Starting phenix.real_space_refine on Fri Mar 15 12:56:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/03_2024/7udc_26456.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/03_2024/7udc_26456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/03_2024/7udc_26456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/03_2024/7udc_26456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/03_2024/7udc_26456.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udc_26456/03_2024/7udc_26456.pdb" } resolution = 3.7 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 Anisotropic ADP refinement not supported. Converting 5307 atoms to isotropic. 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 35 5.16 5 C 4030 2.51 5 N 1092 2.21 5 O 1268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6425 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4331 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 27, 'TRANS': 514} Chain breaks: 3 Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1716 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Time building chain proxies: 3.78, per 1000 atoms: 0.59 Number of scatterers: 6425 At special positions: 0 Unit cell: (92.88, 109.08, 91.8, 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 35 16.00 O 1268 8.00 N 1092 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS C 36 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.3 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.631A pdb=" N CYS A 44 " --> pdb=" O MET A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.942A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.347A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.745A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 183 removed outlier: 3.581A pdb=" N THR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 179 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.816A pdb=" N ILE A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 313 removed outlier: 4.065A pdb=" N SER A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLN A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 359 Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 361 through 375 removed outlier: 3.893A pdb=" N ASP A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Proline residue: A 392 - end of helix removed outlier: 3.529A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.741A pdb=" N TYR A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 436 through 443 removed outlier: 4.304A pdb=" N ILE A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.848A pdb=" N ASP A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.958A pdb=" N ARG A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.708A pdb=" N LEU A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 28 through 64 Processing helix chain 'B' and resid 68 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.132A pdb=" N ASN B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 149 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 204 through 221 removed outlier: 3.849A pdb=" N GLU B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 228 through 231 removed outlier: 3.756A pdb=" N ASP B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 73 removed outlier: 4.112A pdb=" N GLU C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 removed outlier: 4.021A pdb=" N PHE C 77 " --> pdb=" O ALA C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60 removed outlier: 6.050A pdb=" N LYS A 29 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 57 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 30 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 76 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 32 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 73 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 105 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR A 75 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 102 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR A 129 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.659A pdb=" N TYR A 145 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 537 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY A 568 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 539 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 229 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 266 353 hydrogen bonds defined for protein. 