Starting phenix.real_space_refine on Wed Feb 14 06:22:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/02_2024/7znu_14814_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/02_2024/7znu_14814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/02_2024/7znu_14814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/02_2024/7znu_14814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/02_2024/7znu_14814_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/02_2024/7znu_14814_neut_updated.pdb" } resolution = 4.0 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= 0.001 sd= 0.044 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 64 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: 6 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 S 44 5.16 5 C 5526 2.51 5 N 1534 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4333 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Conformer: "B" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Conformer: "C" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Chain: "B" Number of atoms: 4333 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Conformer: "B" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Conformer: "C" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.97, per 1000 atoms: 1.49 Number of scatterers: 8730 At special positions: 0 Unit cell: (68.06, 91.02, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 S 44 16.00 P 4 15.00 O 1620 8.00 N 1534 7.00 C 5526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.97 Conformation dependent library (CDL) restraints added in 4.4 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 4 sheets defined 62.5% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 18 through 50 Proline residue: A 39 - end of helix removed outlier: 4.400A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 101 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 114 through 153 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 156 through 209 removed outlier: 4.937A pdb=" N ASP A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 233 through 266 removed outlier: 3.700A pdb=" N THR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 315 removed outlier: 4.663A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 381 Processing helix chain 'A' and resid 404 through 407 No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 504 through 520 removed outlier: 5.230A pdb=" N ASN A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 18 through 50 Proline residue: B 39 - end of helix removed outlier: 3.664A pdb=" N ILE B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 101 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 114 through 153 Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 156 through 210 removed outlier: 3.529A pdb=" N VAL B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 230 Processing helix chain 'B' and resid 232 through 266 removed outlier: 3.647A pdb=" N LEU B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 314 removed outlier: 4.712A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 404 through 407 No H-bonds generated for 'chain 'B' and resid 404 through 407' Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 477 through 488 Processing helix chain 'B' and resid 504 through 518 Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing sheet with id= A, first strand: chain 'A' and resid 355 through 359 removed outlier: 3.871A pdb=" N PHE A 356 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 335 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 391 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 538 through 541 Processing sheet with id= C, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.729A pdb=" N ARG B 391 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 364 through 366 removed outlier: 3.517A pdb=" N LEU B 493 " --> pdb=" O THR B 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP B 496 " --> pdb=" O VAL B 414 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2955 1.36 - 1.50: 2158 1.50 - 1.64: 3679 1.64 - 1.77: 0 1.77 - 1.91: 