006 0.001 ARG A 652 *********************** 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 386 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 382 time to evaluate : 1.169 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: A 108 MET cc_start: 0.7956 (tmm) cc_final: 0.7750 (tmm) REVERT: A 156 PHE cc_start: 0.7991 (m-80) cc_final: 0.7653 (m-80) REVERT: A 184 GLU cc_start: 0.8373 (pp20) cc_final: 0.8026 (pm20) REVERT: A 221 MET cc_start: 0.8536 (mmp) cc_final: 0.8147 (mmp) REVERT: A 253 ASP cc_start: 0.7638 (p0) cc_final: 0.7220 (p0) REVERT: A 326 MET cc_start: 0.7516 (tpt) cc_final: 0.7219 (tmm) REVERT: A 333 GLU cc_start: 0.7374 (mp0) cc_final: 0.6901 (mp0) REVERT: A 355 GLN cc_start: 0.7941 (mm110) cc_final: 0.7559 (mm-40) REVERT: A 500 GLU cc_start: 0.8617 (tt0) cc_final: 0.8277 (pt0) REVERT: A 501 LEU cc_start: 0.9534 (mm) cc_final: 0.9011 (mm) REVERT: A 561 THR cc_start: 0.7399 (t) cc_final: 0.7133 (p) REVERT: A 622 ARG cc_start: 0.7894 (ptt90) cc_final: 0.7687 (ptp90) REVERT: B 189 TYR cc_start: 0.8798 (m-10) cc_final: 0.8094 (t80) REVERT: B 222 GLN cc_start: 0.8877 (tm130) cc_final: 0.8636 (tm-30) REVERT: B 416 ILE cc_start: 0.8667 (mm) cc_final: 0.8448 (mm) REVERT: B 419 CYS cc_start: 0.8836 (p) cc_final: 0.8625 (p) REVERT: B 423 LEU cc_start: 0.7948 (mt) cc_final: 0.7700 (pp) REVERT: B 439 ILE cc_start: 0.8758 (mt) cc_final: 0.8554 (mt) REVERT: C 87 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8272 (mtp85) REVERT: C 128 ILE cc_start: 0.8395 (tp) cc_final: 0.8166 (tp) REVERT: C 133 SER cc_start: 0.9337 (t) cc_final: 0.9119 (p) REVERT: C 136 ASN cc_start: 0.8045 (p0) cc_final: 0.7782 (p0) REVERT: C 206 LEU cc_start: 0.8467 (mp) cc_final: 0.8240 (tp) REVERT: D 78 PHE cc_start: 0.8408 (t80) cc_final: 0.8193 (t80) REVERT: D 92 LEU cc_start: 0.7667 (pp) cc_final: 0.7205 (pp) REVERT: D 95 THR cc_start: 0.7831 (m) cc_final: 0.6847 (p) outliers start: 4 outliers final: 0 residues processed: 384 average time/residue: 0.1799 time to fit residues: 102.7936 Evaluate side-chains 281 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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: 5.9990 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 573 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 464 GLN ** C 68 GLN ** 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: 0.5847 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10544 Z= 0.307 Angle : 0.829 13.337 14383 Z= 0.434 Chirality : 0.046 0.252 1672 Planarity : 0.006 0.059 1789 Dihedral : 6.273 30.087 1410 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 1.23 % Allowed : 8.78 % Favored : 89.99 % Rotamer: Outliers : 0.27 % Allowed : 3.96 % 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: -0.94 (0.23), residues: 1299 helix: 1.22 (0.19), residues: 746 sheet: -2.70 (0.42), residues: 112 loop : -3.44 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 36 HIS 0.012 0.002 HIS C 171 PHE 0.041 0.003 PHE B 86 TYR 0.035 0.002 TYR A 345 ARG 0.004 0.001 ARG C 87 *********************** 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 347 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.6812 (m-40) cc_final: 0.6522 (m-40) REVERT: A 184 GLU cc_start: 0.8213 (pp20) cc_final: 0.8006 (pm20) REVERT: A 253 ASP cc_start: 0.8123 (p0) cc_final: 0.7915 (p0) REVERT: A 333 GLU cc_start: 