1050 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: 1.59 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2154 1.34 - 1.46: 1282 1.46 - 1.58: 3018 1.58 - 1.70: 1 1.70 - 1.82: 61 Bond restraints: 6516 Sorted by residual: bond pdb=" CB PRO A 223 " pdb=" CG PRO A 223 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.32e+00 bond pdb=" N PRO A 433 " pdb=" CA PRO A 433 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.11e-01 bond pdb=" CB ASP C 65 " pdb=" CG ASP C 65 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.54e-01 bond pdb=" CA THR B 23 " pdb=" CB THR B 23 " ideal model delta sigma weight residual 1.529 1.540 -0.011 1.62e-02 3.81e+03 4.97e-01 bond pdb=" CA THR B 161 " pdb=" CB THR B 161 " ideal model delta sigma weight residual 1.540 1.521 0.019 2.70e-02 1.37e+03 4.82e-01 ... (remaining 6511 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.42: 159 106.42 - 113.32: 3647 113.32 - 120.22: 2280 120.22 - 127.13: 2642 127.13 - 134.03: 48 Bond angle restraints: 8776 Sorted by residual: angle pdb=" CA PRO A 223 " pdb=" N PRO A 223 " pdb=" CD PRO A 223 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 angle pdb=" CB MET A 374 " pdb=" CG MET A 374 " pdb=" SD MET A 374 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" N GLU B 73 " pdb=" CA GLU B 73 " pdb=" CB GLU B 73 " ideal model delta sigma weight residual 110.28 114.20 -3.92 1.55e+00 4.16e-01 6.39e+00 angle pdb=" C ARG A 275 " pdb=" N VAL A 276 " pdb=" CA VAL A 276 " ideal model delta sigma weight residual 121.97 126.52 -4.55 1.80e+00 3.09e-01 6.38e+00 angle pdb=" N PRO A 223 " pdb=" CD PRO A 223 " pdb=" CG PRO A 223 " ideal model delta sigma weight residual 103.20 99.51 3.69 1.50e+00 4.44e-01 6.04e+00 ... (remaining 8771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3646 17.89 - 35.78: 349 35.78 - 53.66: 67 53.66 - 71.55: 18 71.55 - 89.44: 5 Dihedral angle restraints: 4085 sinusoidal: 1702 harmonic: 2383 Sorted by residual: dihedral pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " pdb=" CD GLU A 66 " pdb=" OE1 GLU A 66 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN B 50 " pdb=" CB ASN B 50 " pdb=" CG ASN B 50 " pdb=" OD1 ASN B 50 " ideal model delta sinusoidal sigma weight residual -90.00 -153.56 63.56 2 2.00e+01 2.50e-03 9.62e+00 dihedral pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " pdb=" OD1 ASP B 27 " ideal model delta sinusoidal sigma weight residual -30.00 -83.15 53.15 1 2.00e+01 2.50e-03 9.61e+00 ... (remaining 4082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 678 0.032 - 0.064: 225 0.064 - 0.096: 76 0.096 - 0.127: 22 0.127 - 0.159: 5 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA PRO A 223 " pdb=" N PRO A 223 " pdb=" C PRO A 223 " pdb=" CB PRO A 223 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA GLU B 73 " pdb=" N GLU B 73 " pdb=" C GLU B 73 " pdb=" CB GLU B 73 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1003 not shown) Planarity restraints: 1129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 222 " -0.065 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO A 223 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 369 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLU A 369 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU A 369 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 370 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 78 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 79 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.022 5.00e-02 4.00e+02 ... (remaining 1126 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 512 2.74 - 3.28: 6563 3.28 - 3.82: 10244 3.82 - 4.36: 11465 4.36 - 4.90: 20211 