94 Bond restraints: 8886 Sorted by residual: bond pdb=" N SER B 473 " pdb=" CA SER B 473 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.26e+00 bond pdb=" N SER A 473 " pdb=" CA SER A 473 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.85e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" CA SER A 473 " pdb=" CB SER A 473 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.69e-02 3.50e+03 1.06e+00 ... (remaining 8881 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.85: 189 106.85 - 114.18: 5389 114.18 - 121.51: 4539 121.51 - 128.84: 1877 128.84 - 136.18: 66 Bond angle restraints: 12060 Sorted by residual: angle pdb=" N VAL A 16 " pdb=" CA VAL A 16 " pdb=" C VAL A 16 " ideal model delta sigma weight residual 111.56 107.98 3.58 8.60e-01 1.35e+00 1.74e+01 angle pdb=" N ILE B 454 " pdb=" CA ILE B 454 " pdb=" C ILE B 454 " ideal model delta sigma weight residual 113.53 109.76 3.77 9.80e-01 1.04e+00 1.48e+01 angle pdb=" N HIS B 451 " pdb=" CA HIS B 451 " pdb=" C HIS B 451 " ideal model delta sigma weight residual 114.04 110.19 3.85 1.24e+00 6.50e-01 9.66e+00 angle pdb=" CA MET A 154 " pdb=" C MET A 154 " pdb=" O MET A 154 " ideal model delta sigma weight residual 121.50 117.85 3.65 1.25e+00 6.40e-01 8.53e+00 angle pdb=" CA MET B 154 " pdb=" C MET B 154 " pdb=" O MET B 154 " ideal model delta sigma weight residual 121.50 117.86 3.64 1.25e+00 6.40e-01 8.50e+00 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 4944 23.61 - 47.22: 329 47.22 - 70.83: 25 70.83 - 94.44: 6 94.44 - 118.05: 4 Dihedral angle restraints: 5308 sinusoidal: 2074 harmonic: 3234 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -178.06 118.05 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 -176.41 116.41 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 -174.82 114.83 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 797 0.026 - 0.051: 368 0.051 - 0.077: 170 0.077 - 0.103: 76 0.103 - 0.129: 11 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ILE B 392 " pdb=" N ILE B 392 " pdb=" C ILE B 392 " pdb=" CB ILE B 392 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 526 " pdb=" N ILE A 526 " pdb=" C ILE A 526 " pdb=" CB ILE A 526 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 1419 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C MET B 134 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B 134 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 135 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C MET A 134 " -0.034 2.00e-02 2.50e+03 pdb=" O MET A 134 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 135 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 278 " -0.008 2.00e-02 2.50e+03 9.66e-03 1.63e+00 pdb=" CG PHE B 278 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 278 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 278 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 278 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 278 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 278 " 0.000 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 380 2.72 - 3.26: 9544 3.26 - 3.81: 14798 3.81 - 4.35: 16081 4.35 - 4.90: 27582 Nonbonded interactions: 68385 Sorted by model distance: nonbonded pdb=" OE1 GLN B 478 " pdb=" OG SER B 500 " model vdw 2.173 2.440 nonbonded pdb=" O SER B 458 " pdb=" OG1 THR B 463 " model vdw 2.189 2.440 nonbonded pdb=" OE2 GLU A 343 " pdb=" OH TYR A 352 " model vdw 2.212 2.440 nonbonded pdb=" O TYR A 263 " pdb=" OG1 THR A 266 " model vdw 2.241 2.440 nonbonded pdb=" OD1 ASP B 327 " pdb=" OG SER B 403 " model vdw 2.249 2.440 ... (remaining 68380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 602)) } 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=0.25 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 8.030 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 39.670 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 0.029 8886 Z= 0.185 Angle : 0.635 6.267 12060 Z= 0.366 Chirality : 0.038 0.129 1422 Planarity : 0.003 0.030 1530 Dihedral : 15.162 118.054 3212 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.16 