Starting phenix.real_space_refine on Sun Aug 4 13:46:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqa_38571/08_2024/8xqa_38571.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqa_38571/08_2024/8xqa_38571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqa_38571/08_2024/8xqa_38571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqa_38571/08_2024/8xqa_38571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqa_38571/08_2024/8xqa_38571.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqa_38571/08_2024/8xqa_38571.cif" } resolution = 3.54 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= 0.002 sd= 0.029 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 60 5.16 5 C 6924 2.51 5 N 1758 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 872": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5301 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 17, 'TRANS': 660} Chain breaks: 2 Chain: "B" Number of atoms: 5301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5301 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 17, 'TRANS': 660} Chain breaks: 2 Time building chain proxies: 6.32, per 1000 atoms: 0.60 Number of scatterers: 10602 At special positions: 0 Unit cell: (101.52, 109.08, 116.64, 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 60 16.00 O 1860 8.00 N 1758 7.00 C 6924 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: 4.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 4.262A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.099A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.557A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.725A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.892A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.614A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 381 through 413 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.434A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.899A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.768A pdb=" N ASP A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.849A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.509A pdb=" N LEU A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.622A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 removed outlier: 3.759A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 854 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.830A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.405A pdb=" N VAL B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.203A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.551A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.551A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.707A pdb=" N VAL B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 223 through 253 Processing helix chain 'B' and resid 260 through 291 Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 297 through 317 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.524A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 removed outlier: 3.538A pdb=" N VAL B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.970A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 413 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.633A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.288A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 Processing helix chain 'B' and resid 522 through 530 removed outlier: 4.071A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 600 Processing helix chain 'B' and resid 604 through 621 removed outlier: 4.010A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 639 through 653 removed outlier: 4.201A pdb=" N SER B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 855 removed outlier: 4.527A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.870A pdb=" N ILE B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.286A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 942 909 hydrogen bonds defined for protein. 2718 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: 3.36 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3331 1.34 - 1.46: 1932 1.46 - 1.58: 5423 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10798 Sorted by residual: bond pdb=" CA ILE A 488 " pdb=" CB ILE A 488 " ideal model delta sigma weight residual 1.534 1.549 -0.014 6.80e-03 2.16e+04 4.40e+00 bond pdb=" C ILE A 818 " pdb=" N PRO A 819 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.61e+00 bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.57e+00 bond pdb=" CA ILE A 488 " pdb=" C ILE A 488 " ideal model delta sigma weight residual 1.520 1.533 -0.014 8.80e-03 1.29e+04 2.45e+00 bond pdb=" CB PRO B 144 " pdb=" CG PRO B 144 " ideal model delta sigma weight residual 1.492 1.416 0.076 5.00e-02 4.00e+02 2.33e+00 ... (remaining 10793 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.81: 182 105.81 - 112.94: 6040 112.94 - 120.06: 4059 120.06 - 127.19: 4247 127.19 - 134.32: 110 Bond angle restraints: 14638 Sorted by residual: angle pdb=" C SER A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 120.24 125.31 -5.07 6.30e-01 2.52e+00 6.48e+01 angle pdb=" C SER B 487 " pdb=" N ILE B 488 " pdb=" CA ILE B 488 " ideal model delta sigma weight residual 120.24 123.59 -3.35 6.30e-01 2.52e+00 2.83e+01 angle pdb=" CA LEU A 405 " pdb=" CB LEU A 405 " pdb=" CG LEU A 405 " ideal model delta sigma weight residual 116.30 132.04 -15.74 3.50e+00 8.16e-02 2.02e+01 angle pdb=" CA TRP A 635 " pdb=" CB TRP A 635 " pdb=" CG TRP A 635 " ideal model delta sigma weight residual 113.60 121.40 -7.80 1.90e+00 2.77e-01 1.68e+01 angle pdb=" C ILE A 640 " pdb=" N TYR A 641 " pdb=" CA TYR A 641 " ideal model delta sigma weight residual 120.09 124.44 -4.35 1.25e+00 6.40e-01 1.21e+01 ... (remaining 14633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5782 17.82 - 35.64: 481 35.64 - 53.46: 143 53.46 - 71.28: 33 71.28 - 89.10: 5 Dihedral angle restraints: 6444 sinusoidal: 2522 harmonic: 3922 Sorted by residual: dihedral pdb=" CA ILE B 853 " pdb=" C ILE B 853 " pdb=" N ILE B 854 " pdb=" CA ILE B 854 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU A 220 " pdb=" C LEU A 220 " pdb=" N GLY A 221 " pdb=" CA GLY A 221 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA THR B 258 " pdb=" C THR B 258 " pdb=" N SER B 259 " pdb=" CA SER B 259 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1007 0.034 - 0.067: 518 0.067 - 0.101: 145 0.101 - 0.135: 81 0.135 - 0.168: 21 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA LEU A 143 " pdb=" N LEU A 143 " pdb=" C LEU A 143 " pdb=" CB LEU A 143 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ASN A 830 " pdb=" N ASN A 830 " pdb=" C ASN A 830 " pdb=" CB ASN A 830 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB ILE B 486 " pdb=" CA ILE B 486 " pdb=" CG1 ILE B 486 " pdb=" CG2 ILE B 486 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1769 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 467 