Nonbonded interactions: 48995 Sorted by model distance: nonbonded pdb=" NZ LYS A 29 " pdb=" OE1 GLU A 72 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR A 75 " pdb=" OD2 ASP A 90 " model vdw 2.285 2.440 nonbonded pdb=" O GLN A 175 " pdb=" OG1 THR A 178 " model vdw 2.286 2.440 nonbonded pdb=" NH1 ARG A 464 " pdb=" OD2 ASP A 484 " model vdw 2.307 2.520 nonbonded pdb=" OD1 ASN A 442 " pdb=" ND2 ASN A 586 " model vdw 2.316 2.520 ... (remaining 48990 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 1.540 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.260 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.003 0.126 6516 Z= 0.188 Angle : 0.539 8.760 8776 Z= 0.296 Chirality : 0.038 0.159 1006 Planarity : 0.004 0.096 1129 Dihedral : 14.902 89.440 2522 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.31), residues: 788 helix: 2.44 (0.25), residues: 447 sheet: 0.47 (0.78), residues: 54 loop : -0.74 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 563 HIS 0.007 0.001 HIS B 213 PHE 0.017 0.001 PHE B 33 TYR 0.013 0.001 TYR A 531 ARG 0.003 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.8709 (tpp) cc_final: 0.8468 (tpp) REVERT: B 45 ASP cc_start: 0.8487 (t0) cc_final: 0.7605 (t0) REVERT: B 98 GLN cc_start: 0.8250 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 141 TYR cc_start: 0.9249 (t80) cc_final: 0.9010 (t80) REVERT: C 62 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8241 (tm-30) outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.1606 time to fit residues: 30.4352 Evaluate side-chains 107 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6516 Z= 0.256 Angle : 0.518 6.753 8776 Z= 0.273 Chirality : 0.040 0.144 1006 Planarity : 0.004 0.042 1129 Dihedral : 3.591 14.619 864 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.81 % Allowed : 8.89 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.31), residues: 788 helix: 2.47 (0.25), residues: 453 sheet: 0.57 (0.78), residues: 54 loop : -0.83 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.004 0.001 HIS A 347 PHE 0.012 0.001 PHE B 127 TYR 0.018 0.001 TYR B 243 ARG 0.004 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 305 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7919 (tmm-80) REVERT: A 355 MET cc_start: 0.8980 (tpp) cc_final: 0.8766 (mmm) REVERT: A 387 MET cc_start: 0.8603 (mmm) cc_final: 0.8263 (mmm) REVERT: A 428 GLN cc_start: 0.8822 (tp40) cc_final: 0.8405 (tp-100) REVERT: B 30 MET cc_start: 0.7104 (tpp) cc_final: 0.6702 (tpp) REVERT: B 45 ASP cc_start: 0.8473 (t0) cc_final: 0.7573 (t0) REVERT: B 77 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 98 GLN cc_start: 0.8247 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 141 TYR cc_start: 0.9283 (t80) cc_final: 0.8754 (t80) REVERT: C 62 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8576 (tm-30) outliers start: 13 outliers final: 9 residues processed: 129 average time/residue: 0.1724 time to fit residues: 29.8782 Evaluate side-chains 120 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 77 optimal weight: 0.3980 chunk 64 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6516 Z= 0.141 Angle : 0.470 7.285 8776 Z= 0.245 Chirality : 0.037 0.144 1006 Planarity : 0.003 0.039 1129 Dihedral : 3.435 12.617 864 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.11 % Allowed : 12.50 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.30), residues: 788 helix: 2.66 (0.24), residues: 453 sheet: 0.68 (0.77), residues: 55 loop : -0.84 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 563 HIS 0.003 0.000 HIS B 239 PHE 0.007 0.001 PHE B 33 TYR 0.022 0.001 TYR B 243 ARG 0.006 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8245 (pt) cc_final: 0.8043 (pt) REVERT: A 305 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7937 (tmm-80) REVERT: A 387 MET cc_start: 0.8630 (mmm) cc_final: 0.8285 (mmm) REVERT: A 407 ILE cc_start: 0.9280 (tt) cc_final: 0.9021 (mt) REVERT: A 428 GLN cc_start: 0.8879 (tp40) cc_final: 0.8525 (tp-100) REVERT: B 45 ASP cc_start: 0.8486 (t0) cc_final: 