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 1.40 (0.25), residues: 1112 helix: 2.47 (0.19), residues: 702 sheet: -2.10 (0.65), residues: 58 loop : -1.87 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 62 HIS 0.005 0.001 HIS B 85 PHE 0.022 0.001 PHE B 278 TYR 0.012 0.001 TYR A 13 ARG 0.003 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.001 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: A 19 THR cc_start: 0.7310 (p) cc_final: 0.7059 (p) REVERT: A 21 THR cc_start: 0.9315 (m) cc_final: 0.9064 (p) REVERT: A 68 PHE cc_start: 0.6427 (m-10) cc_final: 0.6222 (m-10) REVERT: A 71 MET cc_start: 0.7901 (mtm) cc_final: 0.7603 (ptm) REVERT: A 154 MET cc_start: 0.7756 (mmp) cc_final: 0.7389 (mmp) REVERT: A 233 PHE cc_start: 0.7204 (m-10) cc_final: 0.6956 (m-80) REVERT: A 254 MET cc_start: 0.8603 (mmm) cc_final: 0.8382 (mmm) REVERT: A 278 PHE cc_start: 0.7952 (m-10) cc_final: 0.7454 (m-10) REVERT: A 482 ILE cc_start: 0.8396 (pt) cc_final: 0.8072 (mt) REVERT: A 503 ASP cc_start: 0.7668 (t70) cc_final: 0.7377 (t70) REVERT: B 1 MET cc_start: 0.6247 (mtm) cc_final: 0.4157 (tpt) REVERT: B 41 LEU cc_start: 0.8747 (mt) cc_final: 0.8224 (tp) REVERT: B 68 PHE cc_start: 0.8091 (t80) cc_final: 0.7544 (t80) REVERT: B 96 TYR cc_start: 0.9327 (t80) cc_final: 0.9113 (t80) REVERT: B 181 LYS cc_start: 0.8236 (ptmm) cc_final: 0.7958 (tttt) REVERT: B 288 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.7314 (mtt90) REVERT: B 299 THR cc_start: 0.9281 (m) cc_final: 0.8975 (p) REVERT: B 437 THR cc_start: 0.6264 (t) cc_final: 0.5852 (p) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2237 time to fit residues: 93.2028 Evaluate side-chains 183 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.0030 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 349 GLN B 512 GLN B 519 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8886 Z= 0.238 Angle : 0.752 13.235 12060 Z= 0.372 Chirality : 0.045 0.229 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.507 107.249 1234 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.38 % Allowed : 16.02 % Favored : 81.60 % 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: 1.21 (0.25), residues: 1112 helix: 2.12 (0.19), residues: 730 sheet: -1.04 (0.78), residues: 48 loop : -2.02 (0.28), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 239 HIS 0.004 0.001 HIS B 190 PHE 0.039 0.002 PHE B 281 TYR 0.016 0.002 TYR B 352 ARG 0.007 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6538 (m-10) cc_final: 0.6309 (m-10) REVERT: A 71 MET cc_start: 0.8006 (mtm) cc_final: 0.7678 (ptm) REVERT: A 154 MET cc_start: 0.7632 (mmp) cc_final: 0.7338 (mmp) REVERT: A 158 MET cc_start: 0.7995 (ppp) cc_final: 0.7783 (mpp) REVERT: A 248 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8423 (ppp) REVERT: A 270 MET cc_start: 0.5780 (tpp) cc_final: 0.4558 (tpp) REVERT: A 297 ASN cc_start: 0.8244 (m110) cc_final: 0.7358 (m110) REVERT: A 307 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7689 (tp30) REVERT: A 482 ILE cc_start: 0.8535 (pt) cc_final: 0.8193 (mt) REVERT: A 503 ASP cc_start: 0.7643 (t70) cc_final: 0.7436 (t70) REVERT: B 1 MET cc_start: 0.6408 (mtm) cc_final: 0.4102 (tpt) REVERT: B 41 LEU cc_start: 0.8756 (mt) cc_final: 0.8206 (tp) REVERT: B 181 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7880 (tttt) REVERT: B 239 TRP cc_start: 0.6995 (m-10) cc_final: 0.6044 (m-10) REVERT: B 288 ARG cc_start: 0.8698 (mtt-85) cc_final: 0.8098 (mtt90) REVERT: B 312 MET cc_start: 0.8256 (tpt) cc_final: 0.8004 (ttp) REVERT: B 384 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7148 (m) REVERT: B 437 THR cc_start: 0.6329 (t) cc_final: 0.5925 (p) outliers start: 22 outliers final: 15 residues processed: 203 average time/residue: 0.1909 time to fit residues: 54.4849 Evaluate side-chains 172 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 537 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.0670 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8886 Z= 0.198 Angle : 0.724 12.923 12060 Z= 0.361 Chirality : 0.043 0.289 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.392 