Starting phenix.real_space_refine on Fri Nov 15 09:02:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/11_2024/8t57_41044.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/11_2024/8t57_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/11_2024/8t57_41044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/11_2024/8t57_41044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/11_2024/8t57_41044.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/11_2024/8t57_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-5513/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: 7.59, per 1000 atoms: 0.90 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: 2.60 Conformation dependent library (CDL) restraints added in 925.1 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: 0.97 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: 2.45 Time building geometry restraints manager: 2.87 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: 0.00 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: 0.530 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.710 Find NCS groups from input model: 0.220 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- 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 : 0.950 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: 1.0071 time to fit residues: 164.7403 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 : 1.227 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.952 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 96 average time/residue: 0.9142 time to fit residues: 96.1300 Evaluate side-chains 72 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE 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 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 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 0.0020 chunk 31 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8692 Z= 0.170 Angle : 0.537 5.030 11780 Z= 0.279 Chirality : 0.042 0.136 1362 Planarity : 0.005 0.044 1398 Dihedral : 8.957 59.983 1566 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.65 % Allowed : 9.85 % Favored : 87.50 % 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: 2.21 (0.27), residues: 984 helix: 1.81 (0.19), residues: 698 sheet: 1.47 (1.10), residues: 24 loop : 0.71 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 504 HIS 0.003 0.001 HIS A 168 PHE 0.014 0.001 PHE A 99 TYR 0.018 0.002 TYR B 170 ARG 0.003 0.000 ARG B 175 *********************** 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: 24 poor density : 87 time to evaluate : 0.995 Fit side-chains REVERT: A 426 MET cc_start: 0.8014 (mmt) cc_final: 0.7642 (mmt) REVERT: B 426 MET cc_start: 0.7891 (mmt) cc_final: 0.6797 (mmt) REVERT: B 585 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6087 (mt) outliers start: 24 outliers final: 8 residues processed: 103 average time/residue: 0.8070 time to fit residues: 91.8886 Evaluate side-chains 76 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 511 ILE Chi-restraints excluded: chain A residue 688 ARG 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 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 68 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.004 0.045 8692 Z= 0.231 Angle : 0.555 9.246 11780 Z= 0.282 Chirality : 0.043 0.140 1362 Planarity : 0.005 0.046 1398 Dihedral : 8.967 59.949 1562 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.65 % Allowed : 10.29 % 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: 2.19 (0.27), residues: 984 helix: 1.79 (0.19), residues: 698 sheet: 1.09 (1.12), residues: 24 loop : 0.75 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 504 HIS 0.002 0.001 HIS B 168 PHE 0.024 0.002 PHE A 415 TYR 0.014 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 103 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.972 Fit side-chains REVERT: B 426 MET cc_start: 0.7946 (mmt) cc_final: 0.7721 (mmt) REVERT: B 585 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6345 (mt) outliers start: 24 outliers final: 14 residues processed: 93 average time/residue: 0.8673 time to fit residues: 89.0889 Evaluate side-chains 84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 414 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 457 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 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 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 1 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8692 Z= 0.176 Angle : 0.522 7.882 11780 Z= 0.264 Chirality : 0.042 0.130 1362 Planarity : 0.005 0.048 1398 Dihedral : 8.685 59.032 1562 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.21 % Allowed : 11.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.27), residues: 984 helix: 2.06 (0.19), residues: 686 sheet: 0.78 (1.11), residues: 24 loop : 0.62 (0.41), residues: 274 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 0.016 0.001 PHE A 99 TYR 0.012 0.002 TYR B 577 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 99 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.875 Fit side-chains REVERT: B 426 MET cc_start: 0.7998 (mmt) cc_final: 0.7611 (mmt) REVERT: B 474 PHE cc_start: 0.7579 (m-80) cc_final: 0.7309 (m-10) REVERT: B 585 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6310 (mt) outliers start: 20 outliers final: 8 residues processed: 90 average time/residue: 0.8801 time to fit residues: 87.2091 Evaluate side-chains 80 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 511 ILE 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 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 19 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN B 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3253 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= 0.193 Angle : 0.534 9.665 11780 Z= 0.268 Chirality : 0.042 0.132 1362 Planarity : 0.005 0.051 1398 Dihedral : 8.665 58.009 1562 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.32 % Allowed : 11.28 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.27), residues: 984 helix: 2.07 (0.19), residues: 686 sheet: -0.30 (0.98), residues: 30 loop : 0.67 (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 0.001 PHE B 415 TYR 0.012 0.001 TYR A 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 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.981 Fit side-chains REVERT: B 426 MET cc_start: 0.7995 (mmt) cc_final: 0.7612 (mmt) REVERT: B 474 PHE cc_start: 