Starting phenix.real_space_refine on Fri Mar 14 06:17:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rra_24657/03_2025/7rra_24657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rra_24657/03_2025/7rra_24657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2025/7rra_24657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2025/7rra_24657.map" model { file = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2025/7rra_24657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2025/7rra_24657.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6164 2.51 5 N 1686 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9608 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4804 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Chain: "A" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4804 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 22, 'TRANS': 579} Chain breaks: 1 Time building chain proxies: 5.80, per 1000 atoms: 0.60 Number of scatterers: 9608 At special positions: 0 Unit cell: (112.77, 80.55, 144.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1714 8.00 N 1686 7.00 C 6164 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 66.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 89 through 124 Processing helix chain 'A' and resid 127 through 174 removed outlier: 4.565A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 193 through 236 removed outlier: 4.260A pdb=" N ASP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 4.201A pdb=" N ASP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 5.177A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 288 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 299 through 339 removed outlier: 3.985A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 330 " --> pdb=" O TRP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 356 Proline residue: A 350 - end of helix removed outlier: 4.114A pdb=" N THR A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 4.799A pdb=" N ALA A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 442 removed outlier: 4.841A pdb=" N LYS A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 592 Processing helix chain 'A' and resid 607 through 621 removed outlier: 4.148A pdb=" N LYS A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.906A pdb=" N TYR A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 82 Processing helix chain 'B' and resid 89 through 124 Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 142 through 175 Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 199 through 236 Proline residue: B 218 - end of helix removed outlier: 4.202A pdb=" N ASP B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 265 through 288 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 299 through 355 removed outlier: 3.908A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 330 " --> pdb=" O TRP B 326 " (cutoff:3.500A) Proline residue: B 350 - end of helix removed outlier: 4.114A pdb=" N THR B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 374 through 442 removed outlier: 4.841A pdb=" N LYS B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'B' and resid 573 through 583 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 608 through 621 Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.906A pdb=" N TYR B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 466 through 469 removed outlier: 3.787A pdb=" N ILE A 475 " --> pdb=" O TYR A 532 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 679 through 683 removed outlier: 7.458A pdb=" N LEU A 654 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ILE A 505 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER A 656 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N GLY A 507 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 466 through 469 removed outlier: 3.787A pdb=" N ILE B 475 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 503 through 507 removed outlier: 6.537A pdb=" N HIS B 669 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR B 506 " --> pdb=" O HIS B 669 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 671 " --> pdb=" O THR B 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=D 623 hydrogen bonds defined for protein. 