Starting phenix.real_space_refine on Thu Mar 13 05:39:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t57_41044/03_2025/8t57_41044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t57_41044/03_2025/8t57_41044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t57_41044/03_2025/8t57_41044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t57_41044/03_2025/8t57_41044.map" model { file = "/net/cci-nas-00/data/ceres_data/8t57_41044/03_2025/8t57_41044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t57_41044/03_2025/8t57_41044.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 26 5.16 5 C 5752 2.51 5 N 1270 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8466 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4033 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 29, 'TRANS': 474} Chain breaks: 5 Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Unusual residues: {'CLR': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Restraints were copied for chains: B Time building chain proxies: 7.70, per 1000 atoms: 0.91 Number of scatterers: 8466 At special positions: 0 Unit cell: (85.49, 120.51, 85.49, 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 26 16.00 O 1418 8.00 N 1270 7.00 C 5752 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: 2.27 Conformation dependent library (CDL) restraints added in 949.6 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 80.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 73 through 81 Processing helix chain 'A' and resid 82 through 109 Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 130 through 139 removed outlier: 6.746A pdb=" N ILE A 136 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 137 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 182 removed outlier: 3.611A pdb=" N HIS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.783A pdb=" N VAL A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.614A pdb=" N ALA A 347 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 368 Processing helix chain 'A' and resid 411 through 420 removed outlier: 3.502A pdb=" N PHE A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 475 through 478 removed outlier: 6.597A pdb=" N LYS A 478 " --> pdb=" O LEU A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'A' and resid 540 through 562 Proline residue: A 546 - end of helix removed outlier: 3.908A pdb=" N PHE A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 587 Processing helix chain 'A' and resid 598 through 624 Processing helix chain 'A' and resid 626 through 633 Processing helix chain 'A' and resid 634 through 651 removed outlier: 3.565A pdb=" N VAL A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 659 through 674 removed outlier: 3.671A pdb=" N ARG A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 4.083A pdb=" N SER A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 82 through 109 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 130 through 139 removed outlier: 6.746A pdb=" N ILE B 136 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 137 " --> pdb=" O PHE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 182 removed outlier: 3.611A pdb=" N HIS B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.782A pdb=" N VAL B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 removed outlier: 3.614A pdb=" N ALA B 347 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 368 Processing helix chain 'B' and resid 411 through 420 removed outlier: 3.502A pdb=" N PHE B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 457 through 463 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 475 through 478 removed outlier: 6.598A pdb=" N LYS B 478 " --> pdb=" O LEU B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 479 through 486 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'B' and resid 540 through 562 Proline residue: B 546 - end of helix removed outlier: 3.909A pdb=" N PHE B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 587 Processing helix chain 'B' and resid 598 through 624 Processing helix chain 'B' and resid 626 through 633 Processing helix chain 'B' and resid 634 through 651 removed outlier: 3.565A pdb=" N VAL B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 Processing