Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 01:26:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/04_2023/7znu_14814_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/04_2023/7znu_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_14814/04_2023/7znu_14814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/04_2023/7znu_14814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/04_2023/7znu_14814_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znu_14814/04_2023/7znu_14814_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-1.21rc1-4938/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: 12.67, per 1000 atoms: 1.45 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: 3.77 Conformation dependent library (CDL) restraints added in 3.6 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: 0.91 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: 2.50 Time building geometry restraints manager: 3.99 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: 1.870 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: 8.180 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 37.350 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.140 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2285 time to fit residues: 95.4407 Evaluate side-chains 175 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4073 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** 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: 0.7720 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8886 Z= 0.228 Angle : 0.749 13.130 12060 Z= 0.373 Chirality : 0.045 0.221 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.512 107.097 1234 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer Outliers : 2.60 % 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: 1.22 (0.25), residues: 1112 helix: 2.11 (0.19), residues: 732 sheet: -1.04 (0.78), residues: 48 loop : -2.01 (0.29), residues: 332 *********************** 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 206 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 198 average time/residue: 0.1970 time to fit residues: 55.4822 Evaluate side-chains 166 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0874 time to fit residues: 3.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3712 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= 0.197 Angle : 0.729 12.934 12060 Z= 0.366 Chirality : 0.044 0.293 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.374 103.896 1234 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.95 % Rotamer Outliers : 0.54 % 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: 1.25 (0.25), residues: 1112 helix: 2.16 (0.19), residues: 726 sheet: -0.77 (0.63), residues: 74 loop : -2.11 (0.30), residues: 312 *********************** 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 176 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 173 average time/residue: 0.1841 time to fit residues: 45.9607 Evaluate side-chains 157 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 8886 Z= 0.213 Angle : 0.749 17.170 12060 Z= 0.371 Chirality : 0.044 0.320 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.362 103.358 1234 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer Outliers : 1.84 % 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: 1.25 (0.25), residues: 1112 helix: 2.09 (0.19), residues: 726 sheet: -0.83 (0.77), residues: 48 loop : -1.85 (0.30), residues: 338 *********************** 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 178 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 167 average time/residue: 0.1777 time to fit residues: 43.9173 Evaluate side-chains 158 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0888 time to fit residues: 3.0300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 8886 Z= 0.296 Angle : 0.779 11.172 12060 Z= 0.406 Chirality : 0.046 0.299 1422 Planarity : 0.004 0.033 1530 Dihedral : 7.683 106.817 1234 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer Outliers : 1.73 % 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: 0.85 (0.25), residues: 1112 helix: 1.79 (0.19), residues: 724 sheet: -2.06 (0.72), residues: 44 loop : -1.80 (0.31), residues: 344 *********************** 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 177 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 168 average time/residue: 0.1855 time to fit residues: 45.9500 Evaluate side-chains 162 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0913 time to fit residues: 3.3526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 0.0040 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7794 moved from start: 0.4827 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= 0.199 Angle : 0.759 20.440 12060 Z= 0.378 Chirality : 0.044 0.237 1422 Planarity : 0.004 0.032 1530 Dihedral : 7.430 100.144 1234 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer Outliers : 1.08 % 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: 1.10 (0.26), residues: 1112 helix: 1.94 (0.19), residues: 726 sheet: -0.60 (0.78), residues: 48 loop : -1.88 (0.30), residues: 338 *********************** 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 173 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 165 average time/residue: 0.1753 time to fit residues: 42.9494 Evaluate side-chains 160 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0882 time to fit residues: 2.5561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** 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: 0.7866 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8886 Z= 0.249 Angle : 0.779 20.845 12060 Z= 0.393 Chirality : 0.045 0.299 1422 Planarity : 0.004 0.044 1530 Dihedral : 7.470 102.236 1234 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer Outliers : 0.65 % 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: 0.94 (0.26), residues: 1112 helix: 1.84 (0.19), residues: 726 sheet: -0.77 (0.60), residues: 74 loop : -2.02 (0.32), residues: 312 *********************** 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 160 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 158 average time/residue: 0.1767 time to fit residues: 42.0167 Evaluate side-chains 152 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0876 time to fit residues: 1.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 0.0050 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** 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: 0.7809 moved from start: 0.5187 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= 0.193 Angle : 0.787 19.510 12060 Z= 0.386 Chirality : 0.045 0.377 1422 Planarity : 0.004 0.035 1530 Dihedral : 7.385 97.850 1234 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer Outliers : 0.43 % 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: 1.00 (0.26), residues: 1112 helix: 1.93 (0.19), residues: 718 sheet: -0.67 (0.61), residues: 74 loop : -2.04 (0.32), residues: 320 *********************** 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 164 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 161 average time/residue: 0.1875 time to fit residues: 44.3108 Evaluate side-chains 154 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0964 time to fit residues: 1.9525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.0060 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** 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: 0.7794 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8886 Z= 0.196 Angle : 0.783 24.413 12060 Z= 0.386 Chirality : 0.045 0.402 1422 Planarity : 0.004 0.030 1530 Dihedral : 7.311 95.157 1234 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer Outliers : 0.32 % 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: 0.96 (0.26), residues: 1112 helix: 1.88 (0.19), residues: 716 sheet: -0.71 (0.60), residues: 74 loop : -1.97 (0.33), residues: 322 *********************** 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 160 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 159 average time/residue: 0.1684 time to fit residues: 39.9183 Evaluate side-chains 155 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0929 time to fit residues: 1.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0040 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 overall best weight: 0.2810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7774 moved from start: 0.5314 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= 0.185 Angle : 0.774 22.591 12060 Z= 0.380 Chirality : 0.045 0.395 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.296 94.049 1234 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer Outliers : 0.22 % 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: 1.02 (0.26), residues: 1112 helix: 1.90 (0.19), residues: 716 sheet: -0.65 (0.60), residues: 74 loop : -1.88 (0.33), residues: 322 ********************** 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 156 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.1612 time to fit residues: 37.7755 Evaluate side-chains 153 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0070 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 4 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.101049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080549 restraints weight = 195448.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086638 restraints weight = 60021.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090910 restraints weight = 24080.317| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8886 Z= 0.186 Angle : 0.771 22.299 12060 Z= 0.380 Chirality : 0.044 0.395 1422 Planarity : 0.004 0.030 1530 Dihedral : 7.264 93.215 1234 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer Outliers : 0.11 % 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: 1.94 (0.19), residues: 712 sheet: -0.59 (0.59), residues: 74 loop : -1.86 (0.33), residues: 326 =============================================================================== Job complete usr+sys time: 2001.25 seconds wall clock time: 37 minutes 0.75 seconds (2220.75 seconds total)