0.7571 (m-80) cc_final: 0.7322 (m-10) outliers start: 21 outliers final: 9 residues processed: 93 average time/residue: 0.8366 time to fit residues: 86.5514 Evaluate side-chains 85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 514 LEU 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 644 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.0370 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8692 Z= 0.177 Angle : 0.527 10.700 11780 Z= 0.265 Chirality : 0.043 0.223 1362 Planarity : 0.005 0.054 1398 Dihedral : 8.550 59.439 1562 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.43 % Allowed : 11.73 % Favored : 85.84 % 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: 2.40 (0.27), residues: 984 helix: 2.09 (0.20), residues: 686 sheet: -0.35 (0.99), residues: 30 loop : 0.67 (0.41), residues: 268 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 0.016 0.001 PHE B 99 TYR 0.013 0.001 TYR A 469 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 101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.913 Fit side-chains REVERT: A 426 MET cc_start: 0.8005 (mmt) cc_final: 0.7654 (mmt) REVERT: A 474 PHE cc_start: 0.7605 (m-80) cc_final: 0.7362 (m-10) REVERT: B 426 MET cc_start: 0.7990 (mmt) cc_final: 0.7519 (mmt) outliers start: 22 outliers final: 13 residues processed: 95 average time/residue: 0.7814 time to fit residues: 82.4031 Evaluate side-chains 87 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 504 TRP Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 162 SER 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 504 TRP 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 29 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8692 Z= 0.175 Angle : 0.531 9.666 11780 Z= 0.265 Chirality : 0.043 0.198 1362 Planarity : 0.005 0.055 1398 Dihedral : 8.465 59.775 1562 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.77 % Allowed : 12.94 % Favored : 85.29 % 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: 2.44 (0.27), residues: 984 helix: 2.13 (0.20), residues: 684 sheet: -0.40 (0.99), residues: 30 loop : 0.64 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.002 0.000 HIS B 168 PHE 0.022 0.001 PHE B 415 TYR 0.014 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 93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.900 Fit side-chains REVERT: A 425 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8360 (mt) REVERT: A 426 MET cc_start: 0.7993 (mmt) cc_final: 0.7579 (mmt) REVERT: B 426 MET cc_start: 0.7993 (mmt) cc_final: 0.7521 (mmt) outliers start: 16 outliers final: 10 residues processed: 89 average time/residue: 0.8190 time to fit residues: 80.5392 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 : 0.887 ------------------------------------------------------------------------------- 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 B residue 162 SER 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 504 TRP 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 92 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8692 Z= 0.182 Angle : 0.545 9.508 11780 Z= 0.271 Chirality : 0.043 0.289 1362 Planarity : 0.005 0.055 1398 Dihedral : 8.407 59.304 1562 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.10 % Allowed : 13.05 % Favored : 84.85 % 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: 2.41 (0.27), residues: 984 helix: 2.11 (0.20), residues: 686 sheet: -0.50 (1.00), residues: 30 loop : 0.63 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 504 HIS 0.001 0.000 HIS B 168 PHE 0.017 0.001 PHE A 99 TYR 0.015 0.001 TYR A 469 ARG 0.002 0.000 ARG B 688 *********************** 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 101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.929 Fit side-chains REVERT: A 426 MET cc_start: 0.8049 (mmt) cc_final: 0.7574 (mmt) REVERT: B 425 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8377 (mt) REVERT: B 426 MET cc_start: 0.8000 (mmt) cc_final: 0.7626 (mmt) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.8180 time to fit residues: 87.0753 Evaluate side-chains 89 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 428 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 425 ILE 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 644 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3529 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= 0.205 Angle : 0.556 9.519 11780 Z= 0.277 Chirality : 0.043 0.252 1362 Planarity : 0.005 0.058 1398 Dihedral : 8.493 58.231 1562 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.77 % Allowed : 13.61 % Favored : 84.62 % 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: 2.33 (0.27), residues: 984 helix: 2.03 (0.20), residues: 688 sheet: -0.55 (1.00), residues: 30 loop : 0.65 (0.41), residues: 266 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 0.024 0.002 PHE A 415 TYR 0.016 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 96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.101 Fit side-chains REVERT: A 426 MET cc_start: 0.8050 (mmt) cc_final: 0.7603 (mmt) REVERT: B 426 MET cc_start: 0.8039 (mmt) cc_final: 0.7638 (mmt) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.8476 time to fit residues: 86.5089 Evaluate side-chains 87 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 428 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 162 SER 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 504 TRP 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 73 optimal weight: 0.0270 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.127894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.104913 restraints weight = 12810.879| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.90 r_work: 0.3366 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8692 Z= 0.176 Angle : 0.545 9.502 11780 Z= 0.272 Chirality : 0.043 0.243 1362 Planarity : 0.005 0.060 1398 Dihedral : 8.394 58.191 1562 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.55 % Allowed : 14.05 % Favored : 84.40 % 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: 2.45 (0.27), residues: 984 helix: 2.13 (0.20), residues: 688 sheet: -0.52 (1.00), residues: 30 loop : 0.66 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 504 HIS 0.001 0.000 HIS B 168 PHE 0.016 0.001 PHE A 99 TYR 0.012 0.001 TYR A 577 ARG 0.004 0.000 ARG A 672 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.78 seconds wall clock time: 50 minutes 30.97 seconds (3030.97 seconds total)