103.999 1234 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 1.62 % Allowed : 20.13 % Favored : 78.25 % 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: 1.21 (0.25), residues: 1112 helix: 2.14 (0.19), residues: 724 sheet: -0.76 (0.64), residues: 74 loop : -2.12 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 239 HIS 0.003 0.001 HIS B 546 PHE 0.049 0.002 PHE B 281 TYR 0.035 0.002 TYR B 96 ARG 0.008 0.001 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 TYR cc_start: 0.8412 (m-10) cc_final: 0.8181 (m-10) REVERT: A 68 PHE cc_start: 0.6580 (m-10) cc_final: 0.6319 (m-10) REVERT: A 71 MET cc_start: 0.8001 (mtm) cc_final: 0.7661 (ptm) REVERT: A 130 TRP cc_start: 0.7928 (m-10) cc_final: 0.7412 (m-10) REVERT: A 154 MET cc_start: 0.7542 (mmp) cc_final: 0.7246 (mmp) REVERT: A 254 MET cc_start: 0.8551 (mmm) cc_final: 0.8208 (ttp) REVERT: A 270 MET cc_start: 0.5143 (tpp) cc_final: 0.4793 (tpp) REVERT: A 297 ASN cc_start: 0.8249 (m110) cc_final: 0.6939 (m110) REVERT: A 307 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7597 (tp30) REVERT: A 482 ILE cc_start: 0.8517 (pt) cc_final: 0.8150 (mt) REVERT: A 503 ASP cc_start: 0.7621 (t70) cc_final: 0.7345 (t70) REVERT: B 1 MET cc_start: 0.6372 (mtm) cc_final: 0.4076 (tpt) REVERT: B 41 LEU cc_start: 0.8733 (mt) cc_final: 0.8183 (tp) REVERT: B 181 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7833 (tttt) REVERT: B 239 TRP cc_start: 0.6639 (m-10) cc_final: 0.5756 (m-10) REVERT: B 254 MET cc_start: 0.8413 (mtp) cc_final: 0.8134 (tpt) REVERT: B 288 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8093 (mtt90) REVERT: B 297 ASN cc_start: 0.8015 (m-40) cc_final: 0.7582 (t0) REVERT: B 437 THR cc_start: 0.6138 (t) cc_final: 0.5742 (p) outliers start: 15 outliers final: 9 residues processed: 175 average time/residue: 0.1700 time to fit residues: 43.3461 Evaluate side-chains 164 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 515 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8886 Z= 0.332 Angle : 0.808 15.455 12060 Z= 0.415 Chirality : 0.046 0.271 1422 Planarity : 0.005 0.040 1530 Dihedral : 7.719 108.422 1234 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 2.81 % Allowed : 20.24 % Favored : 76.95 % 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: 0.79 (0.25), residues: 1112 helix: 1.75 (0.19), residues: 722 sheet: -1.14 (0.58), residues: 84 loop : -2.02 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP A 239 HIS 0.005 0.001 HIS A 442 PHE 0.048 0.003 PHE B 278 TYR 0.025 0.002 TYR A 96 ARG 0.006 0.001 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6700 (m-10) cc_final: 0.6405 (m-10) REVERT: A 71 MET cc_start: 0.8288 (mtm) cc_final: 0.7928 (ptm) REVERT: A 102 MET cc_start: 0.8287 (tpp) cc_final: 0.7530 (tpp) REVERT: A 307 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7617 (tp30) REVERT: A 482 ILE cc_start: 0.8640 (pt) cc_final: 0.8201 (mt) REVERT: B 1 MET cc_start: 0.6818 (mtm) cc_final: 0.4473 (tpt) REVERT: B 181 LYS cc_start: 0.8334 (ptmm) cc_final: 0.8059 (tttt) REVERT: B 239 TRP cc_start: 0.6762 (m-10) cc_final: 0.5670 (m-10) REVERT: B 288 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.7902 (mtt90) REVERT: B 292 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9204 (mm) REVERT: B 297 ASN cc_start: 0.8129 (m-40) cc_final: 0.7017 (t0) outliers start: 26 outliers final: 19 residues processed: 174 average time/residue: 0.1817 time to fit residues: 45.3835 Evaluate side-chains 166 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 537 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8886 Z= 0.195 Angle : 0.767 14.443 12060 Z= 0.376 Chirality : 0.046 0.382 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.491 100.688 1234 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 1.52 % Allowed : 21.75 % Favored : 76.73 % 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: 1.06 (0.26), residues: 1112 helix: 1.93 (0.19), residues: 726 sheet: -0.81 (0.76), residues: 48 loop : -1.89 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A 239 HIS 0.009 0.001 HIS B 137 PHE 0.045 0.002 PHE B 278 TYR 