0.7200 (mp0) cc_final: 0.6904 (mp0) REVERT: A 355 GLN cc_start: 0.7703 (mm110) cc_final: 0.7466 (mm-40) REVERT: A 500 GLU cc_start: 0.8709 (tt0) cc_final: 0.8385 (pt0) REVERT: A 501 LEU cc_start: 0.9488 (mm) cc_final: 0.9045 (mm) REVERT: A 561 THR cc_start: 0.7553 (t) cc_final: 0.7267 (p) REVERT: B 103 VAL cc_start: 0.8415 (t) cc_final: 0.7553 (t) REVERT: B 184 GLU cc_start: 0.9017 (mp0) cc_final: 0.8773 (tp30) REVERT: B 189 TYR cc_start: 0.8823 (m-10) cc_final: 0.8075 (t80) REVERT: B 214 HIS cc_start: 0.6512 (m-70) cc_final: 0.6275 (m-70) REVERT: B 397 SER cc_start: 0.8201 (t) cc_final: 0.7852 (p) REVERT: C 87 ARG cc_start: 0.8348 (mtp85) cc_final: 0.7922 (mtp85) REVERT: C 133 SER cc_start: 0.9332 (t) cc_final: 0.9102 (p) REVERT: C 171 HIS cc_start: 0.8629 (m-70) cc_final: 0.8350 (m-70) REVERT: C 206 LEU cc_start: 0.8478 (mp) cc_final: 0.8228 (tp) REVERT: D 26 LEU cc_start: 0.7914 (mp) cc_final: 0.7613 (mp) REVERT: D 92 LEU cc_start: 0.7576 (pp) cc_final: 0.7267 (pp) REVERT: D 95 THR cc_start: 0.7148 (m) cc_final: 0.6516 (p) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.1809 time to fit residues: 94.8766 Evaluate side-chains 274 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 379 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.6064 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= 0.284 Angle : 0.792 11.974 14383 Z= 0.416 Chirality : 0.044 0.204 1672 Planarity : 0.005 0.063 1789 Dihedral : 6.122 28.646 1410 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 1.15 % Allowed : 8.78 % Favored : 90.07 % Rotamer: Outliers : 0.45 % Allowed : 3.24 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % 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: -0.98 (0.23), residues: 1299 helix: 1.07 (0.19), residues: 748 sheet: -2.53 (0.43), residues: 112 loop : -3.29 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 36 HIS 0.016 0.002 HIS C 197 PHE 0.040 0.002 PHE B 86 TYR 0.041 0.002 TYR B 389 ARG 0.009 0.001 ARG A 657 *********************** 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 353 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 348 time to evaluate : 1.177 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 34 ASN cc_start: 0.6365 (m-40) cc_final: 0.6097 (m-40) REVERT: A 108 MET cc_start: 0.7996 (tmm) cc_final: 0.7778 (tmm) REVERT: A 184 GLU cc_start: 0.8229 (pp20) cc_final: 0.7977 (pm20) REVERT: A 326 MET cc_start: 0.8100 (tmm) cc_final: 0.7724 (tmm) REVERT: A 328 VAL cc_start: 0.7202 (p) cc_final: 0.6862 (m) REVERT: A 355 GLN cc_start: 0.7705 (mm110) cc_final: 0.7310 (mm-40) REVERT: A 500 GLU cc_start: 0.8660 (tt0) cc_final: 0.8326 (pt0) REVERT: A 501 LEU cc_start: 0.9461 (mm) cc_final: 0.8951 (mm) REVERT: B 93 MET cc_start: 0.9115 (mmp) cc_final: 0.8545 (mmm) REVERT: B 103 VAL cc_start: 0.8581 (t) cc_final: 0.7478 (t) REVERT: B 135 ASN cc_start: 0.8078 (p0) cc_final: 0.7803 (p0) REVERT: B 139 MET cc_start: 0.8401 (mmp) cc_final: 0.8173 (mmm) REVERT: B 184 GLU cc_start: 0.9091 (mp0) cc_final: 0.8891 (tp30) REVERT: B 222 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8740 (tm-30) REVERT: B 253 ILE cc_start: 0.8392 (mt) cc_final: 0.8090 (tp) REVERT: B 257 ASP cc_start: 0.7271 (m-30) cc_final: 0.7027 (m-30) REVERT: B 393 VAL cc_start: 0.8816 (m) cc_final: 0.8506 (p) REVERT: B 397 SER cc_start: 0.8253 (t) cc_final: 