1746 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: 2.49 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3146 1.34 - 1.46: 2073 1.46 - 1.58: 4525 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9818 Sorted by residual: bond pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.62e+00 bond pdb=" N GLU A 498 " pdb=" CA GLU A 498 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.05e+00 bond pdb=" N MET B 539 " pdb=" CA MET B 539 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.29e+00 bond pdb=" N GLU B 498 " pdb=" CA GLU B 498 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.37e-02 5.33e+03 7.25e+00 bond pdb=" N MET B 501 " pdb=" CA MET B 501 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.14e+00 ... (remaining 9813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 12915 1.56 - 3.11: 308 3.11 - 4.67: 45 4.67 - 6.22: 19 6.22 - 7.78: 7 Bond angle restraints: 13294 Sorted by residual: angle pdb=" N GLN A 611 " pdb=" CA GLN A 611 " pdb=" C GLN A 611 " ideal model delta sigma weight residual 111.71 107.53 4.18 1.15e+00 7.56e-01 1.32e+01 angle pdb=" N GLN B 611 " pdb=" CA GLN B 611 " pdb=" C GLN B 611 " ideal model delta sigma weight residual 111.71 107.57 4.14 1.15e+00 7.56e-01 1.30e+01 angle pdb=" CA GLU B 498 " pdb=" C GLU B 498 " pdb=" O GLU B 498 " ideal model delta sigma weight residual 121.99 118.13 3.86 1.14e+00 7.69e-01 1.14e+01 angle pdb=" CA GLN B 472 " pdb=" C GLN B 472 " pdb=" O GLN B 472 " ideal model delta sigma weight residual 122.03 117.84 4.19 1.25e+00 6.40e-01 1.13e+01 angle pdb=" CA GLN A 472 " pdb=" C GLN A 472 " pdb=" O GLN A 472 " ideal model delta sigma weight residual 122.03 117.86 4.17 1.25e+00 6.40e-01 1.11e+01 ... (remaining 13289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 5211 16.04 - 32.08: 491 32.08 - 48.12: 159 48.12 - 64.16: 12 64.16 - 80.20: 9 Dihedral angle restraints: 5882 sinusoidal: 2376 harmonic: 3506 Sorted by residual: dihedral pdb=" CA ARG B 69 " pdb=" CB ARG B 69 " pdb=" CG ARG B 69 " pdb=" CD ARG B 69 " ideal model delta sinusoidal sigma weight residual -60.00 -113.42 53.42 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA ARG A 69 " pdb=" CB ARG A 69 " pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " ideal model delta sinusoidal sigma weight residual -60.00 -113.37 53.37 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA TYR B 406 " pdb=" C TYR B 406 " pdb=" N LYS B 407 " pdb=" CA LYS B 407 " ideal model delta harmonic sigma weight residual 180.00 -165.18 -14.82 0 5.00e+00 4.00e-02 8.78e+00 ... (remaining 5879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1191 0.047 - 0.095: 228 0.095 - 0.142: 58 0.142 - 0.190: 5 0.190 - 0.237: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA HIS A 283 " pdb=" N HIS A 283 " pdb=" C HIS A 283 " pdb=" CB HIS A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL B 183 " pdb=" N VAL B 183 " pdb=" C VAL B 183 " pdb=" CB VAL B 183 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 1481 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 618 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C MET A 618 " -0.033 2.00e-02 2.50e+03 pdb=" O MET A 618 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 619 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 618 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C MET B 618 " -0.033 2.00e-02 2.50e+03 pdb=" O MET B 618 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 619 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 349 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 350 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " -0.021 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2033 2.79 - 3.32: 10073 3.32 - 3.84: 15830 3.84 - 4.37: 17559 4.37 - 4.90: 29272 Nonbonded interactions: 74767 Sorted by model distance: nonbonded pdb=" O GLU A 376 " pdb=" OG SER A 379 " model vdw 2.261 3.040 nonbonded pdb=" O GLU B 376 " pdb=" OG SER B 379 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU B 272 " pdb=" NE2 GLN B 316 " model vdw 2.314 3.120 nonbonded pdb=" OE2 GLU A 272 " pdb=" NE2 GLN A 316 " model vdw 2.314 3.120 nonbonded pdb=" NH2 ARG B 280 " pdb=" OE1 GLN A 195 " model vdw 2.327 3.120 ... (remaining 74762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.540 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 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 0.042 9818 Z= 0.196 Angle : 0.593 7.776 13294 Z= 0.338 Chirality : 0.040 0.237 1484 Planarity : 0.003 0.037 1688 Dihedral : 13.752 80.198 3626 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1196 helix: 2.17 (0.18), residues: 816 sheet: 1.98 (0.48), residues: 88 loop : -1.51 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 601 HIS 0.003 0.001 HIS A 283 PHE 0.007 0.001 PHE A 385 TYR 0.020 0.001 TYR A 171 ARG 0.003 0.000 ARG B 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 428 ASP cc_start: 0.7080 (t0) cc_final: 0.6569 (t70) REVERT: B 501 MET cc_start: 0.5014 (ppp) cc_final: 0.3868 (ppp) REVERT: A 428 ASP cc_start: 0.7418 (t0) cc_final: 0.7054 (t0) REVERT: A 501 MET cc_start: 0.6363 (ppp) cc_final: 0.5200 (ppp) REVERT: A 674 ASP cc_start: 0.6859 (p0) cc_final: 0.6351 (p0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2817 time to fit residues: 38.3806 Evaluate side-chains 72 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.095512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.085743 restraints weight = 72022.