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LEU A 467 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 467 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 468 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 467 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C LEU B 467 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU B 467 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL B 468 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 271 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C VAL B 271 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL B 271 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 272 " -0.014 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2635 2.79 - 3.32: 10575 3.32 - 3.85: 18310 3.85 - 4.37: 20137 4.37 - 4.90: 35202 Nonbonded interactions: 86859 Sorted by model distance: nonbonded pdb=" O VAL A 468 " pdb=" OG1 THR A 472 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 631 " pdb=" OG SER A 634 " model vdw 2.271 3.040 nonbonded pdb=" O ALA B 307 " pdb=" OG1 THR B 311 " model vdw 2.320 3.040 nonbonded pdb=" O VAL B 468 " pdb=" OG1 THR B 472 " model vdw 2.322 3.040 nonbonded pdb=" O GLY B 369 " pdb=" OG1 THR B 373 " model vdw 2.322 3.040 ... (remaining 86854 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.005 0.076 10798 Z= 0.342 Angle : 0.762 15.739 14638 Z= 0.438 Chirality : 0.048 0.168 1772 Planarity : 0.007 0.057 1796 Dihedral : 14.998 89.102 3904 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.62 % Allowed : 11.50 % Favored : 81.88 % 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: -1.20 (0.20), residues: 1344 helix: -0.55 (0.13), residues: 1140 sheet: None (None), residues: 0 loop : -1.16 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 635 HIS 0.004 0.001 HIS B 889 PHE 0.021 0.002 PHE B 455 TYR 0.015 0.002 TYR A 191 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 471 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8323 (m) cc_final: 0.7904 (m) REVERT: A 112 ILE cc_start: 0.8385 (mt) cc_final: 0.8020 (mm) REVERT: A 116 VAL cc_start: 0.8318 (p) cc_final: 0.8083 (p) REVERT: A 124 GLU cc_start: 0.7502 (tp30) cc_final: 0.6559 (tp30) REVERT: A 147 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7868 (mt) REVERT: A 160 MET cc_start: 0.7722 (mmm) cc_final: 0.7334 (mmt) REVERT: A 168 ILE cc_start: 0.7750 (tt) cc_final: 0.7546 (tp) REVERT: A 186 MET cc_start: 0.6658 (mtp) cc_final: 0.6416 (mtp) REVERT: A 188 LEU cc_start: 0.8553 (tp) cc_final: 0.8219 (tt) REVERT: A 205 MET cc_start: 0.7655 (mmm) cc_final: 0.6965 (mpp) REVERT: A 209 ASP cc_start: 0.6253 (m-30) cc_final: 0.5960 (m-30) REVERT: A 213 VAL cc_start: 0.8983 (t) cc_final: 0.8782 (t) REVERT: A 217 LEU cc_start: 0.8228 (mt) cc_final: 0.7954 (mt) REVERT: A 218 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7685 (mtmt) REVERT: A 229 ILE cc_start: 0.8531 (mm) cc_final: 0.8323 (mm) REVERT: A 236 LEU cc_start: 0.8031 (mm) cc_final: 0.7642 (mp) REVERT: A 237 ASN cc_start: 0.7930 (t0) cc_final: 0.7692 (t0) REVERT: A 245 PHE cc_start: 0.8209 (t80) cc_final: 0.7993 (t80) REVERT: A 257 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7733 (pp) REVERT: A 292 HIS cc_start: 0.8355 (m-70) cc_final: 0.7819 (m-70) REVERT: A 312 TYR cc_start: 0.8300 (t80) cc_final: 0.8078 (t80) REVERT: A 361 ASN cc_start: 0.8537 (m-40) cc_final: 0.8092 (m110) REVERT: A 367 MET cc_start: 0.7709 (mtp) cc_final: 0.7504 (mtm) REVERT: A 372 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 431 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.8116 (mmt90) REVERT: A 454 LYS cc_start: 0.8299 (mttm) cc_final: 0.7808 (mttm) REVERT: A 477 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 479 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7241 (ttp80) REVERT: A 481 LEU cc_start: 0.8568 (mt) cc_final: 0.8222 (mt) REVERT: A 499 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7090 (ttp80) REVERT: A 506 ASN cc_start: 0.7983 (m110) cc_final: 0.7650 (m110) REVERT: A 531 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6846 (mm-30) REVERT: A 578 MET cc_start: 0.8108 (ttm) cc_final: 0.7812 (ttm) REVERT: A 579 MET cc_start: 0.7926 (mmm) cc_final: 0.7371 (mmm) REVERT: A 585 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7986 (ttp-170) REVERT: A 597 GLN cc_start: 0.7513 (mt0) cc_final: 0.7268 (mt0) REVERT: A 613 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 645 LYS cc_start: 0.8969 (tptp) cc_final: 0.8402 (tptp) REVERT: A 843 TYR cc_start: 0.8550 (t80) cc_final: 0.7757 (t80) REVERT: A 848 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 849 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 852 LYS cc_start: 0.8216 (mttp) cc_final: 0.7928 (mttp) REVERT: A 862 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8357 (mmtm) REVERT: A 866 GLU cc_start: 0.7209 (tp30) cc_final: 0.6985 (tp30) REVERT: A 875 ARG cc_start: 0.7655 (tpt90) cc_final: 0.7245 (tpt90) REVERT: A 880 LYS cc_start: 0.8221 (tptp) cc_final: 0.7777 (tptp) REVERT: A 900 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7405 (tp40) REVERT: A 925 MET cc_start: 0.7843 (mmm) cc_final: 0.7507 (mmm) REVERT: A 938 MET cc_start: 0.8412 (mmm) cc_final: 0.8201 (mmm) REVERT: B 77 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8012 (m) REVERT: B 84 SER cc_start: 0.8179 (t) cc_final: 0.7691 (p) REVERT: B 109 LEU cc_start: 0.7963 (mt) cc_final: 0.7711 (mt) REVERT: B 122 LEU cc_start: 0.8412 (mt) cc_final: 0.8199 (mm) REVERT: B 124 GLU cc_start: 0.7383 (tp30) cc_final: 0.6744 (tp30) REVERT: B 145 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7904 (m) REVERT: B 149 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6857 (tm-30) REVERT: B 152 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8066 (t80) REVERT: B 195 PHE cc_start: 0.7476 (t80) cc_final: 0.7179 (t80) REVERT: B 249 MET cc_start: 0.7435 (tmm) cc_final: 0.7027 (tmm) REVERT: B 278 TRP cc_start: 0.8410 (t-100) cc_final: 0.8103 (t-100) REVERT: B 292 HIS cc_start: 0.8309 (m-70) cc_final: 0.7988 (m-70) REVERT: B 335 ASN cc_start: 0.8253 (t0) cc_final: 0.7813 (t0) REVERT: B 337 GLU cc_start: 0.7754 (mp0) cc_final: 0.7383 (mp0) REVERT: B 338 LYS cc_start: 0.8071 (mttm) cc_final: 0.7846 (mttm) REVERT: B 388 LEU cc_start: 0.8568 (tt) cc_final: 0.8351 (tt) REVERT: B 390 ILE cc_start: 0.8477 (mm) cc_final: 0.8256 (mm) REVERT: B 397 ILE cc_start: 0.8215 (mm) cc_final: 0.7896 (mm) REVERT: B 443 GLU cc_start: 0.7639 (tp30) cc_final: 0.7166 (tp30) REVERT: B 454 LYS cc_start: 0.7981 (tppt) cc_final: 0.7758 (mmtm) REVERT: B 499 ARG cc_start: 0.7647 (ptp90) cc_final: 0.7343 (ptp90) REVERT: B 500 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7449 (tpt90) REVERT: B 527 THR cc_start: 0.8232 (p) cc_final: 0.7805 (p) REVERT: B 531 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6368 (mm-30) REVERT: B 579 MET cc_start: 0.7803 (mmm) cc_final: 0.7372 (mmm) REVERT: B 586 MET cc_start: 0.7762 (tmm) cc_final: 0.6380 (tmm) REVERT: B 588 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7540 (ttpp) REVERT: B 590 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6320 (mm-30) REVERT: B 591 LYS cc_start: 0.8232 (mtmp) cc_final: 0.7930 (mtmp) REVERT: B 595 TRP cc_start: 0.7943 (m100) cc_final: 0.7704 (m100) REVERT: B 613 GLN cc_start: 0.7518 (tm-30) cc_final: 0.6922 (tm-30) REVERT: B 645 LYS cc_start: 0.8496 (tptp) cc_final: 0.7904 (tptp) REVERT: B 841 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8260 (mtpp) REVERT: B 843 TYR cc_start: 0.8324 (t80) cc_final: 0.7460 (t80) REVERT: B 847 GLU cc_start: 0.7855 (tp30) cc_final: 0.7497 (tp30) REVERT: B 848 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 852 LYS cc_start: 0.8626 (mttp) cc_final: 0.8235 (mttp) REVERT: B 876 LEU cc_start: 0.8167 (mt) cc_final: 0.7946 (mt) REVERT: B 880 LYS cc_start: 0.7972 (tmmt) cc_final: 0.7725 (tmmt) REVERT: B 907 ASN cc_start: 0.7574 (m-40) cc_final: 0.6487 (m-40) REVERT: B 908 HIS cc_start: 0.7707 (m-70) cc_final: 0.7172 (m-70) REVERT: B 911 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6632 (mt-10) REVERT: B 913 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 915 GLU cc_start: 0.7599 (tt0) cc_final: 0.7209 (tt0) REVERT: B 928 HIS cc_start: 0.7140 (t70) cc_final: 0.6846 (t70) REVERT: B 943 ASN cc_start: 0.7286 (p0) cc_final: 0.7046 (p0) outliers start: 76 outliers final: 25 residues processed: 513 average time/residue: 0.2643 time to fit residues: 181.2280 Evaluate side-chains 477 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 443 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 374 GLN A 421 ASN A 502 HIS A 506 ASN A 917 GLN B 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 421 ASN B 502 HIS B 506 ASN B 624 GLN B 877 GLN B 886 GLN B 917 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10798 Z= 0.172 Angle : 0.555 10.979 14638 Z= 0.297 Chirality : 0.038 0.264 1772 Planarity : 0.004 0.052 1796 Dihedral : 8.162 70.929 1503 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.75 % Allowed : 17.16 % Favored : 77.09 % 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: 0.93 (0.22), residues: 1344 helix: 0.95 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.94 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 523 HIS 0.004 0.001 HIS B 889 PHE 0.025 0.001 PHE B 163 TYR 0.015 0.001 TYR B 594 ARG 0.005 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 465 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7478 (mmtm) cc_final: 0.7227 (mmtm) REVERT: A 85 CYS cc_start: 0.8351 (m) cc_final: 0.8022 (m) REVERT: A 112 ILE cc_start: 0.8384 (mt) cc_final: 0.8054 (mm) REVERT: A 124 GLU cc_start: 0.7622 (tp30) cc_final: 0.6699 (tp30) REVERT: A 128 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7406 (ttp-170) REVERT: A 160 MET cc_start: 0.7755 (mmm) cc_final: 0.7374 (mmt) REVERT: A 168 ILE cc_start: 0.7728 (tt) cc_final: 0.7519 (tp) REVERT: A 186 MET cc_start: 0.6723 (mtp) cc_final: 0.6452 (mtp) REVERT: A 197 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 205 MET cc_start: 0.7614 (mmm) cc_final: 0.7296 (mpp) REVERT: A 217 LEU cc_start: 0.8451 (mt) cc_final: 0.8197 (mt) REVERT: A 218 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7686 (mtmt) REVERT: A 237 ASN cc_start: 0.7923 (t0) cc_final: 0.7715 (t0) REVERT: A 257 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7563 (pp) REVERT: A 292 HIS cc_start: 0.8264 (m-70) cc_final: 0.7732 (m-70) REVERT: A 335 ASN cc_start: 0.8685 (t0) cc_final: 0.8331 (t0) REVERT: A 401 MET cc_start: 0.7203 (mtm) cc_final: 0.6993 (mtm) REVERT: A 406 PHE cc_start: 0.7687 (m-80) cc_final: 0.7468 (m-80) REVERT: A 454 LYS cc_start: 0.8410 (mttm) cc_final: 0.8084 (mttm) REVERT: A 477 LEU cc_start: 0.8600 (tt) cc_final: 0.8216 (tt) REVERT: A 479 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7383 (ttp80) REVERT: A 481 LEU cc_start: 0.8523 (mt) cc_final: 0.8252 (mt) REVERT: A 486 ILE cc_start: 0.8474 (mt) cc_final: 0.8191 (tt) REVERT: A 499 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7143 (ttp80) REVERT: A 502 HIS cc_start: 0.7821 (t-90) cc_final: 0.7226 (t-90) REVERT: A 506 ASN cc_start: 0.7999 (m-40) cc_final: 0.7445 (m-40) REVERT: A 578 MET cc_start: 0.8167 (ttm) cc_final: 0.7893 (ttm) REVERT: A 579 MET cc_start: 0.7947 (mmm) cc_final: 0.7376 (mmm) REVERT: A 596 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7800 (tmmt) REVERT: A 597 GLN cc_start: 0.7475 (mt0) cc_final: 0.7244 (mt0) REVERT: A 613 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 622 LYS cc_start: 0.7962 (tttp) cc_final: 0.7711 (tttp) REVERT: A 645 LYS cc_start: 0.8956 (tptp) cc_final: 0.8344 (tptp) REVERT: A 843 TYR cc_start: 0.8588 (t80) cc_final: 0.7839 (t80) REVERT: A 848 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 852 LYS cc_start: 0.8176 (mttp) cc_final: 0.7940 (mttp) REVERT: A 862 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8384 (mmtm) REVERT: A 866 GLU cc_start: 0.7258 (tp30) cc_final: 0.7035 (tp30) REVERT: A 868 LYS cc_start: 0.8642 (mmmm) cc_final: 0.7858 (mmmm) REVERT: A 875 ARG cc_start: 0.7617 (tpt90) cc_final: 0.7143 (tpt90) REVERT: A 880 LYS cc_start: 0.8225 (tptp) cc_final: 0.7781 (tptp) REVERT: A 900 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7503 (tp40) REVERT: A 912 THR cc_start: 0.8436 (m) cc_final: 0.8232 (p) REVERT: A 925 MET cc_start: 0.7924 (mmm) cc_final: 0.7601 (mmm) REVERT: A 931 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7240 (mm-30) REVERT: B 77 VAL cc_start: 0.8255 (t) cc_final: 0.7939 (m) REVERT: B 84 SER cc_start: 0.8077 (t) cc_final: 0.7675 (p) REVERT: B 109 LEU cc_start: 0.7913 (mt) cc_final: 0.7615 (mt) REVERT: B 124 GLU cc_start: 0.7443 (tp30) cc_final: 0.7176 (tp30) REVERT: B 149 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6964 (tm-30) REVERT: B 233 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 249 MET cc_start: 0.7523 (tmm) cc_final: 0.7058 (tmm) REVERT: B 278 TRP cc_start: 0.8358 (t-100) cc_final: 0.8024 (t-100) REVERT: B 300 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 337 GLU cc_start: 0.7687 (mp0) cc_final: 0.7396 (mp0) REVERT: B 351 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.8073 (tpp-160) REVERT: B 384 ASP cc_start: 0.6967 (m-30) cc_final: 0.6716 (m-30) REVERT: B 390 ILE cc_start: 0.8494 (mm) cc_final: 0.8266 (mm) REVERT: B 420 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7733 (mtm-85) REVERT: B 443 GLU cc_start: 0.7667 (tp30) cc_final: 0.7211 (tp30) REVERT: B 499 ARG cc_start: 0.7617 (ptp90) cc_final: 0.7301 (ptp90) REVERT: B 500 ARG cc_start: 0.7823 (tpt90) cc_final: 0.7430 (tpt90) REVERT: B 512 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 517 PHE cc_start: 0.7523 (m-10) cc_final: 0.7261 (m-80) REVERT: B 527 THR cc_start: 0.8248 (p) cc_final: 0.7550 (p) REVERT: B 579 MET cc_start: 0.7787 (mmm) cc_final: 0.7427 (mmm) REVERT: B 581 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6024 (pp20) REVERT: B 586 MET