helix chain 'B' and resid 659 through 674 removed outlier: 3.670A pdb=" N ARG B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 684 removed outlier: 4.083A pdb=" N SER B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.897A pdb=" N SER A 222 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 220 through 224 removed outlier: 3.897A pdb=" N SER B 222 " --> pdb=" O SER B 307 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1671 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: 2.37 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1283 1.30 - 1.43: 2361 1.43 - 1.55: 4707 1.55 - 1.67: 301 1.67 - 1.80: 40 Bond restraints: 8692 Sorted by residual: bond pdb=" C10 CLR B 802 " pdb=" C9 CLR B 802 " ideal model delta sigma weight residual 1.551 1.715 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" C10 CLR A 802 " pdb=" C9 CLR A 802 " ideal model delta sigma weight residual 1.551 1.715 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" C4 CLR B 802 " pdb=" C5 CLR B 802 " ideal model delta sigma weight residual 1.506 1.660 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C4 CLR A 802 " pdb=" C5 CLR A 802 " ideal model delta sigma weight residual 1.506 1.659 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C10 CLR A 801 " pdb=" C9 CLR A 801 " ideal model delta sigma weight residual 1.551 1.704 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 8687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10242 2.36 - 4.73: 1324 4.73 - 7.09: 184 7.09 - 9.46: 28 9.46 - 11.82: 2 Bond angle restraints: 11780 Sorted by residual: angle pdb=" C SER B 562 " pdb=" N PRO B 563 " pdb=" CA PRO B 563 " ideal model delta sigma weight residual 119.56 128.55 -8.99 1.02e+00 9.61e-01 7.77e+01 angle pdb=" C SER A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.74e+01 angle pdb=" C TYR A 658 " pdb=" N PRO A 659 " pdb=" CA PRO A 659 " ideal model delta sigma weight residual 120.21 127.68 -7.47 9.60e-01 1.09e+00 6.06e+01 angle pdb=" C TYR B 658 " pdb=" N PRO B 659 " pdb=" CA PRO B 659 " ideal model delta sigma weight residual 120.21 127.65 -7.44 9.60e-01 1.09e+00 6.01e+01 angle pdb=" C LEU A 410 " pdb=" N PRO A 411 " pdb=" CA PRO A 411 " ideal model delta sigma weight residual 119.82 127.26 -7.44 9.80e-01 1.04e+00 5.76e+01 ... (remaining 11775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 4982 15.82 - 31.64: 250 31.64 - 47.46: 46 47.46 - 63.28: 34 63.28 - 79.09: 4 Dihedral angle restraints: 5316 sinusoidal: 2338 harmonic: 2978 Sorted by residual: dihedral pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CA LEU A 652 " pdb=" CB LEU A 652 " ideal model delta harmonic sigma weight residual 122.80 131.22 -8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" N LEU B 652 " pdb=" C LEU B 652 " pdb=" CA LEU B 652 " pdb=" CB LEU B 652 " ideal model delta harmonic sigma weight residual 122.80 131.16 -8.36 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" C TRP B 599 " pdb=" N TRP B 599 " pdb=" CA TRP B 599 " pdb=" CB TRP B 599 " ideal model delta harmonic sigma weight residual -122.60 -130.71 8.11 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 912 0.102 - 0.203: 338 0.203 - 0.304: 80 0.304 - 0.406: 16 0.406 - 0.507: 16 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CB ILE B 368 " pdb=" CA ILE B 368 " pdb=" CG1 ILE B 368 " pdb=" CG2 ILE B 368 " both_signs ideal model delta sigma weight residual False 2.64 3.13 -0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 1359 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 24 " -0.052 2.00e-02 2.50e+03 3.15e-02 1.98e+01 pdb=" CG TYR B 24 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 24 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 24 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 24 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 24 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 24 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 24 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " 0.052 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR A 24 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " -0.059 2.00e-02 2.50e+03 2.98e-02 1.78e+01 pdb=" CG TYR B 215 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " -0.037 