0.7579 (t0) REVERT: B 77 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 62 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8501 (tm-30) outliers start: 8 outliers final: 7 residues processed: 122 average time/residue: 0.1801 time to fit residues: 29.5578 Evaluate side-chains 116 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6516 Z= 0.194 Angle : 0.483 9.470 8776 Z= 0.249 Chirality : 0.039 0.142 1006 Planarity : 0.003 0.037 1129 Dihedral : 3.432 14.154 864 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 13.61 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.30), residues: 788 helix: 2.74 (0.24), residues: 453 sheet: 0.51 (0.77), residues: 54 loop : -0.84 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 288 HIS 0.004 0.001 HIS A 347 PHE 0.013 0.001 PHE B 127 TYR 0.024 0.001 TYR B 243 ARG 0.008 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.784 Fit side-chains REVERT: A 163 GLN cc_start: 0.8056 (mm110) cc_final: 0.7835 (mp10) REVERT: A 276 VAL cc_start: 0.9270 (m) cc_final: 0.8820 (p) REVERT: A 305 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7985 (tmm-80) REVERT: A 374 MET cc_start: 0.8967 (mmm) cc_final: 0.8738 (mmm) REVERT: A 387 MET cc_start: 0.8611 (mmm) cc_final: 0.8273 (mmm) REVERT: A 407 ILE cc_start: 0.9301 (tt) cc_final: 0.9098 (tt) REVERT: A 550 MET cc_start: 0.8695 (ttm) cc_final: 0.8351 (mtp) REVERT: A 579 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8049 (mm) REVERT: B 45 ASP cc_start: 0.8510 (t0) cc_final: 0.7588 (t0) REVERT: B 77 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8121 (tm-30) REVERT: B 98 GLN cc_start: 0.8250 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 131 MET cc_start: 0.8832 (tpp) cc_final: 0.8153 (mpp) outliers start: 11 outliers final: 8 residues processed: 121 average time/residue: 0.1665 time to fit residues: 27.6277 Evaluate side-chains 117 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6516 Z= 0.178 Angle : 0.480 9.461 8776 Z= 0.245 Chirality : 0.038 0.143 1006 Planarity : 0.003 0.037 1129 Dihedral : 3.401 13.857 864 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.94 % Allowed : 13.47 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 788 helix: 2.78 (0.24), residues: 454 sheet: 0.49 (0.77), residues: 54 loop : -0.85 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 288 HIS 0.006 0.001 HIS B 58 PHE 0.009 0.001 PHE B 127 TYR 0.024 0.001 TYR B 243 ARG 0.005 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.767 Fit side-chains REVERT: A 163 GLN cc_start: 0.8090 (mm110) cc_final: 0.7850 (mp10) REVERT: A 276 VAL cc_start: 0.9258 (m) cc_final: 0.8804 (p) REVERT: A 305 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7981 (tmm-80) REVERT: A 374 MET cc_start: 0.8977 (mmm) cc_final: 0.8764 (mmm) REVERT: A 387 MET cc_start: 0.8633 (mmm) cc_final: 0.8288 (mmm) REVERT: A 407 ILE cc_start: 0.9316 (tt) cc_final: 0.9107 (tt) REVERT: A 429 HIS cc_start: 0.8483 (t-170) cc_final: 0.8107 (t70) REVERT: A 550 MET cc_start: 0.8700 (ttm) cc_final: 0.8479 (mtp) REVERT: A 579 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8035 (mm) REVERT: B 45 ASP cc_start: 0.8501 (t0) cc_final: 0.7596 (t0) REVERT: B 77 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 98 GLN cc_start: 0.8230 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 138 GLN cc_start: 0.9286 (mt0) cc_final: 0.9076 (tt0) outliers start: 14 outliers final: 9 residues processed: 125 average time/residue: 0.1644 time to fit residues: 28.0090 Evaluate side-chains 122 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6516 Z= 0.170 Angle : 0.480 8.635 8776 Z= 0.245 Chirality : 0.038 0.142 1006 Planarity : 0.003 0.037 1129 Dihedral : 3.382 13.722 864 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.81 % Allowed : 14.44 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.30), residues: 788 helix: 2.73 (0.24), residues: 454 sheet: 0.51 (0.77), residues: 54 loop : -0.89 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 563 HIS 0.003 0.001 HIS B 58 PHE 0.020 0.001 PHE B 127 TYR 