cc_start: 0.7688 (tmm) cc_final: 0.6010 (tmm) REVERT: B 588 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7784 (ttpp) REVERT: B 590 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6730 (mm-30) REVERT: B 591 LYS cc_start: 0.8198 (mtmp) cc_final: 0.7946 (mtmp) REVERT: B 595 TRP cc_start: 0.7968 (m100) cc_final: 0.7704 (m100) REVERT: B 596 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8162 (mmmt) REVERT: B 613 GLN cc_start: 0.7452 (tm-30) cc_final: 0.6956 (tm-30) REVERT: B 635 TRP cc_start: 0.5449 (m100) cc_final: 0.5212 (m100) REVERT: B 645 LYS cc_start: 0.8499 (tptp) cc_final: 0.7941 (tptp) REVERT: B 825 VAL cc_start: 0.8408 (t) cc_final: 0.8180 (p) REVERT: B 826 ASN cc_start: 0.7909 (t0) cc_final: 0.7567 (m110) REVERT: B 841 LYS cc_start: 0.8512 (ttmm) cc_final: 0.7994 (ttmm) REVERT: B 843 TYR cc_start: 0.8297 (t80) cc_final: 0.7639 (t80) REVERT: B 847 GLU cc_start: 0.7874 (tp30) cc_final: 0.7493 (tp30) REVERT: B 848 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7895 (mt-10) REVERT: B 876 LEU cc_start: 0.8166 (mt) cc_final: 0.7940 (mt) REVERT: B 881 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6777 (mm-30) REVERT: B 889 HIS cc_start: 0.8043 (m90) cc_final: 0.7097 (m90) REVERT: B 907 ASN cc_start: 0.7617 (m-40) cc_final: 0.6505 (m-40) REVERT: B 908 HIS cc_start: 0.7862 (m-70) cc_final: 0.7264 (m-70) REVERT: B 911 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6653 (mp0) REVERT: B 913 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 915 GLU cc_start: 0.7667 (tt0) cc_final: 0.7266 (tt0) REVERT: B 928 HIS cc_start: 0.7157 (t70) cc_final: 0.6862 (t70) REVERT: B 938 MET cc_start: 0.7781 (tpp) cc_final: 0.7571 (tpp) REVERT: B 943 ASN cc_start: 0.7275 (p0) cc_final: 0.7075 (p0) outliers start: 66 outliers final: 34 residues processed: 495 average time/residue: 0.2750 time to fit residues: 179.0695 Evaluate side-chains 489 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 449 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 913 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 0.0770 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 900 GLN B 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 421 ASN B 506 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10798 Z= 0.163 Angle : 0.573 13.486 14638 Z= 0.293 Chirality : 0.038 0.250 1772 Planarity : 0.004 0.046 1796 Dihedral : 7.130 68.173 1483 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.66 % Allowed : 19.43 % Favored : 74.91 % 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: 1.71 (0.23), residues: 1344 helix: 1.48 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.77 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 523 HIS 0.014 0.001 HIS B 502 PHE 0.022 0.001 PHE A 245 TYR 0.014 0.001 TYR A 392 ARG 0.005 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 456 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7477 (mmtm) cc_final: 0.7036 (mmtm) REVERT: A 85 CYS cc_start: 0.8298 (m) cc_final: 0.8030 (m) REVERT: A 112 ILE cc_start: 0.8393 (mt) cc_final: 0.8061 (mm) REVERT: A 124 GLU cc_start: 0.7616 (tp30) cc_final: 0.6727 (tp30) REVERT: A 125 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 128 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7422 (ttp-170) REVERT: A 160 MET cc_start: 0.7730 (mmm) cc_final: 0.7360 (mmt) REVERT: A 186 MET cc_start: 0.6680 (mtp) cc_final: 0.6448 (mtp) REVERT: A 199 MET cc_start: 0.7700 (mmm) cc_final: 0.7334 (mmm) REVERT: A 205 MET cc_start: 0.7611 (mmm) cc_final: 0.7410 (mmm) REVERT: A 217 LEU cc_start: 0.8330 (mt) cc_final: 0.8094 (mt) REVERT: A 237 ASN cc_start: 0.7918 (t0) cc_final: 0.7692 (t0) REVERT: A 257 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7588 (pp) REVERT: A 292 HIS cc_start: 0.8231 (m-70) cc_final: 0.7696 (m-70) REVERT: A 337 GLU cc_start: 0.7287 (mp0) cc_final: 0.6698 (mp0) REVERT: A 387 TYR cc_start: 0.7958 (m-10) cc_final: 0.7603 (m-10) REVERT: A 427 TRP cc_start: 0.8611 (t-100) cc_final: 0.8409 (t-100) REVERT: A 454 LYS cc_start: 0.8410 (mttm) cc_final: 0.8184 (mttm) REVERT: A 477 LEU cc_start: 0.8572 (tt) cc_final: 0.8266 (tt) REVERT: A 479 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7418 (ttp80) REVERT: A 481 LEU cc_start: 0.8465 (mt) cc_final: 0.8240 (mt) REVERT: A 486 ILE cc_start: 0.8514 (mt) cc_final: 0.8214 (tt) REVERT: A 499 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7160 (ttp80) REVERT: A 502 HIS cc_start: 0.7827 (t-90) cc_final: 0.7341 (t-90) REVERT: A 506 ASN cc_start: 0.7974 (m-40) cc_final: 0.7481 (m-40) REVERT: A 514 SER cc_start: 0.8278 (p) cc_final: 0.8047 (p) REVERT: A 578 MET cc_start: 0.8128 (ttm) cc_final: 0.7883 (ttm) REVERT: A 579 MET cc_start: 0.7864 (mmm) cc_final: 0.7299 (mmm) REVERT: A 596 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7763 (tmmt) REVERT: A 597 GLN cc_start: 0.7452 (mt0) cc_final: 0.7213 (mt0) REVERT: A 611 LEU cc_start: 0.8280 (tp) cc_final: 0.8038 (tp) REVERT: A 613 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 614 HIS cc_start: 0.7458 (m90) cc_final: 0.7253 (m90) REVERT: A 616 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 622 LYS cc_start: 0.8005 (tttp) cc_final: 0.7612 (tttp) REVERT: A 645 LYS cc_start: 0.8970 (tptp) cc_final: 0.8698 (tptp) REVERT: A 843 TYR cc_start: 0.8597 (t80) cc_final: 0.7886 (t80) REVERT: A 848 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 849 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 862 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8410 (mmtm) REVERT: A 866 GLU cc_start: 0.7250 (tp30) cc_final: 0.7009 (tp30) REVERT: A 868 LYS cc_start: 0.8573 (mmmm) cc_final: 0.7798 (mmmm) REVERT: A 875 ARG cc_start: 0.7647 (tpt90) cc_final: 0.7164 (tpt90) REVERT: A 880 LYS cc_start: 0.8244 (tptp) cc_final: 0.7782 (tptp) REVERT: A 900 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7437 (tp40) REVERT: A 912 THR cc_start: 0.8475 (m) cc_final: 0.8246 (p) REVERT: A 925 MET cc_start: 0.7901 (mmm) cc_final: 0.7592 (mmm) REVERT: A 931 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 940 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: B 81 ILE cc_start: 0.7897 (mt) cc_final: 0.7602 (mt) REVERT: B 84 SER cc_start: 0.8024 (t) cc_final: 0.7628 (p) REVERT: B 109 LEU cc_start: 0.7915 (mt) cc_final: 0.7570 (mt) REVERT: B 124 GLU cc_start: 0.7522 (tp30) cc_final: 0.7179 (tp30) REVERT: B 140 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7585 (mm110) REVERT: B 149 GLU cc_start: 0.7393 (tm-30) cc_final: 0.6993 (tm-30) REVERT: B 152 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 199 MET cc_start: 0.7539 (tpp) cc_final: 0.7205 (mmm) REVERT: B 233 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 269 LEU cc_start: 0.7978 (tp) cc_final: 0.7631 (tp) REVERT: B 278 TRP cc_start: 0.8354 (t-100) cc_final: 0.8049 (t-100) REVERT: B 284 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7829 (mmmm) REVERT: B 288 PHE cc_start: 0.7876 (t80) cc_final: 0.7656 (t80) REVERT: B 300 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6936 (mt-10) REVERT: B 320 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6928 (mm-30) REVERT: B 337 GLU cc_start: 0.7673 (mp0) cc_final: 0.7396 (mp0) REVERT: B 351 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8239 (tpp-160) REVERT: B 361 ASN cc_start: 0.8150 (m-40) cc_final: 0.7925 (m-40) REVERT: B 384 ASP cc_start: 0.7044 (m-30) cc_final: 0.6844 (m-30) REVERT: B 390 ILE cc_start: 0.8463 (mm) cc_final: 0.8256 (mm) REVERT: B 420 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7552 (mtm-85) REVERT: B 475 GLN cc_start: 0.7564 (tp40) cc_final: 0.7227 (tp40) REVERT: B 499 ARG cc_start: 0.7561 (ptp90) cc_final: 0.7277 (ptp90) REVERT: B 500 ARG cc_start: 0.7809 (tpt90) cc_final: 0.7439 (tpt90) REVERT: B 506 ASN cc_start: 0.8440 (m-40) cc_final: 0.8182 (m110) REVERT: B 512 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 517 PHE cc_start: 0.7530 (m-10) cc_final: 0.7289 (m-80) REVERT: B 527 THR cc_start: 0.7951 (p) cc_final: 0.7371 (p) REVERT: B 531 GLU cc_start: 0.6324 (mm-30) cc_final: 0.6081 (mm-30) REVERT: B 579 MET cc_start: 0.7782 (mmm) cc_final: 0.7412 (mmm) REVERT: B 581 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6017 (pp20) REVERT: B 586 MET cc_start: 0.7731 (tmm) cc_final: 0.6088 (tmm) REVERT: B 588 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7833 (ttpp) REVERT: B 590 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6683 (mm-30) REVERT: B 595 TRP cc_start: 0.7966 (m100) cc_final: 0.7707 (m100) REVERT: B 596 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8175 (mmmt) REVERT: B 613 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 645 LYS cc_start: 0.8490 (tptp) cc_final: 0.7991 (tptp) REVERT: B 825 VAL cc_start: 0.8498 (t) cc_final: 0.8267 (p) REVERT: B 826 ASN cc_start: 0.7926 (t0) cc_final: 0.7532 (m110) REVERT: B 837 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.6895 (m-80) REVERT: B 841 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8116 (ttmm) REVERT: B 843 TYR cc_start: 0.8201 (t80) cc_final: 0.7752 (t80) REVERT: B 847 GLU cc_start: 0.7839 (tp30) cc_final: 0.7491 (tp30) REVERT: B 848 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7925 (mt-10) REVERT: B 850 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8021 (p) REVERT: B 872 GLU cc_start: 0.8099 (tp30) cc_final: 0.7360 (tp30) REVERT: B 876 LEU cc_start: 0.8174 (mt) cc_final: 0.7598 (mt) REVERT: B 881 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6707 (mm-30) REVERT: B 907 ASN cc_start: 0.7638 (m-40) cc_final: 0.6562 (m-40) REVERT: B 908 HIS cc_start: 0.7922 (m-70) cc_final: 0.7495 (m-70) REVERT: B 911 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6676 (mt-10) REVERT: B 913 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8767 (mt) REVERT: B 915 GLU cc_start: 0.7632 (tt0) cc_final: 0.7211 (tt0) REVERT: B 924 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7708 (pp20) REVERT: B 928 HIS cc_start: 0.7128 (t70) cc_final: 0.6834 (t70) outliers start: 65 outliers final: 39 residues processed: 482 average time/residue: 0.2694 time to fit residues: 171.0491 Evaluate side-chains 498 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 450 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10798 Z= 0.186 Angle : 0.558 13.892 14638 Z= 0.289 Chirality : 0.038 0.227 1772 Planarity : 0.004 0.046 1796 Dihedral : 6.748 58.219 1480 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.10 % Allowed : 20.64 % Favored : 73.26 % 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: 2.10 (0.23), residues: 1344 helix: 1.74 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.64 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 523 HIS 0.002 0.000 HIS B 889 PHE 0.015 0.001 PHE A 457 TYR 0.017 0.001 TYR A 392 ARG 0.006 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 445 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7392 (mmtm) cc_final: 0.7116 (mmtm) REVERT: A 85 CYS cc_start: 0.8285 (m) cc_final: 0.7907 (m) REVERT: A 112 ILE cc_start: 0.8397 (mt) cc_final: 0.8072 (mm) REVERT: A 124 GLU cc_start: 0.7615 (tp30) cc_final: 0.6751 (tp30) REVERT: A 125 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 160 MET cc_start: 0.7724 (mmm) cc_final: 0.7360 (mmt) REVERT: A 186 MET cc_start: 0.6685 (mtp) cc_final: 0.6450 (mtp) REVERT: A 199 MET cc_start: 0.7660 (mmm) cc_final: 0.7231 (mmm) REVERT: A 205 MET cc_start: 0.7610 (mmm) cc_final: 0.7257 (mmm) REVERT: A 217 LEU cc_start: 0.8341 (mt) cc_final: 0.8098 (mt) REVERT: A 218 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7633 (ttmt) REVERT: A 237 ASN cc_start: 0.7938 (t0) cc_final: 0.7696 (t0) REVERT: A 292 HIS cc_start: 0.8196 (m-70) cc_final: 0.7585 (m-70) REVERT: A 335 ASN cc_start: 0.8655 (t0) cc_final: 0.8369 (t0) REVERT: A 337 GLU cc_start: 0.7290 (mp0) cc_final: 0.6700 (mp0) REVERT: A 387 TYR cc_start: 0.7937 (m-10) cc_final: 0.7579 (m-10) REVERT: A 431 ARG cc_start: 0.8246 (mmt180) cc_final: 0.8015 (mmt180) REVERT: A 454 LYS cc_start: 0.8423 (mttm) cc_final: 0.8135 (mttm) REVERT: A 477 LEU cc_start: 0.8547 (tt) cc_final: 0.8249 (tt) REVERT: A 479 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7454 (ttp80) REVERT: A 481 LEU cc_start: 0.8467 (mt) cc_final: 0.8205 (mt) REVERT: A 499 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7184 (ttp80) REVERT: A 502 HIS cc_start: 0.7854 (t-90) cc_final: 0.7390 (t-90) REVERT: A 506 ASN cc_start: 0.7981 (m-40) cc_final: 0.7501 (m-40) REVERT: A 514 SER cc_start: 0.8303 (p) cc_final: 0.8077 (p) REVERT: A 578 MET cc_start: 0.8162 (ttm) cc_final: 0.7925 (ttm) REVERT: A 579 MET cc_start: 0.7900 (mmm) cc_final: 0.7350 (mmm) REVERT: A 596 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7782 (tmmt) REVERT: A 597 GLN cc_start: 0.7441 (mt0) cc_final: 0.7218 (mt0) REVERT: A 611 LEU cc_start: 0.8259 (tp) cc_final: 0.7980 (tp) REVERT: A 613 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 645 LYS cc_start: 0.8966 (tptp) cc_final: 0.8339 (tptp) REVERT: A 826 ASN cc_start: 0.7376 (t0) cc_final: 0.7035 (t0) REVERT: A 843 TYR cc_start: 0.8602 (t80) cc_final: 0.7975 (t80) REVERT: A 848 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 849 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 862 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8403 (mmtm) REVERT: A 866 GLU cc_start: 0.7293 (tp30) cc_final: 0.7040 (tp30) REVERT: A 868 LYS cc_start: 0.8578 (mmmm) cc_final: 0.7788 (mmmm) REVERT: A 875 ARG cc_start: 0.7682 (tpt90) cc_final: 0.7443 (tpt90) REVERT: A 880 LYS cc_start: 0.8269 (tptp) cc_final: 0.7830 (tptp) REVERT: A 900 GLN cc_start: 0.8155 (tm130) cc_final: 0.7434 (tp40) REVERT: A 912 THR cc_start: 0.8492 (m) cc_final: 0.8256 (p) REVERT: A 925 MET cc_start: 0.7970 (mmm) cc_final: 0.7722 (mmm) REVERT: A 931 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 938 MET cc_start: 0.8512 (mmm) cc_final: 0.8198 (mmm) REVERT: A 940 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7512 (ttm-80) REVERT: B 81 ILE cc_start: 0.7893 (mt) cc_final: 0.7609 (mt) REVERT: B 84 SER cc_start: 0.8029 (t) cc_final: 0.7630 (p) REVERT: B 109 LEU cc_start: 0.7912 (mt) cc_final: 0.7587 (mt) REVERT: B 124 GLU cc_start: 0.7522 (tp30) cc_final: 0.7161 (tp30) REVERT: B 140 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7588 (mm110) REVERT: B 149 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7033 (tm-30) REVERT: B 152 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7930 (t80) REVERT: B 199 MET cc_start: 0.7430 (tpp) cc_final: 0.7221 (mmm) REVERT: B 233 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 246 ASN cc_start: 0.8135 (m-40) cc_final: 0.7901 (m-40) REVERT: B 249 MET cc_start: 0.7538 (tmm) cc_final: 0.7047 (tmm) REVERT: B 269 LEU cc_start: 0.7994 (tp) cc_final: 0.7659 (tp) REVERT: B 278 TRP cc_start: 0.8352 (t-100) cc_final: 0.8055 (t-100) REVERT: B 300 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6849 (mt-10) REVERT: B 335 ASN cc_start: 0.8258 (t0) cc_final: 0.8036 (t0) REVERT: B 337 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 351 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8043 (tpp-160) REVERT: B 390 ILE cc_start: 0.8481 (mm) cc_final: 0.8272 (mm) REVERT: B 399 ARG cc_start: 0.8527 (ttt90) cc_final: 0.8221 (tpt170) REVERT: B 443 GLU cc_start: 0.7715 (tp30) cc_final: 0.7128 (tp30) REVERT: B 475 GLN cc_start: 0.7482 (tp40) cc_final: 0.7171 (tp40) REVERT: B 499 ARG cc_start: 0.7577 (ptp90) cc_final: 0.7279 (ptp90) REVERT: B 500 ARG cc_start: 0.7818 (tpt90) cc_final: 0.7412 (tpp80) REVERT: B 517 PHE cc_start: 0.7476 (m-10) cc_final: 0.7274 (m-80) REVERT: B 527 THR cc_start: 0.8131 (p) cc_final: 0.7501 (p) REVERT: B 579 MET cc_start: 0.7736 (mmm) cc_final: 0.7307 (mmm) REVERT: B 581 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5972 (pp20) REVERT: B 586 MET cc_start: 0.7667 (tmm) cc_final: 0.5936 (tmm) REVERT: B 588 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7906 (ttpp) REVERT: B 590 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6711 (mm-30) REVERT: B 595 TRP cc_start: 0.7953 (m100) cc_final: 0.7660 (m100) REVERT: B 613 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6960 (tm-30) REVERT: B 645 LYS cc_start: 0.8529 (tptp) cc_final: 0.7998 (tptp) REVERT: B 825 VAL cc_start: 0.8512 (t) cc_final: 0.8274 (p) REVERT: B 826 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7557 (m110) REVERT: B 837 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: B 841 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8210 (ttmm) REVERT: B 843 TYR cc_start: 0.8145 (t80) cc_final: 0.7853 (t80) REVERT: B 847 GLU cc_start: 0.7834 (tp30) cc_final: 0.7557 (tp30) REVERT: B 848 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 850 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7978 (p) REVERT: B 876 LEU cc_start: 0.8161 (mt) cc_final: 0.7866 (mt) REVERT: B 880 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7661 (tmmt) REVERT: B 881 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 885 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7658 (pp) REVERT: B 907 ASN cc_start: 0.7663 (m-40) cc_final: 0.6606 (m-40) REVERT: B 908 HIS cc_start: 0.7946 (m-70) cc_final: 0.7510 (m-70) REVERT: B 911 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6680 (mt-10) REVERT: B 916 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8362 (tt) REVERT: B 928 HIS cc_start: 0.7143 (t70) cc_final: 0.6843 (t70) REVERT: B 929 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7243 (mtpp) outliers start: 70 outliers final: 40 residues processed: 469 average time/residue: 0.2774 time to fit residues: 171.6003 Evaluate side-chains 490 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 440 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 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 270 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10798 Z= 0.223 Angle : 0.593 14.489 14638 Z= 0.304 Chirality : 0.040 0.275 1772 Planarity : 0.004 0.047 1796 Dihedral : 6.254 59.697 1468 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 6.45 % Allowed : 20.82 % Favored : 72.74 % 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 (0.23), residues: 1344 helix: 1.78 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.41 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.003 0.000 HIS A 614 PHE 0.021 0.001 PHE B 288 TYR 0.015 0.001 TYR B 837 ARG 0.011 0.001 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 445 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7408 (mmtm) cc_final: 0.7112 (mmtm) REVERT: A 85 CYS cc_start: 0.8347 (m) cc_final: 0.8009 (m) REVERT: A 108 ILE cc_start: 0.8331 (mt) cc_final: 0.8061 (mp) REVERT: A 112 ILE cc_start: 0.8409 (mt) cc_final: 0.8088 (mm) REVERT: A 124 GLU cc_start: 0.7630 (tp30) cc_final: 0.6891 (tp30) REVERT: A 125 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 155 ASP cc_start: 0.7383 (t0) cc_final: 0.7172 (t0) REVERT: A 160 MET cc_start: 0.7739 (mmm) cc_final: 0.7347 (mmt) REVERT: A 186 MET cc_start: 0.6602 (mtp) cc_final: 0.6397 (mtp) REVERT: A 205 MET cc_start: 0.7619 (mmm) cc_final: 0.7215 (mmm) REVERT: A 217 LEU cc_start: 0.8364 (mt) cc_final: 0.8116 (mt) REVERT: A 218 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7687 (ttmt) REVERT: A 237 ASN cc_start: 0.7919 (t0) cc_final: 0.7710 (t0) REVERT: A 292 HIS cc_start: 0.8220 (m-70) cc_final: 0.7638 (m-70) REVERT: A 319 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6614 (mt) REVERT: A 335 ASN cc_start: 0.8671 (t0) cc_final: 0.8425 (t0) REVERT: A 337 GLU cc_start: 0.7269 (mp0) cc_final: 0.6684 (mp0) REVERT: A 387 TYR cc_start: 0.7943 (m-10) cc_final: 0.7629 (m-10) REVERT: A 431 ARG cc_start: 0.8264 (mmt180) cc_final: 0.8014 (mmt-90) REVERT: A 454 LYS cc_start: 0.8427 (mttm) cc_final: 0.8125 (mttm) REVERT: A 477 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8275 (tt) REVERT: A 479 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7510 (ttp80) REVERT: A 481 LEU cc_start: 0.8494 (mt) cc_final: 0.8231 (mt) REVERT: A 486 ILE cc_start: 0.8511 (mt) cc_final: 0.8101 (tt) REVERT: A 488 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8343 (tp) REVERT: A 491 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7543 (ttm110) REVERT: A 499 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7190 (ttp80) REVERT: A 502 HIS cc_start: 0.7913 (t-90) cc_final: 0.7402 (t-90) REVERT: A 506 ASN cc_start: 0.8007 (m-40) cc_final: 0.7496 (m-40) REVERT: A 514 SER cc_start: 0.8330 (p) cc_final: 0.8108 (p) REVERT: A 578 MET cc_start: 0.8168 (ttm) cc_final: 0.7927 (ttm) REVERT: A 579 MET cc_start: 0.7907 (mmm) cc_final: 0.7368 (mmm) REVERT: A 596 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7786 (tmmt) REVERT: A 597 GLN cc_start: 0.7506 (mt0) cc_final: 0.7272 (mt0) REVERT: A 611 LEU cc_start: 0.8240 (tp) cc_final: 0.7972 (tp) REVERT: A 613 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 622 LYS