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.087488 restraints weight = 43534.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.088694 restraints weight = 29675.352| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9818 Z= 0.238 Angle : 0.608 8.294 13294 Z= 0.319 Chirality : 0.040 0.205 1484 Planarity : 0.004 0.027 1688 Dihedral : 4.072 17.676 1344 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: 1.67 (0.24), residues: 1196 helix: 1.88 (0.17), residues: 798 sheet: 1.95 (0.45), residues: 88 loop : -1.23 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 339 HIS 0.004 0.001 HIS A 97 PHE 0.012 0.002 PHE B 71 TYR 0.025 0.002 TYR B 171 ARG 0.004 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 PHE cc_start: 0.8002 (t80) cc_final: 0.6795 (t80) REVERT: B 155 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7049 (mt-10) REVERT: B 428 ASP cc_start: 0.8344 (t0) cc_final: 0.7785 (t70) REVERT: B 501 MET cc_start: 0.5714 (ppp) cc_final: 0.4775 (ppp) REVERT: B 539 MET cc_start: 0.9006 (mpp) cc_final: 0.8731 (mpp) REVERT: A 146 PHE cc_start: 0.8021 (t80) cc_final: 0.6846 (t80) REVERT: A 428 ASP cc_start: 0.7975 (t0) cc_final: 0.7574 (t70) REVERT: A 501 MET cc_start: 0.6493 (ppp) cc_final: 0.5702 (ppp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2462 time to fit residues: 32.5103 Evaluate side-chains 72 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS B 502 HIS A 299 HIS ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.092668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.082901 restraints weight = 72725.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.084630 restraints weight = 44216.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.085829 restraints weight = 30016.860| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9818 Z= 0.282 Angle : 0.644 9.624 13294 Z= 0.341 Chirality : 0.042 0.182 1484 Planarity : 0.005 0.053 1688 Dihedral : 4.392 19.032 1344 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % 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 (0.23), residues: 1196 helix: 1.34 (0.17), residues: 810 sheet: 1.50 (0.45), residues: 92 loop : -1.67 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 339 HIS 0.005 0.001 HIS A 169 PHE 0.020 0.002 PHE A 175 TYR 0.037 0.002 TYR A 171 ARG 0.005 0.001 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ILE cc_start: 0.7277 (mm) cc_final: 0.7062 (mm) REVERT: B 155 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 325 LEU cc_start: 0.7458 (mp) cc_final: 0.7001 (mp) REVERT: B 428 ASP cc_start: 0.8441 (t0) cc_final: 0.7871 (t70) REVERT: B 501 MET cc_start: 0.6372 (ppp) cc_final: 0.5158 (ppp) REVERT: A 146 PHE cc_start: 0.7893 (t80) cc_final: 0.6899 (t80) REVERT: A 172 ARG cc_start: 0.7088 (mmp-170) cc_final: 0.6781 (mmp80) REVERT: A 186 MET cc_start: 0.6354 (tmm) cc_final: 0.6067 (tmm) REVERT: A 428 ASP cc_start: 0.8071 (t0) cc_final: 0.7657 (t0) REVERT: A 501 MET cc_start: 0.7046 (ppp) cc_final: 0.6016 (ppp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2262 time to fit residues: 28.7568 Evaluate side-chains 73 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN A 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.094128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.084349 restraints weight = 71803.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.086122 restraints weight = 43403.