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3280 2.89 - 3.39: 8658 3.39 - 3.89: 14173 3.89 - 4.40: 18020 4.40 - 4.90: 27840 Nonbonded interactions: 71971 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" NZ LYS A 174 " model vdw 2.385 3.120 nonbonded pdb=" OD1 ASP B 75 " pdb=" NZ LYS B 174 " model vdw 2.385 3.120 nonbonded pdb=" CB GLU A 510 " pdb=" OE1 GLU A 510 " model vdw 2.412 2.752 nonbonded pdb=" CB GLU B 510 " pdb=" OE1 GLU B 510 " model vdw 2.412 2.752 nonbonded pdb=" N PRO A 335 " pdb=" O PRO A 335 " model vdw 2.508 2.496 ... (remaining 71966 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 individual isotropic 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: 0.330 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.070 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.027 0.164 8692 Z= 1.715 Angle : 1.654 11.819 11780 Z= 1.110 Chirality : 0.120 0.507 1362 Planarity : 0.008 0.031 1398 Dihedral : 11.192 79.094 3380 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.77 (0.25), residues: 984 helix: 0.45 (0.18), residues: 706 sheet: 2.58 (0.99), residues: 24 loop : 0.92 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.007 TRP A 599 HIS 0.007 0.003 HIS A 614 PHE 0.039 0.006 PHE A 99 TYR 0.059 0.009 TYR B 215 ARG 0.005 0.001 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.823 Fit side-chains REVERT: A 426 MET cc_start: 0.8327 (mmt) cc_final: 0.7787 (mmt) REVERT: B 426 MET cc_start: 0.8314 (mmt) cc_final: 0.7575 (mmt) outliers start: 0 outliers final: 2 residues processed: 151 average time/residue: 0.9306 time to fit residues: 152.1996 Evaluate side-chains 68 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 109 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 543 GLN B 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.124971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101763 restraints weight = 12896.297| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.89 r_work: 0.3331 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8692 Z= 0.305 Angle : 0.650 6.919 11780 Z= 0.336 Chirality : 0.047 0.173 1362 Planarity : 0.005 0.040 1398 Dihedral : 9.913 56.812 1566 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.54 % Allowed : 8.08 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 984 helix: 1.53 (0.19), residues: 694 sheet: 1.32 (1.09), residues: 24 loop : 0.44 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 599 HIS 0.008 0.002 HIS A 223 PHE 0.023 0.002 PHE A 415 TYR 0.019 0.002 TYR B 577 ARG 0.002 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.862 Fit side-chains REVERT: A 132 ASP cc_start: 0.8318 (m-30) cc_final: 0.8078 (p0) REVERT: A 145 LYS cc_start: 0.8020 (mptt) cc_final: 0.7745 (mmpt) REVERT: A 174 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8521 (mtpp) REVERT: B 174 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8497 (mtpp) outliers start: 23 outliers final: 9 residues processed: 96 average time/residue: 0.8900 time to fit residues: 93.6457 Evaluate side-chains 74 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.126029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.103084 restraints weight = 13129.600| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.92 r_work: 0.3342 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8692 Z= 0.222 Angle : 0.552 5.225 11780 Z= 0.286 Chirality : 0.044 0.144 1362 Planarity : 0.005 0.042 1398 Dihedral : 9.173 59.011 1566 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.21 % Allowed : 9.51 % Favored : 87.28 % 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: 1.99 (0.26), residues: 984 helix: 1.68 (0.19), residues: 696 sheet: 1.28 (1.10), residues: 24 loop : 0.56 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 504 HIS 0.002 0.001 HIS B 149 PHE 0.018 0.001 PHE A 99 TYR 0.014 0.002 TYR B 577 ARG 0.002 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.878 Fit side-chains REVERT: A 145 LYS cc_start: 0.7991 (mptt) cc_final: 0.7781 (mmpt) REVERT: A 543 GLN cc_start: 0.8174 (mt0) cc_final: 0.7923 (tm-30) REVERT: B 131 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7369 (ttt) REVERT: B 145 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7676 (mmpt) REVERT: B 468 