Starting phenix.real_space_refine on Thu Mar 14 19:50:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/03_2024/7psl_13613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/03_2024/7psl_13613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/03_2024/7psl_13613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/03_2024/7psl_13613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/03_2024/7psl_13613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psl_13613/03_2024/7psl_13613_updated.pdb" } resolution = 3.3 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= 0.070 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 34 5.16 5 C 6190 2.51 5 N 1634 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9612 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4756 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 17, 'TRANS': 582} Chain: "B" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4756 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 17, 'TRANS': 582} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'LOP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'LOP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.60, per 1000 atoms: 0.58 Number of scatterers: 9612 At special positions: 0 Unit cell: (109.647, 76.167, 142.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 4 15.00 O 1750 8.00 N 1634 7.00 C 6190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 2 sheets defined 63.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 105 through 139 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 152 through 200 removed outlier: 4.073A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 211 through 233 Processing helix chain 'A' and resid 237 through 253 Processing helix chain 'A' and resid 256 through 303 removed outlier: 3.519A pdb=" N ALA A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 315 through 367 removed outlier: 3.939A pdb=" N ILE A 366 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 413 Proline residue: A 388 - end of helix removed outlier: 5.535A pdb=" N PHE A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 505 through 511 removed outlier: 4.351A pdb=" N VAL A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 533 removed outlier: 4.741A pdb=" N GLY A 533 " --> pdb=" O ASN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 552 through 555 No H-bonds generated for 'chain 'A' and resid 552 through 555' Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 605 through 618 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 105 through 139 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 152 through 200 removed outlier: 4.074A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 200 " --> pdb=" O GLN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 211 through 233 Processing helix chain 'B' and resid 237 through 253 Processing helix chain 'B' and resid 256 through 303 removed outlier: 3.518A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 315 through 367 removed outlier: 3.938A pdb=" N ILE B 366 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 413 Proline residue: B 388 - end of helix removed outlier: 5.535A pdb=" N PHE B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 505 through 511 removed outlier: 4.351A pdb=" N VAL B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 4.741A pdb=" N GLY B 533 " --> pdb=" O ASN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 552 through 555 No H-bonds generated for 'chain 'B' and resid 552 through 555' Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 605 through 618 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 666 through 690 Processing sheet with id= A, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.224A pdb=" N ALA A 466 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 645 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 468 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 642 through 645 removed outlier: 6.224A pdb=" N ALA B 466 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 645 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 468 " --> pdb=" O LEU B 645 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1728 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: 2.77 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1552 1.31 - 1.43: 2487 1.43 - 1.56: 5683 1.56 - 1.68: 4 1.68 - 1.81: 62 Bond restraints: 9788 Sorted by residual: bond pdb=" C24 LOP B 701 " pdb=" O6 LOP B 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C24 LOP A 701 " pdb=" O6 LOP A 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C6 LOP A 701 " pdb=" O5 LOP A 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C6 LOP B 701 " pdb=" O5 LOP B 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.569 1.519 0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 9783 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.28: 118 105.28 - 112.45: 5188 112.45 - 119.62: 3063 119.62 - 126.79: 4749 126.79 - 133.96: 108 Bond angle restraints: 13226 Sorted by residual: angle pdb=" N ILE B 526 " pdb=" CA ILE B 526 " pdb=" C ILE B 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE A 526 " pdb=" CA ILE A 526 " pdb=" C ILE A 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ILE A 154 " pdb=" CA ILE A 154 " pdb=" C ILE A 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" O3 LOP A 701 " pdb=" P1 LOP A 701 " pdb=" O4 LOP A 701 " ideal model delta sigma weight residual 120.67 109.36 11.31 3.00e+00 1.11e-01 1.42e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5158 17.54 - 35.07: 574 35.07 - 52.61: 134 52.61 - 70.14: 24 70.14 - 87.68: 4 Dihedral angle restraints: 5894 sinusoidal: 2420 harmonic: 3474 Sorted by residual: dihedral pdb=" CA ASP A 374 " pdb=" CB ASP A 374 " pdb=" CG ASP A 374 " pdb=" OD1 ASP A 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.21 59.21 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B 374 " pdb=" CB ASP B 374 " pdb=" CG ASP B 374 " pdb=" OD1 ASP B 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ARG B 484 " pdb=" C ARG B 484 " pdb=" N PHE B 485 " pdb=" CA PHE B 485 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 ... (remaining 5891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1096 0.039 - 0.078: 329 0.078 - 0.116: 83 0.116 - 0.155: 14 0.155 - 0.194: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C4 LOP B 701 " pdb=" C3 LOP B 701 " pdb=" C5 LOP B 701 " pdb=" O5 LOP B 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" C4 LOP A 701 " pdb=" C3 LOP A 701 " pdb=" C5 LOP A 701 " pdb=" O5 LOP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" C PRO A 129 " pdb=" CB PRO A 129 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1521 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 128 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 129 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 128 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 129 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 387 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 388 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.016 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2334 2.79 - 3.32: 9964 3.32 - 3.84: 15480 3.84 - 4.37: 17627 4.37 - 4.90: 31523 Nonbonded interactions: 76928 Sorted by model distance: nonbonded pdb=" OD1 ASP A 499 " pdb=" N ILE A 500 " model vdw 2.258 2.520 nonbonded pdb=" OD1 ASP B 499 " pdb=" N ILE B 500 " model vdw 2.259 2.520 nonbonded pdb=" NZ LYS A 531 " pdb=" O ILE A 535 " model vdw 2.297 2.520 nonbonded pdb=" NZ LYS B 531 " pdb=" O ILE B 535 " model vdw 2.297 2.520 nonbonded pdb=" O THR A 273 " pdb=" OG1 THR A 277 " model vdw 2.311 2.440 ... (remaining 76923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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=0.00 max=1.00 mean=0.94 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: 1.290 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: 7.500 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.120 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.006 0.072 9788 Z= 0.415 Angle : 0.649 11.311 13226 Z= 0.342 Chirality : 0.040 0.194 1524 Planarity : 0.003 0.034 1664 Dihedral : 15.096 87.681 3650 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -3.04 (0.22), residues: 1196 helix: -0.93 (0.17), residues: 778 sheet: -3.80 (0.67), residues: 56 loop : -4.02 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 PHE 0.012 0.001 PHE A 132 TYR 0.008 0.001 TYR B 310 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7884 (ttp80) REVERT: A 649 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7013 (mtp-110) REVERT: A 665 SER cc_start: 0.8387 (m) cc_final: 0.8121 (p) REVERT: A 668 ARG cc_start: 0.8517 (mtp180) cc_final: 0.8178 (mtm180) REVERT: B 312 ASN cc_start: 0.8628 (m110) cc_final: 0.8422 (m110) REVERT: B 668 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8130 (mtm180) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2637 time to fit residues: 45.7695 Evaluate side-chains 100 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 606 HIS B 127 GLN B 196 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9788 Z= 0.278 Angle : 0.563 7.336 13226 Z= 0.290 Chirality : 0.041 0.220 1524 Planarity : 0.004 0.038 1664 Dihedral : 8.300 57.904 1378 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.87 % Allowed : 12.21 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1196 helix: 0.94 (0.19), residues: 790 sheet: -3.70 (0.67), residues: 56 loop : -3.23 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 279 HIS 0.005 0.001 HIS B 197 PHE 0.021 0.002 PHE A 132 TYR 0.029 0.002 TYR B 310 ARG 0.003 0.000 ARG B 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7888 (ttp80) REVERT: A 216 ARG cc_start: 0.6888 (ttp80) cc_final: 0.6664 (ttp80) REVERT: A 594 MET cc_start: 0.7316 (mmt) cc_final: 0.7111 (mmt) REVERT: B 148 VAL cc_start: 0.8824 (p) cc_final: 0.8616 (m) REVERT: B 668 ARG cc_start: 0.8511 (mtp180) cc_final: 0.8179 (mtm180) outliers start: 9 outliers final: 8 residues processed: 155 average time/residue: 0.2309 time to