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.087347 restraints weight = 29634.634| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9818 Z= 0.191 Angle : 0.565 8.249 13294 Z= 0.296 Chirality : 0.039 0.144 1484 Planarity : 0.005 0.060 1688 Dihedral : 4.251 19.833 1344 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 (0.24), residues: 1196 helix: 1.61 (0.17), residues: 812 sheet: 1.47 (0.47), residues: 88 loop : -1.62 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 339 HIS 0.006 0.001 HIS A 299 PHE 0.011 0.001 PHE A 517 TYR 0.032 0.002 TYR B 171 ARG 0.006 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ILE cc_start: 0.7476 (mm) cc_final: 0.7253 (mm) REVERT: B 146 PHE cc_start: 0.7951 (t80) cc_final: 0.6806 (t80) REVERT: B 155 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 172 ARG cc_start: 0.7220 (mmp-170) cc_final: 0.6917 (mmp80) REVERT: B 325 LEU cc_start: 0.7597 (mp) cc_final: 0.7196 (mp) REVERT: B 428 ASP cc_start: 0.8377 (t0) cc_final: 0.7809 (t70) REVERT: B 501 MET cc_start: 0.6270 (ppp) cc_final: 0.5159 (ppp) REVERT: B 548 MET cc_start: 0.3765 (ppp) cc_final: 0.3517 (ppp) REVERT: A 146 PHE cc_start: 0.7927 (t80) cc_final: 0.6879 (t80) REVERT: A 172 ARG cc_start: 0.7155 (mmp-170) cc_final: 0.6952 (mmp80) REVERT: A 186 MET cc_start: 0.6383 (tmm) cc_final: 0.6038 (tmm) REVERT: A 428 ASP cc_start: 0.7854 (t0) cc_final: 0.7570 (t70) REVERT: A 501 MET cc_start: 0.7057 (ppp) cc_final: 0.5966 (ppp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2265 time to fit residues: 28.7626 Evaluate side-chains 73 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 50 optimal weight: 0.3980 chunk 13 optimal weight: 0.0670 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.096002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.086318 restraints weight = 71502.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.088166 restraints weight = 43146.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.089403 restraints weight = 29217.099| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9818 Z= 0.153 Angle : 0.546 10.544 13294 Z= 0.278 Chirality : 0.038 0.188 1484 Planarity : 0.004 0.047 1688 Dihedral : 4.134 20.125 1344 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 1.65 (0.24), residues: 1196 helix: 1.94 (0.17), residues: 814 sheet: 1.53 (0.48), residues: 88 loop : -1.57 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 137 HIS 0.004 0.001 HIS A 299 PHE 0.028 0.001 PHE B 130 TYR 0.022 0.001 TYR A 171 ARG 0.004 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 PHE cc_start: 0.8034 (t80) cc_final: 0.6781 (t80) REVERT: B 155 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 172 ARG cc_start: 0.6976 (mmp-170) cc_final: 0.6674 (mmp80) REVERT: B 325 LEU cc_start: 0.7647 (mp) cc_final: 0.7382 (mp) REVERT: B 428 ASP cc_start: 0.8276 (t0) cc_final: 0.7728 (t70) REVERT: B 501 MET cc_start: 0.6285 (ppp) cc_final: 0.5159 (ppp) REVERT: B 539 MET cc_start: 0.9107 (mpp) cc_final: 0.8837 (mpp) REVERT: B 548 MET cc_start: 0.3787 (ppp) cc_final: 0.3453 (ppp) REVERT: B 602 LYS cc_start: 0.6379 (mmtt) cc_final: 0.6097 (mmtt) REVERT: A 146 PHE cc_start: 0.8019 (t80) cc_final: 0.6824 (t80) REVERT: A 155 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7077 (mt-10) REVERT: A 186 MET cc_start: 0.6333 (tmm) cc_final: 0.5943 (tmm) REVERT: A 428 ASP cc_start: 0.7736 (t0) cc_final: 0.7429 (t0) REVERT: A 501 MET cc_start: 0.6929 (ppp) cc_final: 0.5698 (ppp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2550 time to fit residues: 34.1071 Evaluate side-chains 78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.092329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.082909 restraints weight = 72567.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.084627 restraints weight = 44533.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.085795 restraints weight = 30440.198| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9818 Z= 0.249 Angle : 0.627 9.786 13294 Z= 0.331 Chirality : 0.041 0.177 1484 Planarity : 0.005 0.042 1688 Dihedral : 4.385 20.408 1344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1196 helix: 1.50 (0.17), residues: 806 sheet: 1.39 (0.48), residues: 92 loop : -1.59 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 595 HIS 0.006 0.001 HIS A 299 PHE 0.015 0.002 PHE A 175 TYR 0.031 0.002 TYR A 171 ARG 0.013 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.122 Fit side-chains REVERT: B 146 PHE cc_start: 0.8049 (t80) cc_final: 0.6934 (t80) REVERT: B 155 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 172 ARG cc_start: 0.7309 (mmp-170) cc_final: 0.6907 (mmp80) REVERT: B 325 LEU cc_start: 0.7632 (mp) cc_final: 0.7314 (mp) REVERT: B 428 ASP cc_start: 0.8393 (t0) cc_final: 0.7854 (t70) REVERT: B 501 MET cc_start: 0.6691 (ppp) cc_final: 0.5718 (ppp) REVERT: B 539 MET cc_start: 0.9204 (mpp) cc_final: 0.8872 (mpp) REVERT: A 146 PHE cc_start: 0.8041 (t80) cc_final: 0.7003 (t80) REVERT: A 155 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 186 MET cc_start: 0.6474 (tmm) cc_final: 0.6005 (tmm) REVERT: A 428 ASP cc_start: 0.7863 (t0) cc_final: 0.7522 (t0) REVERT: A 501 MET cc_start: 0.6554 (ppp) cc_final: 0.5885 (ppp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2809 time to fit residues: 34.9259 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.093905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.084434 restraints weight = 72282.