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7667 (tm) REVERT: B 474 PHE cc_start: 0.7872 (m-80) cc_final: 0.7584 (m-80) REVERT: B 585 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6339 (mt) outliers start: 29 outliers final: 16 residues processed: 102 average time/residue: 0.9400 time to fit residues: 104.5170 Evaluate side-chains 87 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.126271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103414 restraints weight = 13044.389| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.93 r_work: 0.3343 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8692 Z= 0.198 Angle : 0.540 8.614 11780 Z= 0.274 Chirality : 0.043 0.135 1362 Planarity : 0.005 0.046 1398 Dihedral : 8.931 59.572 1566 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.88 % Allowed : 10.07 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 984 helix: 1.78 (0.19), residues: 698 sheet: 1.18 (1.11), residues: 24 loop : 0.72 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 504 HIS 0.002 0.001 HIS B 168 PHE 0.025 0.001 PHE A 415 TYR 0.016 0.002 TYR B 170 ARG 0.002 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.880 Fit side-chains REVERT: A 131 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7447 (ttt) REVERT: A 145 LYS cc_start: 0.7948 (mptt) cc_final: 0.7691 (mmpt) REVERT: A 560 PHE cc_start: 0.8851 (t80) cc_final: 0.8617 (t80) REVERT: A 657 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 670 ASP cc_start: 0.7641 (m-30) cc_final: 0.7075 (m-30) REVERT: B 585 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6476 (mt) outliers start: 26 outliers final: 14 residues processed: 93 average time/residue: 0.8551 time to fit residues: 87.4631 Evaluate side-chains 88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.0670 chunk 81 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104399 restraints weight = 12969.961| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.92 r_work: 0.3358 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8692 Z= 0.177 Angle : 0.524 7.447 11780 Z= 0.265 Chirality : 0.042 0.132 1362 Planarity : 0.005 0.048 1398 Dihedral : 8.727 59.031 1562 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.65 % Allowed : 10.51 % Favored : 86.84 % 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: 2.38 (0.27), residues: 984 helix: 2.03 (0.19), residues: 686 sheet: 0.91 (1.11), residues: 24 loop : 0.63 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 504 HIS 0.002 0.000 HIS B 168 PHE 0.016 0.001 PHE A 99 TYR 0.013 0.002 TYR A 170 ARG 0.002 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.976 Fit side-chains REVERT: A 145 LYS cc_start: 0.7895 (mptt) cc_final: 0.7653 (mmpt) REVERT: A 560 PHE cc_start: 0.8835 (t80) cc_final: 0.8591 (t80) REVERT: A 670 ASP cc_start: 0.7584 (m-30) cc_final: 0.6997 (m-30) REVERT: B 426 MET cc_start: 0.7499 (mmt) cc_final: 0.7210 (mmt) REVERT: B 468 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7708 (tm) REVERT: B 585 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6441 (mt) REVERT: B 670 ASP cc_start: 0.7534 (m-30) cc_final: 0.7162 (m-30) outliers start: 24 outliers final: 8 residues processed: 97 average time/residue: 0.8151 time to fit residues: 87.2766 Evaluate side-chains 82 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103914 restraints weight = 12844.726| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.89 r_work: 0.3355 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8692 Z= 0.201 Angle : 0.535 9.584 11780 Z= 0.269 Chirality : 0.042 0.134 1362 Planarity : 0.005 0.050 1398 Dihedral : 8.727 57.761 1562 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.77 % Allowed : 10.73 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 984 helix: 2.03 (0.19), residues: 686 sheet: -0.27 (0.98), residues: 30 loop : 0.66 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 504 HIS 0.002 0.001 HIS B 168 PHE 0.024 0.002 PHE B 415 TYR 0.013 0.001 TYR B 577 ARG 0.003 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.833 Fit side-chains REVERT: A 145 LYS cc_start: 0.7905 (mptt) cc_final: 0.7662 (mmpt) REVERT: A 474 PHE cc_start: 0.7802 (m-80) cc_final: 0.7519 (m-10) REVERT: A 560 PHE cc_start: 0.8840 (t80) cc_final: 0.8581 (t80) REVERT: A 585 