0.7741 (p) REVERT: B 439 ILE cc_start: 0.8785 (mt) cc_final: 0.8575 (mt) REVERT: C 87 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8065 (mtp85) REVERT: C 109 ARG cc_start: 0.7321 (tpp-160) cc_final: 0.7025 (mmm160) REVERT: C 133 SER cc_start: 0.9319 (t) cc_final: 0.9098 (p) REVERT: C 206 LEU cc_start: 0.8477 (mp) cc_final: 0.8222 (tp) outliers start: 5 outliers final: 0 residues processed: 350 average time/residue: 0.1746 time to fit residues: 92.5210 Evaluate side-chains 272 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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: 9.9990 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 573 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5886 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10544 Z= 0.320 Angle : 0.810 13.566 14383 Z= 0.425 Chirality : 0.046 0.302 1672 Planarity : 0.006 0.061 1789 Dihedral : 6.127 27.989 1410 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.16 % Favored : 89.92 % Rotamer: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1299 helix: 1.02 (0.19), residues: 742 sheet: -2.45 (0.44), residues: 112 loop : -3.24 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 67 HIS 0.011 0.002 HIS C 197 PHE 0.039 0.003 PHE B 86 TYR 0.038 0.002 TYR D 56 ARG 0.009 0.001 ARG A 432 *********************** 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 325 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 1.069 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 34 ASN cc_start: 0.6426 (m-40) cc_final: 0.6102 (m-40) REVERT: A 184 GLU cc_start: 0.8254 (pp20) cc_final: 0.8001 (pm20) REVERT: A 310 GLU cc_start: 0.9121 (tp30) cc_final: 0.8920 (tp30) REVERT: A 326 MET cc_start: 0.7714 (tmm) cc_final: 0.7495 (tmm) REVERT: A 355 GLN cc_start: 0.8046 (mm110) cc_final: 0.7811 (mm-40) REVERT: B 93 MET cc_start: 0.9123 (mmp) cc_final: 0.8536 (mmt) REVERT: B 223 GLN cc_start: 0.8186 (pm20) cc_final: 0.7961 (pm20) REVERT: B 393 VAL cc_start: 0.8818 (m) cc_final: 0.8519 (p) REVERT: B 397 SER cc_start: 0.8233 (t) cc_final: 0.7753 (p) REVERT: B 423 LEU cc_start: 0.8070 (mm) cc_final: 0.7835 (pp) REVERT: C 109 ARG cc_start: 0.7374 (tpp-160) cc_final: 0.7069 (mmm160) REVERT: C 133 SER cc_start: 0.9231 (t) cc_final: 0.8923 (p) REVERT: C 206 LEU cc_start: 0.8503 (mp) cc_final: 0.8255 (tp) REVERT: D 95 THR cc_start: 0.6299 (p) cc_final: 0.5531 (p) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.1737 time to fit residues: 84.5542 Evaluate side-chains 259 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10544 Z= 0.307 Angle : 0.817 14.551 14383 Z= 0.425 Chirality : 0.047 0.232 1672 Planarity : 0.006 0.064 1789 Dihedral : 6.068 27.136 1410 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.78 % Favored : 90.22 % Rotamer: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1299 helix: 0.95 (0.19), residues: 740 sheet: -2.36 (0.46), residues: 113 loop : -3.24 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 67 HIS 0.011 0.002 HIS C 197 PHE 0.040 0.003 PHE B 86 TYR 0.046 0.002 TYR B 389 ARG 0.005 0.001 ARG B 108 *********************** 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 323 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.6297 (m-40) cc_final: 0.6002 (m-40) REVERT: A 35 SER cc_start: 0.7037 (m) cc_final: 0.6770 (t) REVERT: A 156 PHE cc_start: 0.7990 (m-80) cc_final: 0.7717 (m-80) REVERT: A 184 GLU cc_start: 0.8304 (pp20) cc_final: 0.7991 (pm20) REVERT: A 347 MET cc_start: 0.8203 (mmm) cc_final: 0.7635 (tpp) REVERT: A 655 ASP cc_start: 0.7285 (p0) cc_final: 0.7072 (p0) REVERT: B 93 MET cc_start: 0.9178 (mmp) cc_final: 0.8939 (mmt) REVERT: B 103 VAL cc_start: 0.8583 (t) cc_final: 0.7881 (t) REVERT: B 116 THR cc_start: 0.6253 (p) cc_final: 0.5880 (p) REVERT: B 184 GLU cc_start: 0.8973 (mp0) cc_final: 0.8642 (tp30) REVERT: B 187 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8547 (mtmt) REVERT: B 223 GLN cc_start: 0.8105 (pm20) cc_final: 0.7881 (pm20) REVERT: B 393 VAL cc_start: 0.8849 (m) cc_final: 0.8491 (p) REVERT: B 397 SER cc_start: 0.8273 (t) cc_final: 0.7763 (p) REVERT: B 423 LEU cc_start: 0.8068 (mm) cc_final: 0.7831 (pp) REVERT: B 439 ILE cc_start: 0.8780 (mt) cc_final: 0.8574 (mt) REVERT: C 109 ARG cc_start: 0.7356 (tpp-160) cc_final: 0.7079 (mmm160) REVERT: C 133 SER cc_start: 0.9198 (t) cc_final: 0.8882 (p) REVERT: C 171 HIS cc_start: 0.8616 (m-70) cc_final: 0.8312 (m-70) REVERT: C 206 LEU cc_start: 0.8506 (mp) cc_final: 0.8271 (tp) REVERT: D 26 LEU cc_start: 0.7639 (mp) cc_final: 0.7366 (mp) REVERT: D 95 THR cc_start: 0.6302 (p) cc_final: 0.5656 (p) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.1711 time to fit residues: 83.4420 Evaluate side-chains 270 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 9.9990 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10544 Z= 0.325 Angle : 0.815 13.970 14383 Z= 0.427 Chirality : 0.046 0.277 1672 Planarity : 0.005 0.064 1789 Dihedral : 6.083 26.853 1410 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.47 % Favored : 89.61 % Rotamer: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.23), residues: 1299 helix: 0.88 (0.19), residues: 734 sheet: -2.39 (0.49), residues: 105 loop : -3.22 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 67 HIS 0.012 0.002 HIS C 197 PHE 0.038 0.003 PHE B 86 TYR 0.035 0.002 TYR D 56 ARG 0.006 0.001 ARG A 652 *********************** 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 327 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 326 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.6351 (m-40) cc_final: 0.5922 (m110) REVERT: A 35 SER cc_start: 0.7200 (m) cc_final: 0.6901 (t) REVERT: A 156 PHE cc_start: 0.8056 (m-80) cc_final: 0.7756 (m-80) REVERT: A 184 GLU cc_start: 0.8313 (pp20) cc_final: 0.7997 (pm20) REVERT: A 221 MET cc_start: 0.7806 (mmm) cc_final: 0.7452 (mmt) REVERT: A 335 PHE cc_start: 0.8071 (m-80) cc_final: 0.7826 (m-10) REVERT: A 347 MET cc_start: 0.8295 (mmm) cc_final: 0.7588 (tpp) REVERT: B 93 MET cc_start: 0.9237 (mmp) cc_final: 0.8928 (mmt) REVERT: B 103 VAL cc_start: 0.8613 (t) cc_final: 0.7870 (t) REVERT: B 116 THR cc_start: 0.6140 (p) cc_final: 0.5573 (p) REVERT: B 222 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8746 (tm-30) REVERT: B 393 VAL cc_start: 0.8798 (m) cc_final: 0.8478 (p) REVERT: B 397 SER cc_start: 0.8308 (t) cc_final: 0.7817 (p) REVERT: B 457 MET cc_start: 0.9040 (mmp) cc_final: 0.8825 (mmm) REVERT: C 109 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.7110 (mmm160) REVERT: C 133 SER cc_start: 0.9090 (t) cc_final: 0.8800 (p) REVERT: C 171 HIS cc_start: 0.8572 (m-70) cc_final: 0.8344 (m-70) REVERT: C 206 LEU cc_start: 0.8475 (mp) cc_final: 0.8259 (tp) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.1691 time to fit residues: 83.4928 Evaluate side-chains 267 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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: 0.6980 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 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: 0.5912 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10544 Z= 0.278 Angle : 0.835 15.327 14383 Z= 0.431 Chirality : 0.048 0.373 1672 Planarity : 0.005 0.063 1789 Dihedral : 5.949 25.584 1410 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.70 % Favored : 90.30 % Rotamer: Outliers : 0.09 % Allowed : 1.26 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1299 helix: 0.78 (0.19), residues: 739 sheet: -2.34 (0.48), residues: 104 loop : -3.16 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 247 HIS 0.011 0.001 HIS C 197 PHE 0.045 0.003 PHE B 86 TYR 0.058 0.002 TYR B 389 ARG 0.006 0.001 ARG A 652 *********************** 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 338 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.184 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 35 SER cc_start: 0.6905 (m) cc_final: 0.6614 (t) REVERT: A 46 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7883 (pttp) REVERT: A 108 MET cc_start: 0.8000 (tmm) cc_final: 0.7784 (tmm) REVERT: A 156 PHE cc_start: 0.8052 (m-80) cc_final: 0.7748 (m-80) REVERT: A 221 MET cc_start: 0.7713 (mmm) cc_final: 0.7396 (mmt) REVERT: A 310 GLU cc_start: 0.8892 (tp30) cc_final: 0.8640 (tm-30) REVERT: A 335 PHE cc_start: 0.8045 (m-80) cc_final: 0.7831 (m-10) REVERT: A 347 MET cc_start: 0.8215 (mmm) cc_final: 0.7673 (tpp) REVERT: A 655 ASP cc_start: 0.7325 (p0) cc_final: 0.7045 (p0) REVERT: B 93 MET cc_start: 0.9279 (mmp) cc_final: 0.8987 (mmt) REVERT: B 103 VAL cc_start: 0.8393 (t) cc_final: 0.7684 (t) REVERT: B 116 THR cc_start: 0.6852 (p) cc_final: 0.5974 (t) REVERT: B 135 ASN cc_start: 0.8035 (p0) cc_final: 0.7539 (p0) REVERT: B 222 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8676 (tm-30) REVERT: B 393 VAL cc_start: 0.8808 (m) cc_final: 0.8458 (p) REVERT: B 397 SER cc_start: 0.8315 (t) cc_final: 0.7786 (p) REVERT: B 423 LEU cc_start: 0.8101 (mm) cc_final: 0.7890 (pp) REVERT: B 439 ILE cc_start: 0.8773 (mt) cc_final: 0.8549 (mt) REVERT: C 109 ARG cc_start: 0.7366 (tpp-160) cc_final: 0.7134 (mmm160) REVERT: C 171 HIS cc_start: 0.8547 (m-70) cc_final: 0.8313 (m-70) REVERT: C 180 ASP cc_start: 0.7571 (t0) cc_final: 0.7258 (t0) REVERT: C 206 LEU cc_start: 0.8510 (mp) cc_final: 0.8254 (tp) REVERT: D 26 LEU cc_start: 0.7474 (mp) cc_final: 0.7079 (mp) REVERT: D 95 THR cc_start: 0.6094 (p) cc_final: 0.5263 (p) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.1670 time to fit residues: 85.0493 Evaluate side-chains 276 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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: 2.9990 chunk 58 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 573 ASN B 163 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5924 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10544 Z= 0.289 Angle : 0.820 10.279 14383 Z= 0.428 Chirality : 0.049 0.457 1672 Planarity : 0.005 0.063 1789 Dihedral : 5.971 29.805 1410 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.08 % Favored : 89.99 % Rotamer: Outliers : 0.18 % Allowed : 0.27 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1299 helix: 0.69 (0.19), residues: 743 sheet: -2.15 (0.48), residues: 102 loop : -3.11 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP D 36 HIS 0.013 0.001 HIS C 197 PHE 0.044 0.002 PHE B 86 TYR 0.038 0.002 TYR D 56 ARG 0.009 0.001 ARG A 652 ********************** 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 327 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 325 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 PHE cc_start: 0.8097 (m-80) cc_final: 0.7851 (m-80) REVERT: A 221 MET cc_start: 0.7669 (mmm) cc_final: 0.7375 (mmt) REVERT: A 253 ASP cc_start: 0.7144 (p0) cc_final: 0.6906 (p0) REVERT: A 257 TRP cc_start: 0.7071 (t60) cc_final: 0.6771 (t60) REVERT: A 310 GLU cc_start: 0.8897 (tp30) cc_final: 0.8656 (tm-30) REVERT: A 347 MET cc_start: 0.8239 (mmm) cc_final: 0.7725 (tpp) REVERT: A 564 THR cc_start: 0.8295 (m) cc_final: 0.8066 (m) REVERT: B 93 MET cc_start: 0.9249 (mmp) cc_final: 0.8948 (mmt) REVERT: B 103 VAL cc_start: 0.8347 (t) cc_final: 0.7998 (t) REVERT: B 167 ILE cc_start: 0.8034 (pt) cc_final: 0.7798 (pt) REVERT: B 222 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8673 (tm-30) REVERT: B 393 VAL cc_start: 0.8782 (m) cc_final: 0.8422 (p) REVERT: B 397 SER cc_start: 0.8307 (t) cc_final: 0.7777 (p) REVERT: B 423 LEU cc_start: 0.8102 (mm) cc_final: 0.7892 (pp) REVERT: B 439 ILE cc_start: 0.8624 (mt) cc_final: 0.8407 (mt) REVERT: B 464 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7701 (tp-100) REVERT: C 109 ARG cc_start: 0.7375 (tpp-160) cc_final: 0.7144 (mmm160) REVERT: C 171 HIS cc_start: 0.8482 (m-70) cc_final: 0.8239 (m-70) REVERT: C 180 ASP cc_start: 0.7533 (t0) cc_final: 0.7075 (t0) REVERT: C 206 LEU cc_start: 0.8487 (mp) cc_final: 0.8266 (tp) REVERT: C 231 THR cc_start: 0.7481 (p) cc_final: 0.7179 (p) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.1756 time to fit residues: 87.4193 Evaluate side-chains 263 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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: 4.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 0.0370 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 305 GLN A 573 ASN B 163 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.095851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085184 restraints weight = 36665.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086864 restraints weight = 24313.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088162 restraints weight = 17674.252| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10544 Z= 0.259 Angle : 0.819 11.737 14383 Z= 0.423 Chirality : 0.047 0.313 1672 Planarity : 0.005 0.061 1789 Dihedral : 5.848 31.206 1410 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.47 % Favored : 90.61 % Rotamer: Outliers : 0.18 % Allowed : 0.90 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.40 % 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 (0.19), residues: 733 sheet: -2.10 (0.48), residues: 102 loop : -3.06 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 36 HIS 0.013 0.001 HIS C 197 PHE 0.045 0.002 PHE B 86 TYR 0.057 0.002 TYR B 389 ARG 0.007 0.001 ARG A 657 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.64 seconds wall clock time: 44 minutes 6.08 seconds (2646.08 seconds total)