0.028 0.002 TYR B 96 ARG 0.005 0.001 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6709 (m-10) cc_final: 0.6392 (m-10) REVERT: A 71 MET cc_start: 0.8217 (mtm) cc_final: 0.7871 (ptm) REVERT: A 254 MET cc_start: 0.8532 (mmm) cc_final: 0.8094 (ttp) REVERT: A 299 THR cc_start: 0.9202 (m) cc_final: 0.9000 (p) REVERT: A 307 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7526 (tp30) REVERT: A 482 ILE cc_start: 0.8512 (pt) cc_final: 0.8103 (mt) REVERT: B 1 MET cc_start: 0.6776 (mtm) cc_final: 0.4419 (tpt) REVERT: B 11 MET cc_start: 0.7283 (tmm) cc_final: 0.7061 (ttt) REVERT: B 102 MET cc_start: 0.7609 (mmm) cc_final: 0.7029 (mmt) REVERT: B 181 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7832 (tttm) REVERT: B 239 TRP cc_start: 0.6680 (m-10) cc_final: 0.5608 (m-10) REVERT: B 270 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5748 (ttm) REVERT: B 288 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.7964 (mtt90) REVERT: B 297 ASN cc_start: 0.8126 (m-40) cc_final: 0.7047 (t0) REVERT: B 312 MET cc_start: 0.8175 (tpt) cc_final: 0.7939 (ttm) outliers start: 14 outliers final: 11 residues processed: 172 average time/residue: 0.1677 time to fit residues: 42.4541 Evaluate side-chains 168 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 515 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 0.0270 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8886 Z= 0.196 Angle : 0.782 18.467 12060 Z= 0.380 Chirality : 0.045 0.283 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.421 99.156 1234 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 1.52 % Allowed : 22.40 % Favored : 76.08 % 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: 1.05 (0.26), residues: 1112 helix: 1.94 (0.19), residues: 728 sheet: -1.23 (0.62), residues: 68 loop : -1.92 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP A 239 HIS 0.006 0.001 HIS B 137 PHE 0.046 0.002 PHE B 281 TYR 0.017 0.001 TYR A 96 ARG 0.005 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8593 (tt) cc_final: 0.8211 (tp) REVERT: A 21 THR cc_start: 0.8769 (m) cc_final: 0.8548 (p) REVERT: A 68 PHE cc_start: 0.6702 (m-10) cc_final: 0.6411 (m-10) REVERT: A 71 MET cc_start: 0.8195 (mtm) cc_final: 0.7863 (ptm) REVERT: A 130 TRP cc_start: 0.8181 (m-10) cc_final: 0.7735 (m-10) REVERT: A 254 MET cc_start: 0.8533 (mmm) cc_final: 0.8131 (ttp) REVERT: A 299 THR cc_start: 0.9179 (m) cc_final: 0.8974 (p) REVERT: A 307 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7517 (tp30) REVERT: A 482 ILE cc_start: 0.8500 (pt) cc_final: 0.8071 (mt) REVERT: B 1 MET cc_start: 0.6781 (mtm) cc_final: 0.4417 (tpt) REVERT: B 11 MET cc_start: 0.7283 (tmm) cc_final: 0.7059 (ttt) REVERT: B 102 MET cc_start: 0.7652 (mmm) cc_final: 0.7101 (mmt) REVERT: B 137 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6709 (m90) REVERT: B 181 LYS cc_start: 0.8165 (ptmm) cc_final: 0.7812 (tttm) REVERT: B 288 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.7871 (mtt90) REVERT: B 297 ASN cc_start: 0.8135 (m-40) cc_final: 0.7743 (t0) REVERT: B 525 ILE cc_start: 0.8583 (mt) cc_final: 0.8322 (mp) outliers start: 14 outliers final: 11 residues processed: 171 average time/residue: 0.1694 time to fit residues: 42.5608 Evaluate side-chains 170 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 515 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8886 Z= 0.240 Angle : 0.781 19.826 12060 Z= 0.387 Chirality : 0.045 0.250 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.448 101.690 1234 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 2.06 % Allowed : 22.19 % Favored : 75.76 % 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: 1.10 (0.26), residues: 1112 helix: 1.90 (0.19), residues: 728 sheet: -0.56 (0.74), residues: 48 loop : -1.77 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A 239 HIS 0.013 0.001 HIS B 137 PHE 0.047 0.002 PHE B 281 TYR 0.024 0.002 TYR A 96 ARG 0.004 0.001 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6792 (m-10) cc_final: 0.6490 (m-10) REVERT: A 71 MET cc_start: 0.8224 (mtm) cc_final: 0.7873 (ptm) REVERT: A 130 TRP cc_start: 0.8269 (m-10) cc_final: 0.7706 (m-10) REVERT: A 154 MET cc_start: 0.8123 (mmm) cc_final: 0.6663 (mmp) REVERT: A 254 MET cc_start: 0.8540 (mmm) cc_final: 0.8208 (ttp) REVERT: A 307 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7536 (tp30) REVERT: A 482 ILE cc_start: 0.8550 (pt) cc_final: 0.8129 (mt) REVERT: B 1 MET cc_start: 0.6826 (mtm) cc_final: 0.4775 (tpt) REVERT: B 11 MET cc_start: 0.7339 (tmm) cc_final: 0.7119 (ttt) REVERT: B 137 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6815 (m90) REVERT: B 181 LYS cc_start: 0.8193 (ptmm) cc_final: 0.7828 (tttm) REVERT: B 297 ASN cc_start: 0.8184 (m-40) cc_final: 0.7805 (t0) REVERT: B 312 MET cc_start: 0.8187 (tpt) cc_final: 0.7898 (ttp) REVERT: B 393 MET cc_start: 0.6196 (tpp) cc_final: 0.5977 (tpp) REVERT: B 525 ILE cc_start: 0.8631 (mt) cc_final: 0.8362 (mp) outliers start: 19 outliers final: 17 residues processed: 169 average time/residue: 0.1755 time to fit residues: 43.8806 Evaluate side-chains 173 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 515 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8886 Z= 0.207 Angle : 0.793 23.212 12060 Z= 0.388 Chirality : 0.045 0.249 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.441 98.137 1234 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 1.95 % Allowed : 22.84 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1112 helix: 1.92 (0.19), residues: 726 sheet: -0.26 (0.77), residues: 46 loop : -1.68 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP A 239 HIS 0.007 0.001 HIS B 519 PHE 0.047 0.002 PHE B 281 TYR 0.024 0.002 TYR A 96 ARG 0.004 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6852 (m-10) cc_final: 0.6510 (m-10) REVERT: A 71 MET cc_start: 0.8221 (mtm) cc_final: 0.7864 (ptm) REVERT: A 130 TRP cc_start: 0.8237 (m-10) cc_final: 0.7715 (m-10) REVERT: A 154 MET cc_start: 0.8064 (mmm) cc_final: 0.6642 (mmp) REVERT: A 254 MET cc_start: 0.8526 (mmm) cc_final: 0.8215 (ttp) REVERT: A 307 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7498 (tp30) REVERT: A 482 ILE cc_start: 0.8492 (pt) cc_final: 0.8097 (mt) REVERT: B 1 MET cc_start: 0.6782 (mtm) cc_final: 0.4707 (tpt) REVERT: B 11 MET cc_start: 0.7345 (tmm) cc_final: 0.7122 (ttt) REVERT: B 102 MET cc_start: 0.7541 (mmm) cc_final: 0.6754 (mmm) REVERT: B 137 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6901 (m-70) REVERT: B 169 TYR cc_start: 0.8561 (m-80) cc_final: 0.7895 (m-80) REVERT: B 181 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7775 (tttm) REVERT: B 239 TRP cc_start: 0.6800 (m-10) cc_final: 0.5752 (m-10) REVERT: B 270 MET cc_start: 0.6398 (tmm) cc_final: 0.6060 (mmt) REVERT: B 297 ASN cc_start: 0.8202 (m-40) cc_final: 0.6838 (t0) REVERT: B 312 MET cc_start: 0.8151 (tpt) cc_final: 0.7913 (ttp) REVERT: B 525 ILE cc_start: 0.8600 (mt) cc_final: 0.8331 (mp) outliers start: 18 outliers final: 15 residues processed: 174 average time/residue: 0.1676 time to fit residues: 42.4257 Evaluate side-chains 171 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 515 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.0170 chunk 63 optimal weight: 3.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8886 Z= 0.194 Angle : 0.775 20.520 12060 Z= 0.378 Chirality : 0.044 0.231 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.383 95.241 1234 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 1.52 % Allowed : 23.27 % Favored : 75.22 % 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: 1.15 (0.26), residues: 1112 helix: 1.97 (0.19), residues: 718 sheet: -0.51 (0.74), residues: 50 loop : -1.74 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 239 HIS 0.005 0.001 HIS B 190 PHE 0.051 0.002 PHE B 281 TYR 0.022 0.001 TYR A 96 ARG 0.004 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6861 (m-10) cc_final: 0.6558 (m-10) REVERT: A 71 MET cc_start: 0.8247 (mtm) cc_final: 0.7889 (ptm) REVERT: A 130 TRP cc_start: 0.8217 (m-10) cc_final: 0.7698 (m-10) REVERT: A 152 MET cc_start: 0.7479 (mmm) cc_final: 0.7243 (mmm) REVERT: A 154 MET cc_start: 0.7970 (mmm) cc_final: 0.6613 (mmp) REVERT: A 254 MET cc_start: 0.8442 (mmm) cc_final: 0.8153 (ttp) REVERT: A 307 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7484 (tp30) REVERT: A 482 ILE cc_start: 0.8482 (pt) cc_final: 0.8076 (mt) REVERT: B 1 MET cc_start: 0.6812 (mtm) cc_final: 0.4673 (tpt) REVERT: B 102 MET cc_start: 0.7585 (mmm) cc_final: 0.6755 (mmm) REVERT: B 169 TYR cc_start: 0.8535 (m-80) cc_final: 0.7887 (m-80) REVERT: B 181 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7718 (tttm) REVERT: B 239 TRP cc_start: 0.6810 (m-10) cc_final: 0.5788 (m-10) REVERT: B 297 ASN cc_start: 0.8205 (m-40) cc_final: 0.6857 (t0) REVERT: B 312 MET cc_start: 0.8133 (tpt) cc_final: 0.7897 (ttm) REVERT: B 525 ILE cc_start: 0.8572 (mt) cc_final: 0.8318 (mp) outliers start: 14 outliers final: 13 residues processed: 172 average time/residue: 0.1975 time to fit residues: 49.1331 Evaluate side-chains 172 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 515 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.0870 chunk 87 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8886 Z= 0.190 Angle : 0.774 20.686 12060 Z= 0.379 Chirality : 0.044 0.240 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.341 94.241 1234 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 1.41 % Allowed : 22.94 % Favored : 75.65 % 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: 1.11 (0.26), residues: 1112 helix: 1.94 (0.19), residues: 718 sheet: -0.45 (0.79), residues: 46 loop : -1.76 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 239 HIS 0.005 0.001 HIS B 190 PHE 0.052 0.002 PHE B 281 TYR 0.024 0.001 TYR A 96 ARG 0.005 0.000 ARG B 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.6849 (m-10) cc_final: 0.6554 (m-10) REVERT: A 71 MET cc_start: 0.8224 (mtm) cc_final: 0.7859 (ptm) REVERT: A 130 TRP cc_start: 0.8183 (m-10) cc_final: 0.7704 (m-10) REVERT: A 152 MET cc_start: 0.7418 (mmm) cc_final: 0.7164 (mmm) REVERT: A 154 MET cc_start: 0.7928 (mmm) cc_final: 0.6584 (mmp) REVERT: A 254 MET cc_start: 0.8435 (mmm) cc_final: 0.8153 (ttp) REVERT: A 307 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7552 (tp30) REVERT: A 482 ILE cc_start: 0.8460 (pt) cc_final: 0.8063 (mt) REVERT: B 1 MET cc_start: 0.6818 (mtm) cc_final: 0.4654 (tpt) REVERT: B 24 MET cc_start: 0.8174 (tpt) cc_final: 0.7898 (tpt) REVERT: B 102 MET cc_start: 0.7518 (mmm) cc_final: 0.6707 (mmm) REVERT: B 169 TYR cc_start: 0.8522 (m-80) cc_final: 0.7907 (m-80) REVERT: B 181 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7640 (tttm) REVERT: B 239 TRP cc_start: 0.6785 (m-10) cc_final: 0.5801 (m-10) REVERT: B 297 ASN cc_start: 0.8215 (m-40) cc_final: 0.6879 (t0) REVERT: B 525 ILE cc_start: 0.8492 (mt) cc_final: 0.8248 (mp) outliers start: 13 outliers final: 13 residues processed: 167 average time/residue: 0.1770 time to fit residues: 42.9591 Evaluate side-chains 168 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 526 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.0670 chunk 63 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 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 = 0.3738 r_free = 0.3738 target = 0.099552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078948 restraints weight = 198275.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083923 restraints weight = 54697.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.087357 restraints weight = 26385.004| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8886 Z= 0.188 Angle : 0.755 19.391 12060 Z= 0.369 Chirality : 0.043 0.227 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.309 95.192 1234 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 1.52 % Allowed : 22.73 % Favored : 75.76 % 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: 1.16 (0.26), residues: 1112 helix: 1.97 (0.19), residues: 718 sheet: -0.61 (0.73), residues: 50 loop : -1.71 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 239 HIS 0.004 0.001 HIS B 190 PHE 0.050 0.002 PHE B 278 TYR 0.023 0.001 TYR A 96 ARG 0.005 0.000 ARG B 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.67 seconds wall clock time: 39 minutes 8.30 seconds (2348.30 seconds total)