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6515 (mt) REVERT: A 670 ASP cc_start: 0.7555 (m-30) cc_final: 0.6916 (m-30) REVERT: B 145 LYS cc_start: 0.7869 (mmpt) cc_final: 0.7547 (mmpt) REVERT: B 426 MET cc_start: 0.7485 (mmt) cc_final: 0.7177 (mmt) REVERT: B 468 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7676 (tm) REVERT: B 474 PHE cc_start: 0.7763 (m-80) cc_final: 0.7466 (m-10) REVERT: B 585 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6378 (mt) REVERT: B 670 ASP cc_start: 0.7592 (m-30) cc_final: 0.7158 (m-30) outliers start: 25 outliers final: 11 residues processed: 95 average time/residue: 0.7623 time to fit residues: 80.1882 Evaluate side-chains 87 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103543 restraints weight = 12989.670| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.90 r_work: 0.3345 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8692 Z= 0.208 Angle : 0.543 10.579 11780 Z= 0.273 Chirality : 0.043 0.142 1362 Planarity : 0.005 0.053 1398 Dihedral : 8.744 59.415 1562 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.77 % Allowed : 11.06 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.27), residues: 984 helix: 2.01 (0.19), residues: 686 sheet: -0.38 (0.98), residues: 30 loop : 0.64 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.002 0.001 HIS B 168 PHE 0.018 0.001 PHE B 99 TYR 0.013 0.001 TYR B 577 ARG 0.002 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.928 Fit side-chains REVERT: A 474 PHE cc_start: 0.7740 (m-80) cc_final: 0.7442 (m-10) REVERT: A 561 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8218 (mm) REVERT: A 585 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6512 (mt) REVERT: A 670 ASP cc_start: 0.7564 (m-30) cc_final: 0.6928 (m-30) REVERT: B 426 MET cc_start: 0.7484 (mmt) cc_final: 0.7146 (mmt) REVERT: B 468 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7708 (tm) REVERT: B 474 PHE cc_start: 0.7727 (m-80) cc_final: 0.7434 (m-10) REVERT: B 585 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6384 (mt) REVERT: B 670 ASP cc_start: 0.7632 (m-30) cc_final: 0.7217 (m-30) outliers start: 25 outliers final: 13 residues processed: 91 average time/residue: 0.7704 time to fit residues: 77.9248 Evaluate side-chains 88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.128064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105298 restraints weight = 13047.387| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.90 r_work: 0.3371 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8692 Z= 0.160 Angle : 0.523 9.668 11780 Z= 0.263 Chirality : 0.042 0.195 1362 Planarity : 0.005 0.054 1398 Dihedral : 8.538 59.915 1562 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.32 % Allowed : 11.73 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.27), residues: 984 helix: 2.14 (0.19), residues: 684 sheet: -0.33 (0.99), residues: 30 loop : 0.71 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.001 0.000 HIS B 168 PHE 0.023 0.001 PHE B 415 TYR 0.013 0.001 TYR B 469 ARG 0.002 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.131 Fit side-chains REVERT: A 413 LEU cc_start: 0.9191 (tp) cc_final: 0.8937 (mt) REVERT: A 426 MET cc_start: 0.7421 (mmt) cc_final: 0.7094 (mmt) REVERT: A 474 PHE cc_start: 0.7674 (m-80) cc_final: 0.7405 (m-10) REVERT: A 561 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8130 (mm) REVERT: A 670 ASP cc_start: 0.7415 (m-30) cc_final: 0.7118 (m-30) REVERT: B 426 MET cc_start: 0.7365 (mmt) cc_final: 0.6992 (mmt) REVERT: B 468 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7645 (tm) REVERT: B 474 PHE cc_start: 0.7668 (m-80) cc_final: 0.7402 (m-10) REVERT: B 561 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8195 (mm) REVERT: B 585 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6321 (mt) REVERT: B 670 ASP cc_start: 0.7573 (m-30) cc_final: 0.7189 (m-30) outliers start: 21 outliers final: 10 residues processed: 93 average time/residue: 0.8846 time to fit residues: 91.5881 Evaluate side-chains 86 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN ** B 328 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 = 0.3832 r_free = 0.3832 target = 0.126974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104026 