0.026 0.001 TYR B 243 ARG 0.004 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.735 Fit side-chains REVERT: A 163 GLN cc_start: 0.8158 (mm110) cc_final: 0.7880 (mp10) REVERT: A 238 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 276 VAL cc_start: 0.9265 (m) cc_final: 0.8814 (p) REVERT: A 305 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7761 (tmm-80) REVERT: A 387 MET cc_start: 0.8631 (mmm) cc_final: 0.8264 (mmm) REVERT: A 407 ILE cc_start: 0.9327 (tt) cc_final: 0.9107 (tt) REVERT: A 429 HIS cc_start: 0.8458 (t-170) cc_final: 0.8042 (t70) REVERT: A 550 MET cc_start: 0.8691 (ttm) cc_final: 0.8487 (mtp) REVERT: B 30 MET cc_start: 0.7101 (tpp) cc_final: 0.6808 (tpp) REVERT: B 77 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 138 GLN cc_start: 0.9274 (mt0) cc_final: 0.9071 (tt0) REVERT: B 141 TYR cc_start: 0.9358 (t80) cc_final: 0.8903 (t80) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.1569 time to fit residues: 26.8536 Evaluate side-chains 123 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6516 Z= 0.173 Angle : 0.484 8.079 8776 Z= 0.246 Chirality : 0.038 0.144 1006 Planarity : 0.003 0.038 1129 Dihedral : 3.359 13.974 864 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 15.42 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.30), residues: 788 helix: 2.76 (0.24), residues: 455 sheet: 0.48 (0.76), residues: 54 loop : -0.87 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 563 HIS 0.004 0.001 HIS B 58 PHE 0.029 0.001 PHE B 127 TYR 0.025 0.001 TYR B 243 ARG 0.003 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.755 Fit side-chains REVERT: A 163 GLN cc_start: 0.8190 (mm110) cc_final: 0.7902 (mp10) REVERT: A 238 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8272 (t0) REVERT: A 276 VAL cc_start: 0.9259 (m) cc_final: 0.8803 (p) REVERT: A 305 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7810 (tmm-80) REVERT: A 387 MET cc_start: 0.8629 (mmm) cc_final: 0.8271 (mmm) REVERT: A 407 ILE cc_start: 0.9340 (tt) cc_final: 0.9110 (tt) REVERT: A 429 HIS cc_start: 0.8442 (t-170) cc_final: 0.8038 (t70) REVERT: B 30 MET cc_start: 0.7061 (tpp) cc_final: 0.6736 (tpp) REVERT: B 77 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 141 TYR cc_start: 0.9386 (t80) cc_final: 0.8979 (t80) REVERT: B 148 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7723 (ptp-110) outliers start: 11 outliers final: 8 residues processed: 122 average time/residue: 0.1571 time to fit residues: 26.4419 Evaluate side-chains 122 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6516 Z= 0.187 Angle : 0.486 8.058 8776 Z= 0.249 Chirality : 0.038 0.142 1006 Planarity : 0.003 0.038 1129 Dihedral : 3.380 14.009 864 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.67 % Allowed : 15.42 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.30), residues: 788 helix: 2.79 (0.24), residues: 455 sheet: 0.50 (0.76), residues: 54 loop : -0.85 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 563 HIS 0.004 0.001 HIS B 58 PHE 0.008 0.001 PHE B 34 TYR 0.027 0.001 TYR B 243 ARG 0.003 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.747 Fit side-chains REVERT: A 163 GLN cc_start: 0.8186 (mm110) cc_final: 0.7885 (mp10) REVERT: A 275 ARG cc_start: 0.8543 (tpp-160) cc_final: 0.8272 (tpp-160) REVERT: A 276 VAL cc_start: 0.9258 (m) cc_final: 0.8799 (p) REVERT: A 387 MET cc_start: 0.8636 (mmm) cc_final: 0.8276 (mmm) REVERT: A 407 ILE cc_start: 0.9345 (tt) cc_final: 0.9108 (tt) REVERT: A 429 HIS cc_start: 0.8455 (t-170) cc_final: 0.8023 (t70) REVERT: B 6 GLN cc_start: 0.8826 (tp40) cc_final: 0.8519 (tp40) REVERT: B 30 MET cc_start: 0.7077 (tpp) cc_final: 0.6748 (tpp) REVERT: B 77 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 141 TYR cc_start: 0.9394 (t80) cc_final: 0.8962 (t80) REVERT: B 148 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7703 (ptm160) outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.1677 time to fit residues: 27.5265 Evaluate side-chains 122 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6516 Z= 0.178 Angle : 0.488 8.361 8776 Z= 0.248 Chirality : 0.038 0.142 1006 Planarity : 0.003 0.038 1129 Dihedral : 3.377 14.455 864 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.81 % Allowed : 15.00 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.30), residues: 788 helix: 2.80 (0.24), residues: 455 sheet: 0.52 (0.75), residues: 54 loop : -0.88 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 563 HIS 0.003 0.001 HIS A 347 PHE 0.007 0.001 PHE B 34 TYR 0.027 0.001 TYR B 243 ARG 0.006 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.762 Fit side-chains REVERT: A 163 GLN cc_start: 0.8188 (mm110) cc_final: 0.7893 (mp10) REVERT: A 275 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.8249 (tpp-160) REVERT: A 276 VAL cc_start: 0.9249 (m) cc_final: 0.8789 (p) REVERT: A 387 MET cc_start: 0.8652 (mmm) cc_final: 0.8128 (mmm) REVERT: A 391 VAL cc_start: 0.9025 (t) cc_final: 0.8791 (t) REVERT: A 407 ILE cc_start: 0.9332 (tt) cc_final: 0.9091 (tt) REVERT: B 6 GLN cc_start: 0.8828 (tp40) cc_final: 0.8513 (tp40) REVERT: B 30 MET cc_start: 0.7095 (tpp) cc_final: 0.6757 (tpp) REVERT: B 77 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 131 MET cc_start: 0.8937 (mmm) cc_final: 0.8202 (mpp) REVERT: B 141 TYR cc_start: 0.9394 (t80) cc_final: 0.9026 (t80) REVERT: B 148 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7665 (ptm160) outliers start: 13 outliers final: 12 residues processed: 122 average time/residue: 0.1656 time to fit residues: 28.3753 Evaluate side-chains 125 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 0.0070 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6516 Z= 0.144 Angle : 0.484 8.709 8776 Z= 0.247 Chirality : 0.038 0.141 1006 Planarity : 0.003 0.038 1129 Dihedral : 3.354 13.432 864 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.81 % Allowed : 15.14 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.30), residues: 788 helix: 2.78 (0.24), residues: 455 sheet: 0.64 (0.75), residues: 54 loop : -0.83 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 563 HIS 0.010 0.001 HIS B 58 PHE 0.006 0.001 PHE B 33 TYR 0.027 0.001 TYR B 243 ARG 0.007 0.000 ARG B 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.793 Fit side-chains REVERT: A 163 GLN cc_start: 0.8184 (mm110) cc_final: 0.7884 (mp10) REVERT: A 275 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8251 (tpp-160) REVERT: A 276 VAL cc_start: 0.9244 (m) cc_final: 0.8785 (p) REVERT: A 387 MET cc_start: 0.8662 (mmm) cc_final: 0.8290 (mmm) REVERT: A 407 ILE cc_start: 0.9325 (tt) cc_final: 0.9082 (tt) REVERT: B 6 GLN cc_start: 0.8807 (tp40) cc_final: 0.8500 (tp40) REVERT: B 30 MET cc_start: 0.7086 (tpp) cc_final: 0.6756 (tpp) REVERT: B 77 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 131 MET cc_start: 0.8945 (mmm) cc_final: 0.8727 (tpp) REVERT: B 141 TYR cc_start: 0.9336 (t80) cc_final: 0.8979 (t80) REVERT: B 148 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7662 (ptm160) outliers start: 13 outliers final: 13 residues processed: 116 average time/residue: 0.1490 time to fit residues: 24.0402 Evaluate side-chains 122 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119858 restraints weight = 8368.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119038 restraints weight = 5491.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120882 restraints weight = 5285.229| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6516 Z= 0.147 Angle : 0.479 8.797 8776 Z= 0.244 Chirality : 0.038 0.141 1006 Planarity : 0.003 0.038 1129 Dihedral : 3.312 13.368 864 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.67 % Allowed : 15.42 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.30), residues: 788 helix: 2.81 (0.24), residues: 455 sheet: 0.65 (0.75), residues: 54 loop : -0.82 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 563 HIS 0.005 0.001 HIS B 58 PHE 0.006 0.001 PHE B 34 TYR 0.027 0.001 TYR B 243 ARG 0.007 0.000 ARG B 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.01 seconds wall clock time: 28 minutes 5.67 seconds (1685.67 seconds total)