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.086210 restraints weight = 44039.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.087403 restraints weight = 29920.290| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9818 Z= 0.188 Angle : 0.587 8.864 13294 Z= 0.303 Chirality : 0.039 0.146 1484 Planarity : 0.004 0.044 1688 Dihedral : 4.296 20.243 1344 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1196 helix: 1.68 (0.17), residues: 806 sheet: 1.40 (0.49), residues: 88 loop : -1.48 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 339 HIS 0.004 0.001 HIS A 299 PHE 0.013 0.001 PHE A 385 TYR 0.028 0.002 TYR A 171 ARG 0.005 0.000 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.7067 (ppp) cc_final: 0.6772 (ppp) REVERT: B 122 ILE cc_start: 0.7488 (mm) cc_final: 0.7284 (mt) REVERT: B 146 PHE cc_start: 0.7890 (t80) cc_final: 0.6705 (t80) REVERT: B 172 ARG cc_start: 0.7213 (mmp-170) cc_final: 0.6886 (mmp80) REVERT: B 186 MET cc_start: 0.6538 (tmm) cc_final: 0.6131 (tmm) REVERT: B 325 LEU cc_start: 0.7590 (mp) cc_final: 0.7191 (mp) REVERT: B 428 ASP cc_start: 0.8340 (t0) cc_final: 0.7807 (t70) REVERT: B 501 MET cc_start: 0.6791 (ppp) cc_final: 0.5827 (ppp) REVERT: B 539 MET cc_start: 0.9055 (mpp) cc_final: 0.8710 (mpp) REVERT: A 130 PHE cc_start: 0.6633 (m-10) cc_final: 0.6252 (m-10) REVERT: A 146 PHE cc_start: 0.7893 (t80) cc_final: 0.6774 (t80) REVERT: A 155 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 186 MET cc_start: 0.6467 (tmm) cc_final: 0.5953 (tmm) REVERT: A 428 ASP cc_start: 0.7805 (t0) cc_final: 0.7483 (t0) REVERT: A 501 MET cc_start: 0.6513 (ppp) cc_final: 0.5844 (ppp) REVERT: A 539 MET cc_start: 0.8493 (mpp) cc_final: 0.8207 (mpp) REVERT: A 548 MET cc_start: 0.3000 (ppp) cc_final: 0.2765 (ppp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2188 time to fit residues: 28.5839 Evaluate side-chains 78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** 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 = 0.4260 r_free = 0.4260 target = 0.094622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.085059 restraints weight = 72594.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.086879 restraints weight = 43767.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.088109 restraints weight = 29545.012| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9818 Z= 0.168 Angle : 0.571 11.652 13294 Z= 0.292 Chirality : 0.039 0.137 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.238 20.000 1344 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.46 (0.24), residues: 1196 helix: 1.78 (0.18), residues: 812 sheet: 1.43 (0.50), residues: 88 loop : -1.52 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS A 299 PHE 0.008 0.001 PHE B 385 TYR 0.026 0.002 TYR A 171 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: B 67 MET cc_start: 0.7063 (ppp) cc_final: 0.6761 (ppp) REVERT: B 146 PHE cc_start: 0.8058 (t80) cc_final: 0.6855 (t80) REVERT: B 155 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7163 (tm-30) REVERT: B 172 ARG cc_start: 0.7137 (mmp-170) cc_final: 0.6853 (mmp80) REVERT: B 346 MET cc_start: 0.7693 (mmp) cc_final: 0.7364 (mmp) REVERT: B 428 ASP cc_start: 0.8280 (t0) cc_final: 0.7746 (t70) REVERT: B 501 MET cc_start: 0.6757 (ppp) cc_final: 0.5756 (ppp) REVERT: B 539 MET cc_start: 0.9066 (mpp) cc_final: 0.8724 (mpp) REVERT: A 146 PHE cc_start: 0.8048 (t80) cc_final: 0.6864 (t80) REVERT: A 155 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 186 MET cc_start: 0.6432 (tmm) cc_final: 0.5903 (tmm) REVERT: A 428 ASP cc_start: 0.7744 (t0) cc_final: 0.7405 (t0) REVERT: A 501 MET cc_start: 0.6452 (ppp) cc_final: 0.5703 (ppp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2405 time to fit residues: 30.5343 Evaluate side-chains 81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** 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 = 0.4265 r_free = 0.4265 target = 0.094805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.085341 restraints weight = 71934.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.087143 restraints weight = 43767.