restraints weight = 12997.977| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.91 r_work: 0.3352 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8692 Z= 0.195 Angle : 0.551 9.357 11780 Z= 0.273 Chirality : 0.044 0.293 1362 Planarity : 0.005 0.055 1398 Dihedral : 8.591 59.421 1562 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.66 % Allowed : 12.72 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.27), residues: 984 helix: 2.08 (0.19), residues: 686 sheet: -0.48 (0.99), residues: 30 loop : 0.70 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 504 HIS 0.002 0.001 HIS B 168 PHE 0.018 0.001 PHE A 99 TYR 0.015 0.002 TYR A 469 ARG 0.002 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.801 Fit side-chains REVERT: A 426 MET cc_start: 0.7555 (mmt) cc_final: 0.7207 (mmt) REVERT: A 474 PHE cc_start: 0.7697 (m-80) cc_final: 0.7449 (m-10) REVERT: A 561 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 585 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6545 (mt) REVERT: A 670 ASP cc_start: 0.7529 (m-30) cc_final: 0.6883 (m-30) REVERT: B 425 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8385 (mt) REVERT: B 426 MET cc_start: 0.7473 (mmt) cc_final: 0.7062 (mmt) REVERT: B 468 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7689 (tm) REVERT: B 474 PHE cc_start: 0.7681 (m-80) cc_final: 0.7407 (m-10) REVERT: B 561 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 585 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6365 (mt) REVERT: B 670 ASP cc_start: 0.7624 (m-30) cc_final: 0.7214 (m-30) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.8446 time to fit residues: 84.6595 Evaluate side-chains 86 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.126138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103219 restraints weight = 12919.997| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.89 r_work: 0.3338 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8692 Z= 0.223 Angle : 0.563 9.530 11780 Z= 0.280 Chirality : 0.044 0.255 1362 Planarity : 0.005 0.055 1398 Dihedral : 8.697 58.300 1562 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.66 % Allowed : 13.38 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 984 helix: 2.01 (0.19), residues: 686 sheet: -0.61 (1.01), residues: 30 loop : 0.57 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 504 HIS 0.002 0.001 HIS B 168 PHE 0.025 0.002 PHE A 415 TYR 0.015 0.002 TYR B 469 ARG 0.002 0.000 ARG B 672 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.362 Fit side-chains REVERT: A 426 MET cc_start: 0.7589 (mmt) cc_final: 0.7216 (mmt) REVERT: A 474 PHE cc_start: 0.7701 (m-80) cc_final: 0.7440 (m-10) REVERT: A 561 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 585 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6497 (mt) REVERT: A 670 ASP cc_start: 0.7540 (m-30) cc_final: 0.6894 (m-30) REVERT: B 426 MET cc_start: 0.7539 (mmt) cc_final: 0.7199 (mmt) REVERT: B 468 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7694 (tm) REVERT: B 474 PHE cc_start: 0.7671 (m-80) cc_final: 0.7420 (m-10) REVERT: B 561 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 670 ASP cc_start: 0.7664 (m-30) cc_final: 0.7248 (m-30) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 0.9719 time to fit residues: 90.3018 Evaluate side-chains 84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 644 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103746 restraints weight = 13035.415| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.91 r_work: 0.3349 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8692 Z= 0.195 Angle : 0.551 9.506 11780 Z= 0.275 Chirality : 0.043 0.232 1362 Planarity : 0.005 0.058 1398 Dihedral : 8.603 57.943 1562 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.44 % Allowed : 13.61 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.27), residues: 984 helix: 2.07 (0.19), residues: 686 sheet: -0.54 (1.00), residues: 30 loop : 0.55 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 504 HIS 0.002 0.001 HIS B 168 PHE 0.017 0.001 PHE A 99 TYR 0.019 0.002 TYR A 469 ARG 0.002 0.000 ARG B 672 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6056.20 seconds wall clock time: 106 minutes 11.91 seconds (6371.91 seconds total)