Starting phenix.real_space_refine (version: dev) on Sun Feb 19 14:59:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/02_2023/5fn2_3237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/02_2023/5fn2_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_3237/02_2023/5fn2_3237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/02_2023/5fn2_3237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/02_2023/5fn2_3237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn2_3237/02_2023/5fn2_3237.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 5.94, 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 - 3.50 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: 4.10 Conformation dependent library (CDL) restraints added in 1.4 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: 0.48 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: 3.17 Time building geometry restraints manager: 4.42 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 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. 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: 0.260 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: 2.350 Check model and map are aligned: 0.140 Process input model: 29.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 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 : 1.733 14.672 14383 Z= 1.239 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 % 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 *********************** 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 : 1.245 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 outliers start: 130 outliers final: 49 residues processed: 525 average time/residue: 0.2114 time to fit residues: 157.2195 Evaluate side-chains 364 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 315 time to evaluate : 1.147 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 49 outliers final: 2 residues processed: 49 average time/residue: 0.1037 time to fit residues: 11.1377 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** 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 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS B 222 GLN B 405 ASN B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 207 ASN D 8 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 10544 Z= 0.306 Angle : 0.951 19.241 14383 Z= 0.484 Chirality : 0.050 0.243 1672 Planarity : 0.006 0.064 1789 Dihedral : 7.106 37.374 1410 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 1.23 % Allowed : 8.55 % Favored : 90.22 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.48 % Twisted Proline : 1.69 % Twisted General : 0.32 % 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: -0.68 (0.24), residues: 1299 helix: 1.83 (0.19), residues: 750 sheet: -3.60 (0.36), residues: 103 loop : -3.91 (0.24), residues: 446 *********************** 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 435 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 424 time to evaluate : 1.292 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 outliers start: 11 outliers final: 1 residues processed: 428 average time/residue: 0.1974 time to fit residues: 123.8956 Evaluate side-chains 287 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0995 time to fit residues: 1.7402 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 428 GLN A 478 ASN A 516 GLN A 562 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 10544 Z= 0.297 Angle : 0.895 18.125 14383 Z= 0.452 Chirality : 0.048 0.233 1672 Planarity : 0.006 0.076 1789 Dihedral : 6.586 35.059 1410 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 1.15 % Allowed : 9.93 % Favored : 88.91 % Rotamer Outliers : 0.45 % 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: -0.81 (0.24), residues: 1299 helix: 1.44 (0.19), residues: 751 sheet: -3.03 (0.39), residues: 100 loop : -3.57 (0.25), residues: 448 *********************** 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 371 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 366 time to evaluate : 1.335 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 outliers start: 5 outliers final: 1 residues processed: 368 average time/residue: 0.1867 time to fit residues: 102.7472 Evaluate side-chains 274 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0950 time to fit residues: 1.7698 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 10544 Z= 0.273 Angle : 0.856 19.373 14383 Z= 0.429 Chirality : 0.047 0.262 1672 Planarity : 0.006 0.075 1789 Dihedral : 6.313 32.360 1410 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 1.08 % Allowed : 9.39 % Favored : 89.53 % Rotamer Outliers : 0.36 % 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: -0.92 (0.23), residues: 1299 helix: 1.24 (0.19), residues: 745 sheet: -2.85 (0.41), residues: 97 loop : -3.40 (0.26), residues: 457 *********************** 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 351 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 349 average time/residue: 0.1853 time to fit residues: 96.5776 Evaluate side-chains 268 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4836 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** 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 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 moved from start: 0.6163 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= 0.312 Angle : 0.844 18.670 14383 Z= 0.428 Chirality : 0.047 0.252 1672 Planarity : 0.006 0.073 1789 Dihedral : 6.259 30.087 1410 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 1.08 % Allowed : 9.47 % Favored : 89.45 % Rotamer Outliers : 0.27 % 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: -1.08 (0.23), residues: 1299 helix: 1.05 (0.19), residues: 745 sheet: -2.75 (0.45), residues: 92 loop : -3.38 (0.25), residues: 462 *********************** 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 336 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 334 average time/residue: 0.1816 time to fit residues: 91.5374 Evaluate side-chains 253 