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.088330 restraints weight = 29747.077| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9818 Z= 0.170 Angle : 0.561 8.468 13294 Z= 0.290 Chirality : 0.039 0.190 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.214 19.659 1344 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.52 (0.24), residues: 1196 helix: 1.83 (0.17), residues: 814 sheet: 1.39 (0.51), residues: 88 loop : -1.52 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS A 299 PHE 0.016 0.001 PHE A 130 TYR 0.025 0.002 TYR A 171 ARG 0.004 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.7049 (ppp) cc_final: 0.6744 (ppp) REVERT: B 146 PHE cc_start: 0.7960 (t80) cc_final: 0.6827 (t80) REVERT: B 155 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 172 ARG cc_start: 0.7124 (mmp-170) cc_final: 0.6834 (mmp80) REVERT: B 346 MET cc_start: 0.7574 (mmp) cc_final: 0.7285 (mmp) REVERT: B 428 ASP cc_start: 0.8157 (t0) cc_final: 0.7673 (t70) REVERT: B 501 MET cc_start: 0.6773 (ppp) cc_final: 0.5828 (ppp) REVERT: B 539 MET cc_start: 0.9060 (mpp) cc_final: 0.8718 (mpp) REVERT: A 146 PHE cc_start: 0.7983 (t80) cc_final: 0.6965 (t80) REVERT: A 155 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 186 MET cc_start: 0.6393 (tmm) cc_final: 0.5849 (tmm) REVERT: A 428 ASP cc_start: 0.7745 (t0) cc_final: 0.7409 (t0) REVERT: A 501 MET cc_start: 0.6443 (ppp) cc_final: 0.5821 (ppp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2647 time to fit residues: 34.3827 Evaluate side-chains 80 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** 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 = 0.4271 r_free = 0.4271 target = 0.095364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.085905 restraints weight = 72119.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.087729 restraints weight = 43726.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.088976 restraints weight = 29620.607| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9818 Z= 0.159 Angle : 0.556 8.469 13294 Z= 0.287 Chirality : 0.039 0.167 1484 Planarity : 0.004 0.039 1688 Dihedral : 4.176 19.770 1344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 1.53 (0.24), residues: 1196 helix: 1.80 (0.18), residues: 832 sheet: 1.44 (0.50), residues: 88 loop : -1.61 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.004 0.001 HIS B 210 PHE 0.008 0.001 PHE A 385 TYR 0.023 0.002 TYR A 171 ARG 0.003 0.000 ARG A 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.7023 (ppp) cc_final: 0.6717 (ppp) REVERT: B 146 PHE cc_start: 0.8079 (t80) cc_final: 0.6824 (t80) REVERT: B 155 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 172 ARG cc_start: 0.7054 (mmp-170) cc_final: 0.6798 (mmp80) REVERT: B 346 MET cc_start: 0.7539 (mmp) cc_final: 0.7275 (mmp) REVERT: B 385 PHE cc_start: 0.3874 (m-10) cc_final: 0.2615 (t80) REVERT: B 428 ASP cc_start: 0.8127 (t0) cc_final: 0.7644 (t70) REVERT: B 501 MET cc_start: 0.6708 (ppp) cc_final: 0.5765 (ppp) REVERT: B 539 MET cc_start: 0.9048 (mpp) cc_final: 0.8719 (mpp) REVERT: A 146 PHE cc_start: 0.7981 (t80) cc_final: 0.6968 (t80) REVERT: A 155 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 186 MET cc_start: 0.6362 (tmm) cc_final: 0.5820 (tmm) REVERT: A 428 ASP cc_start: 0.7701 (t0) cc_final: 0.7362 (t0) REVERT: A 501 MET cc_start: 0.6383 (ppp) cc_final: 0.5768 (ppp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2391 time to fit residues: 31.1522 Evaluate side-chains 81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** 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 = 0.4275 r_free = 0.4275 target = 0.095610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.086223 restraints weight = 71584.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.088053 restraints weight = 43286.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.089295 restraints weight = 29291.991| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9818 Z= 0.159 Angle : 0.556 8.348 13294 Z= 0.284 Chirality : 0.039 0.148 1484 Planarity : 0.004 0.040 1688 Dihedral : 4.136 19.086 1344 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.57 (0.24), residues: 1196 helix: 1.83 (0.17), residues: 832 sheet: 1.42 (0.51), residues: 88 loop : -1.62 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS B 210 PHE 0.007 0.001 PHE A 385 TYR 0.022 0.002 TYR A 171 ARG 0.003 0.000 ARG B 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.02 seconds wall clock time: 50 minutes 47.38 seconds (3047.38 seconds total)