fit residues: 49.1305 Evaluate side-chains 137 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 117 optimal weight: 0.0010 chunk 97 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 346 GLN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9788 Z= 0.196 Angle : 0.521 10.233 13226 Z= 0.262 Chirality : 0.039 0.235 1524 Planarity : 0.003 0.026 1664 Dihedral : 7.907 59.710 1378 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.84 % Allowed : 13.28 % Favored : 84.88 % 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: 0.22 (0.26), residues: 1196 helix: 1.59 (0.19), residues: 788 sheet: -3.64 (0.65), residues: 56 loop : -2.65 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 279 HIS 0.003 0.001 HIS A 606 PHE 0.018 0.001 PHE A 532 TYR 0.035 0.002 TYR B 310 ARG 0.005 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7833 (ttp80) REVERT: A 216 ARG cc_start: 0.6922 (ttp80) cc_final: 0.6644 (ttp80) REVERT: A 481 LEU cc_start: 0.7990 (tp) cc_final: 0.7510 (mp) REVERT: B 216 ARG cc_start: 0.6933 (ttp80) cc_final: 0.6608 (ttp80) REVERT: B 594 MET cc_start: 0.7262 (mmt) cc_final: 0.7004 (mmt) REVERT: B 662 MET cc_start: 0.6325 (mtt) cc_final: 0.6007 (ptp) REVERT: B 668 ARG cc_start: 0.8531 (mtp180) cc_final: 0.8201 (mtm180) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.2353 time to fit residues: 47.5773 Evaluate side-chains 137 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 536 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9788 Z= 0.201 Angle : 0.509 9.646 13226 Z= 0.256 Chirality : 0.039 0.238 1524 Planarity : 0.003 0.029 1664 Dihedral : 7.620 59.517 1378 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.00 % Allowed : 14.53 % Favored : 82.46 % 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: 0.58 (0.26), residues: 1196 helix: 1.81 (0.19), residues: 788 sheet: -3.53 (0.55), residues: 80 loop : -2.16 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.003 0.001 HIS A 606 PHE 0.017 0.001 PHE A 254 TYR 0.030 0.002 TYR B 310 ARG 0.003 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7808 (ttp80) REVERT: A 216 ARG cc_start: 0.6964 (ttp80) cc_final: 0.6690 (ttp80) REVERT: B 216 ARG cc_start: 0.6945 (ttp80) cc_final: 0.6633 (ttp80) REVERT: B 662 MET cc_start: 0.6289 (mtt) cc_final: 0.5989 (mmp) REVERT: B 668 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8208 (mtm180) outliers start: 31 outliers final: 21 residues processed: 158 average time/residue: 0.2288 time to fit residues: 49.8958 Evaluate side-chains 145 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9788 Z= 0.174 Angle : 0.501 10.472 13226 Z= 0.251 Chirality : 0.038 0.244 1524 Planarity : 0.003 0.023 1664 Dihedral : 7.336 59.399 1378 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.71 % Allowed : 15.70 % Favored : 81.59 % 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: 0.91 (0.27), residues: 1196 helix: 2.04 (0.19), residues: 784 sheet: -3.40 (0.57), residues: 80 loop : -1.92 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 656 PHE 0.025 0.001 PHE A 254 TYR 0.026 0.001 TYR B 310 ARG 0.002 0.000 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7770 (ttp80) REVERT: A 216 ARG cc_start: 0.6994 (ttp80) cc_final: 0.6687 (ttp80) REVERT: A 310 TYR cc_start: 0.7863 (m-80) cc_final: 0.7625 (m-80) REVERT: A 668 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7480 (mtm180) REVERT: B 216 ARG cc_start: 0.6958 (ttp80) cc_final: 0.6657 (ttp80) outliers start: 28 outliers final: 19 residues processed: 157 average time/residue: 0.2272 time to fit residues: 49.0903 Evaluate side-chains 147 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9788 Z= 0.245 Angle : 0.536 10.807 13226 Z= 0.267 Chirality : 0.039 0.241 1524 Planarity : 0.003 0.026 1664 Dihedral : 7.257 58.689 1378 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.91 % Allowed : 18.02 % Favored : 79.07 % 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: 0.89 (0.26), residues: 1196 helix: 1.97 (0.19), residues: 784 sheet: -3.39 (0.68), residues: 56 loop : -1.96 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 279 HIS 0.002 0.001 HIS B 197 PHE 0.021 0.002 PHE B 254 TYR 0.022 0.002 TYR B 310 ARG 0.002 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7757 (ttp80) REVERT: A 216 ARG cc_start: 0.6970 (ttp80) cc_final: 0.6639 (ttp80) REVERT: A 668 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7435 (mtm180) REVERT: B 216 ARG cc_start: 0.6944 (ttp80) cc_final: 0.6620 (ttp80) REVERT: B 662 MET cc_start: 0.6418 (mtt) cc_final: 0.6109 (ptt) REVERT: B 668 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8148 (mtm-85) outliers start: 30 outliers final: 27 residues processed: 157 average time/residue: 0.2324 time to fit residues: 50.1769 Evaluate side-chains 157 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9788 Z= 0.263 Angle : 0.544 9.987 13226 Z= 0.273 Chirality : 0.039 0.232 1524 Planarity : 0.003 0.023 1664 Dihedral : 7.250 59.066 1378 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.10 % Allowed : 18.31 % Favored : 78.59 % 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: 0.88 (0.26), residues: 1196 helix: 1.92 (0.19), residues: 784 sheet: -3.36 (0.67), residues: 56 loop : -1.84 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 279 HIS 0.002 0.001 HIS B 197 PHE 0.022 0.002 PHE A 254 TYR 0.021 0.002 TYR A 310 ARG 0.002 0.000 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7763 (ttp80) REVERT: A 216 ARG cc_start: 0.7008 (ttp80) cc_final: 0.6671 (ttp80) REVERT: A 668 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7420 (mtt180) REVERT: B 216 ARG cc_start: 0.7012 (ttp80) cc_final: 0.6661 (ttp80) REVERT: B 662 MET cc_start: 0.6506 (mtt) cc_final: 0.6170 (ptt) REVERT: B 668 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8160 (mtm-85) outliers start: 32 outliers final: 29 residues processed: 158 average time/residue: 0.2259 time to fit residues: 49.2987 Evaluate side-chains 162 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9788 Z= 0.211 Angle : 0.533 9.651 13226 Z= 0.267 Chirality : 0.038 0.213 1524 Planarity : 0.003 0.024 1664 Dihedral : 7.167 59.674 1378 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.00 % Allowed : 18.99 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 1196 helix: 2.03 (0.19), residues: 786 sheet: -3.35 (0.67), residues: 56 loop : -1.77 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 PHE 0.020 0.001 PHE A 254 TYR 0.022 0.001 TYR B 310 ARG 0.002 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7741 (ttp80) REVERT: A 216 ARG cc_start: 0.6982 (ttp80) cc_final: 0.6631 (ttp80) REVERT: A 668 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7617 (mtm180) REVERT: B 216 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6646 (ttp80) REVERT: B 662 MET cc_start: 0.6570 (mtt) cc_final: 0.6364 (ptp) REVERT: B 668 ARG cc_start: 0.8524 (mtp180) cc_final: 0.8267 (mtm180) outliers start: 31 outliers final: 27 residues processed: 158 average time/residue: 0.2299 time to fit residues: 49.9502 Evaluate side-chains 158 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.0030 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9788 Z= 0.171 Angle : 0.515 9.275 13226 Z= 0.258 Chirality : 0.037 0.210 1524 Planarity : 0.003 0.024 1664 Dihedral : 7.007 59.719 1378 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.33 % Allowed : 20.06 % Favored : 77.62 % 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: 1.28 (0.27), residues: 1196 helix: 2.20 (0.19), residues: 786 sheet: -3.28 (0.58), residues: 80 loop : -1.46 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 656 PHE 0.014 0.001 PHE A 179 TYR 0.018 0.001 TYR A 310 ARG 0.002 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7713 (ttp80) REVERT: A 216 ARG cc_start: 0.6990 (ttp80) cc_final: 0.6614 (ttp80) REVERT: A 668 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7625 (mtm180) REVERT: B 216 ARG cc_start: 0.6995 (ttp80) cc_final: 0.6617 (ttp80) outliers start: 24 outliers final: 24 residues processed: 153 average time/residue: 0.2414 time to fit residues: 51.3363 Evaluate side-chains 153 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9788 Z= 0.260 Angle : 0.558 9.530 13226 Z= 0.279 Chirality : 0.039 0.192 1524 Planarity : 0.003 0.024 1664 Dihedral : 7.081 59.225 1378 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.33 % Allowed : 20.06 % Favored : 77.62 % 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: 1.14 (0.26), residues: 1196 helix: 2.09 (0.19), residues: 786 sheet: -3.44 (0.65), residues: 56 loop : -1.67 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 279 HIS 0.002 0.001 HIS B 656 PHE 0.016 0.002 PHE B 350 TYR 0.019 0.002 TYR A 310 ARG 0.003 0.000 ARG B 585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7765 (ttp80) REVERT: A 216 ARG cc_start: 0.6986 (ttp80) cc_final: 0.6614 (ttp80) REVERT: A 668 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7584 (mtm180) REVERT: B 216 ARG cc_start: 0.6980 (ttp80) cc_final: 0.6607 (ttp80) outliers start: 24 outliers final: 23 residues processed: 155 average time/residue: 0.2268 time to fit residues: 48.4536 Evaluate side-chains 160 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 0.0020 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129960 restraints weight = 10510.682| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.56 r_work: 0.3380 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9788 Z= 0.160 Angle : 0.534 9.057 13226 Z= 0.264 Chirality : 0.037 0.214 1524 Planarity : 0.003 0.022 1664 Dihedral : 6.938 59.449 1378 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.03 % Allowed : 20.74 % Favored : 77.23 % 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: 1.38 (0.26), residues: 1196 helix: 2.28 (0.19), residues: 786 sheet: -3.23 (0.59), residues: 80 loop : -1.40 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS A 282 PHE 0.015 0.001 PHE A 179 TYR 0.019 0.001 TYR A 310 ARG 0.004 0.000 ARG A 616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2144.83 seconds wall clock time: 39 minutes 6.46 seconds (2346.46 seconds total)