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1410 time to fit residues: 1.9421 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** B 214 HIS ** 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 ** 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: 0.5731 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 10544 Z= 0.479 Angle : 0.933 20.052 14383 Z= 0.480 Chirality : 0.050 0.320 1672 Planarity : 0.006 0.073 1789 Dihedral : 6.605 29.988 1410 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 28.99 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.47 % Favored : 88.61 % Rotamer Outliers : 0.09 % 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: -1.51 (0.22), residues: 1299 helix: 0.57 (0.18), residues: 737 sheet: -2.50 (0.47), residues: 93 loop : -3.34 (0.25), residues: 469 *********************** 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 316 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 1.275 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 outliers start: 1 outliers final: 1 residues processed: 316 average time/residue: 0.1925 time to fit residues: 91.7814 Evaluate side-chains 238 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1445 time to fit residues: 1.8511 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 125 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 10544 Z= 0.253 Angle : 0.851 19.744 14383 Z= 0.425 Chirality : 0.046 0.227 1672 Planarity : 0.005 0.078 1789 Dihedral : 6.108 29.420 1410 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.77 % Allowed : 8.93 % Favored : 90.30 % Rotamer Outliers : 0.09 % 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: -1.15 (0.23), residues: 1299 helix: 0.86 (0.19), residues: 731 sheet: -1.91 (0.50), residues: 97 loop : -3.24 (0.25), residues: 471 *********************** 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 341 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.1813 time to fit residues: 92.1818 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4652 ------------------------------------------------------------------------------- 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: 1.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 10544 Z= 0.273 Angle : 0.844 19.117 14383 Z= 0.425 Chirality : 0.047 0.267 1672 Planarity : 0.005 0.083 1789 Dihedral : 6.058 29.031 1410 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.78 % Favored : 89.38 % Rotamer Outliers : 0.00 % 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: -1.21 (0.23), residues: 1299 helix: 0.74 (0.19), residues: 733 sheet: -2.07 (0.48), residues: 101 loop : -3.13 (0.26), residues: 465 *********************** 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 326 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1846 time to fit residues: 90.7846 Evaluate side-chains 254 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5006 ------------------------------------------------------------------------------- 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: 0.9980 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** 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 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 10544 Z= 0.238 Angle : 0.856 18.732 14383 Z= 0.427 Chirality : 0.047 0.378 1672 Planarity : 0.005 0.085 1789 Dihedral : 5.944 28.764 1410 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.62 % Favored : 90.38 % Rotamer Outliers : 0.00 % 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: 0.73 (0.19), residues: 738 sheet: -1.82 (0.46), residues: 107 loop : -3.14 (0.27), residues: 454 *********************** 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 327 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1759 time to fit residues: 87.5733 Evaluate side-chains 260 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6747 ------------------------------------------------------------------------------- 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: 0.9990 chunk 58 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.7430 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= 0.268 Angle : 0.860 19.681 14383 Z= 0.433 Chirality : 0.048 0.320 1672 Planarity : 0.006 0.084 1789 Dihedral : 5.898 28.931 1410 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.39 % Favored : 89.61 % Rotamer Outliers : 0.00 % 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: -1.13 (0.23), residues: 1299 helix: 0.74 (0.19), residues: 736 sheet: -1.64 (0.50), residues: 94 loop : -3.08 (0.26), residues: 469 ********************** 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 310 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.283 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 outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1827 time to fit residues: 86.0121 Evaluate side-chains 259 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5189 ------------------------------------------------------------------------------- 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: 0.9980 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 0.2980 chunk 106 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083434 restraints weight = 36829.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.085634 restraints weight = 21644.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087200 restraints weight = 14572.281| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10544 Z= 0.270 Angle : 0.855 19.148 14383 Z= 0.428 Chirality : 0.047 0.268 1672 Planarity : 0.006 0.085 1789 Dihedral : 5.839 29.415 1410 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.16 % Favored : 89.99 % Rotamer Outliers : 0.00 % 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: -1.00 (0.23), residues: 1299 helix: 0.78 (0.19), residues: 729 sheet: -1.56 (0.50), residues: 94 loop : -2.85 (0.27), residues: 476 =============================================================================== Job complete usr+sys time: 2340.62 seconds wall clock time: 43 minutes 50.87 seconds (2630.87 seconds total)