cc_start: 0.7868 (tttp) cc_final: 0.7526 (tttp) REVERT: A 645 LYS cc_start: 0.8982 (tptp) cc_final: 0.8381 (tptp) REVERT: A 843 TYR cc_start: 0.8643 (t80) cc_final: 0.7933 (t80) REVERT: A 848 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 849 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 852 LYS cc_start: 0.8318 (mttp) cc_final: 0.8034 (tttp) REVERT: A 862 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8402 (mmtm) REVERT: A 866 GLU cc_start: 0.7335 (tp30) cc_final: 0.7041 (tp30) REVERT: A 875 ARG cc_start: 0.7682 (tpt90) cc_final: 0.7372 (tpt90) REVERT: A 880 LYS cc_start: 0.8295 (tptp) cc_final: 0.7849 (tptp) REVERT: A 881 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6968 (tm-30) REVERT: A 900 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7493 (tp40) REVERT: A 925 MET cc_start: 0.8020 (mmm) cc_final: 0.7751 (mmm) REVERT: A 938 MET cc_start: 0.8483 (mmm) cc_final: 0.8249 (mmm) REVERT: B 81 ILE cc_start: 0.7930 (mt) cc_final: 0.7615 (mt) REVERT: B 84 SER cc_start: 0.8043 (t) cc_final: 0.7619 (p) REVERT: B 109 LEU cc_start: 0.7935 (mt) cc_final: 0.7616 (mt) REVERT: B 120 VAL cc_start: 0.8444 (t) cc_final: 0.8054 (p) REVERT: B 124 GLU cc_start: 0.7527 (tp30) cc_final: 0.7184 (tp30) REVERT: B 140 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7581 (mm110) REVERT: B 149 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 152 PHE cc_start: 0.8265 (t80) cc_final: 0.7914 (t80) REVERT: B 246 ASN cc_start: 0.8119 (m-40) cc_final: 0.7898 (m-40) REVERT: B 249 MET cc_start: 0.7524 (tmm) cc_final: 0.7034 (tmm) REVERT: B 269 LEU cc_start: 0.8010 (tp) cc_final: 0.7688 (tp) REVERT: B 278 TRP cc_start: 0.8370 (t-100) cc_final: 0.8063 (t-100) REVERT: B 300 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6963 (mt-10) REVERT: B 337 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 351 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8019 (tpp-160) REVERT: B 361 ASN cc_start: 0.8160 (m-40) cc_final: 0.7639 (m110) REVERT: B 384 ASP cc_start: 0.7054 (m-30) cc_final: 0.6749 (m-30) REVERT: B 390 ILE cc_start: 0.8515 (mm) cc_final: 0.8300 (mm) REVERT: B 399 ARG cc_start: 0.8527 (ttt90) cc_final: 0.8203 (tpt170) REVERT: B 420 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: B 443 GLU cc_start: 0.7735 (tp30) cc_final: 0.7156 (tp30) REVERT: B 475 GLN cc_start: 0.7481 (tp40) cc_final: 0.7181 (tp40) REVERT: B 499 ARG cc_start: 0.7618 (ptp90) cc_final: 0.7298 (ptp90) REVERT: B 500 ARG cc_start: 0.7856 (tpt90) cc_final: 0.7479 (tpp80) REVERT: B 512 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 527 THR cc_start: 0.8042 (p) cc_final: 0.7381 (p) REVERT: B 531 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5864 (mm-30) REVERT: B 579 MET cc_start: 0.7724 (mmm) cc_final: 0.7302 (mmm) REVERT: B 581 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5999 (pp20) REVERT: B 586 MET cc_start: 0.7679 (tmm) cc_final: 0.5971 (tmm) REVERT: B 588 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7922 (ttpp) REVERT: B 590 GLU cc_start: 0.7751 (mm-30) cc_final: 0.6741 (mm-30) REVERT: B 595 TRP cc_start: 0.7979 (m100) cc_final: 0.7671 (m100) REVERT: B 596 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8241 (mmmt) REVERT: B 613 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 645 LYS cc_start: 0.8546 (tptp) cc_final: 0.8015 (tptp) REVERT: B 825 VAL cc_start: 0.8524 (t) cc_final: 0.8293 (p) REVERT: B 826 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7561 (m110) REVERT: B 837 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: B 841 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8210 (ttmm) REVERT: B 843 TYR cc_start: 0.8136 (t80) cc_final: 0.7881 (t80) REVERT: B 847 GLU cc_start: 0.7845 (tp30) cc_final: 0.7568 (tp30) REVERT: B 848 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 850 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.7987 (p) REVERT: B 872 GLU cc_start: 0.7920 (tp30) cc_final: 0.7481 (tp30) REVERT: B 876 LEU cc_start: 0.8110 (mt) cc_final: 0.7795 (mt) REVERT: B 880 LYS cc_start: 0.8082 (tmmt) cc_final: 0.7702 (tmmt) REVERT: B 881 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7188 (mm-30) REVERT: B 885 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7539 (pp) REVERT: B 904 THR cc_start: 0.7844 (p) cc_final: 0.7413 (t) REVERT: B 907 ASN cc_start: 0.7637 (m-40) cc_final: 0.6550 (m110) REVERT: B 908 HIS cc_start: 0.7967 (m-70) cc_final: 0.7567 (m-70) REVERT: B 911 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6723 (mt-10) REVERT: B 916 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8358 (tt) REVERT: B 928 HIS cc_start: 0.7167 (t70) cc_final: 0.6849 (t70) outliers start: 74 outliers final: 51 residues processed: 470 average time/residue: 0.2788 time to fit residues: 173.4253 Evaluate side-chains 506 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 442 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 940 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 943 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 506 ASN B 624 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10798 Z= 0.197 Angle : 0.577 14.576 14638 Z= 0.297 Chirality : 0.039 0.216 1772 Planarity : 0.004 0.052 1796 Dihedral : 6.211 58.533 1468 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 6.79 % Allowed : 21.69 % Favored : 71.52 % 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: 2.27 (0.23), residues: 1344 helix: 1.83 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.39 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 635 HIS 0.002 0.000 HIS B 889 PHE 0.013 0.001 PHE A 517 TYR 0.014 0.001 TYR A 313 ARG 0.006 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 449 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7386 (mmtm) cc_final: 0.7184 (mmtm) REVERT: A 85 CYS cc_start: 0.8341 (m) cc_final: 0.8003 (m) REVERT: A 112 ILE cc_start: 0.8416 (mt) cc_final: 0.8078 (mm) REVERT: A 124 GLU cc_start: 0.7545 (tp30) cc_final: 0.6988 (tp30) REVERT: A 125 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 155 ASP cc_start: 0.7367 (t0) cc_final: 0.7167 (t0) REVERT: A 160 MET cc_start: 0.7769 (mmm) cc_final: 0.7368 (mmt) REVERT: A 186 MET cc_start: 0.6604 (mtp) cc_final: 0.6371 (mtp) REVERT: A 199 MET cc_start: 0.7845 (mmm) cc_final: 0.7526 (mmm) REVERT: A 205 MET cc_start: 0.7588 (mmm) cc_final: 0.7352 (mpp) REVERT: A 217 LEU cc_start: 0.8362 (mt) cc_final: 0.8103 (mt) REVERT: A 218 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7701 (ttmt) REVERT: A 237 ASN cc_start: 0.7933 (t0) cc_final: 0.7675 (t0) REVERT: A 250 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7456 (mtmm) REVERT: A 292 HIS cc_start: 0.8217 (m-70) cc_final: 0.7636 (m-70) REVERT: A 319 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6623 (mt) REVERT: A 335 ASN cc_start: 0.8664 (t0) cc_final: 0.8394 (t0) REVERT: A 337 GLU cc_start: 0.7267 (mp0) cc_final: 0.6651 (mp0) REVERT: A 346 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6746 (mt-10) REVERT: A 387 TYR cc_start: 0.7913 (m-10) cc_final: 0.7523 (m-10) REVERT: A 454 LYS cc_start: 0.8371 (mttm) cc_final: 0.8081 (mttm) REVERT: A 477 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 479 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7502 (ttp80) REVERT: A 481 LEU cc_start: 0.8523 (mt) cc_final: 0.8259 (mt) REVERT: A 486 ILE cc_start: 0.8436 (mt) cc_final: 0.7995 (tt) REVERT: A 491 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7604 (ttm110) REVERT: A 499 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7178 (ttp80) REVERT: A 502 HIS cc_start: 0.7879 (t-90) cc_final: 0.7378 (t-90) REVERT: A 506 ASN cc_start: 0.8007 (m-40) cc_final: 0.7566 (m-40) REVERT: A 514 SER cc_start: 0.8350 (p) cc_final: 0.8107 (p) REVERT: A 578 MET cc_start: 0.8130 (ttm) cc_final: 0.7912 (ttm) REVERT: A 579 MET cc_start: 0.7900 (mmm) cc_final: 0.7358 (mmm) REVERT: A 596 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7749 (tmmt) REVERT: A 597 GLN cc_start: 0.7437 (mt0) cc_final: 0.7183 (mt0) REVERT: A 611 LEU cc_start: 0.8262 (tp) cc_final: 0.7976 (tp) REVERT: A 613 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 645 LYS cc_start: 0.8957 (tptp) cc_final: 0.8356 (tptp) REVERT: A 843 TYR cc_start: 0.8638 (t80) cc_final: 0.7960 (t80) REVERT: A 848 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 849 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 852 LYS cc_start: 0.8309 (mttp) cc_final: 0.8038 (tttp) REVERT: A 862 LYS cc_start: 0.8692 (mmtm) cc_final: 0.8434 (mmtm) REVERT: A 866 GLU cc_start: 0.7323 (tp30) cc_final: 0.7031 (tp30) REVERT: A 875 ARG cc_start: 0.7660 (tpt90) cc_final: 0.7367 (tpt90) REVERT: A 880 LYS cc_start: 0.8286 (tptp) cc_final: 0.7827 (tptp) REVERT: A 881 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6953 (tm-30) REVERT: A 900 GLN cc_start: 0.8195 (tm130) cc_final: 0.7962 (tp40) REVERT: A 910 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: A 925 MET cc_start: 0.8013 (mmm) cc_final: 0.7789 (mmm) REVERT: A 931 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 938 MET cc_start: 0.8510 (mmm) cc_final: 0.8243 (mmm) REVERT: B 81 ILE cc_start: 0.7906 (mt) cc_final: 0.7612 (mt) REVERT: B 84 SER cc_start: 0.8041 (t) cc_final: 0.7622 (p) REVERT: B 109 LEU cc_start: 0.7934 (mt) cc_final: 0.7662 (mt) REVERT: B 149 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 199 MET cc_start: 0.7664 (mmm) cc_final: 0.7058 (tpt) REVERT: B 246 ASN cc_start: 0.8108 (m-40) cc_final: 0.7883 (m-40) REVERT: B 269 LEU cc_start: 0.8010 (tp) cc_final: 0.7695 (tp) REVERT: B 278 TRP cc_start: 0.8376 (t-100) cc_final: 0.8069 (t-100) REVERT: B 300 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6972 (mt-10) REVERT: B 337 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: B 351 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8073 (tpp-160) REVERT: B 366 MET cc_start: 0.8129 (tpp) cc_final: 0.7839 (tpp) REVERT: B 387 TYR cc_start: 0.7804 (m-10) cc_final: 0.7396 (m-10) REVERT: B 390 ILE cc_start: 0.8527 (mm) cc_final: 0.8319 (mm) REVERT: B 420 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7659 (mtm-85) REVERT: B 443 GLU cc_start: 0.7726 (tp30) cc_final: 0.7101 (tp30) REVERT: B 475 GLN cc_start: 0.7474 (tp40) cc_final: 0.7177 (tp40) REVERT: B 499 ARG cc_start: 0.7614 (ptp90) cc_final: 0.7290 (ptp90) REVERT: B 500 ARG cc_start: 0.7844 (tpt90) cc_final: 0.7485 (tpp80) REVERT: B 512 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8094 (tp) REVERT: B 527 THR cc_start: 0.8129 (p) cc_final: 0.7358 (p) REVERT: B 531 GLU cc_start: 0.6384 (mm-30) cc_final: 0.5959 (mm-30) REVERT: B 579 MET cc_start: 0.7730 (mmm) cc_final: 0.7364 (mmm) REVERT: B 581 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5880 (pp20) REVERT: B 586 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.5973 (tmm) REVERT: B 588 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7927 (ttpp) REVERT: B 590 GLU cc_start: 0.7708 (mm-30) cc_final: 0.6673 (mm-30) REVERT: B 595 TRP cc_start: 0.8004 (m100) cc_final: 0.7685 (m100) REVERT: B 596 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8239 (mmmt) REVERT: B 613 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7016 (tm-30) REVERT: B 645 LYS cc_start: 0.8523 (tptp) cc_final: 0.7982 (tptp) REVERT: B 825 VAL cc_start: 0.8510 (t) cc_final: 0.8274 (p) REVERT: B 826 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7590 (m110) REVERT: B 837 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: B 841 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8195 (ttmm) REVERT: B 847 GLU cc_start: 0.7770 (tp30) cc_final: 0.7494 (tp30) REVERT: B 848 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 850 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7951 (p) REVERT: B 872 GLU cc_start: 0.7903 (tp30) cc_final: 0.7514 (tp30) REVERT: B 876 LEU cc_start: 0.8084 (mt) cc_final: 0.7794 (mt) REVERT: B 881 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 885 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7511 (pp) REVERT: B 904 THR cc_start: 0.7827 (p) cc_final: 0.7403 (t) REVERT: B 907 ASN cc_start: 0.7639 (m-40) cc_final: 0.6548 (m110) REVERT: B 908 HIS cc_start: 0.7931 (m-70) cc_final: 0.7543 (m-70) REVERT: B 911 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6693 (mt-10) REVERT: B 916 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8344 (tt) REVERT: B 928 HIS cc_start: 0.7163 (t70) cc_final: 0.6858 (t70) REVERT: B 929 LYS cc_start: 0.7753 (mtpp) cc_final: 0.7237 (mtpp) outliers start: 78 outliers final: 51 residues processed: 478 average time/residue: 0.2765 time to fit residues: 174.8705 Evaluate side-chains 506 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 443 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 875 ARG Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10798 Z= 0.192 Angle : 0.588 15.083 14638 Z= 0.305 Chirality : 0.040 0.255 1772 Planarity : 0.004 0.047 1796 Dihedral : 6.182 58.328 1468 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.88 % Allowed : 22.74 % Favored : 70.38 % 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: 2.35 (0.23), residues: 1344 helix: 1.90 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.48 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 635 HIS 0.004 0.001 HIS B 889 PHE 0.022 0.001 PHE B 288 TYR 0.014 0.001 TYR B 837 ARG 0.006 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 443 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8330 (m) cc_final: 0.7910 (m) REVERT: A 112 ILE cc_start: 0.8425 (mt) cc_final: 0.8081 (mm) REVERT: A 124 GLU cc_start: 0.7533 (tp30) cc_final: 0.6629 (tp30) REVERT: A 125 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 155 ASP cc_start: 0.7362 (t0) cc_final: 0.7154 (t0) REVERT: A 160 MET cc_start: 0.7784 (mmm) cc_final: 0.7346 (mmt) REVERT: A 186 MET cc_start: 0.6592 (mtp) cc_final: 0.6367 (mtp) REVERT: A 199 MET cc_start: 0.7764 (mmm) cc_final: 0.7401 (mmm) REVERT: A 205 MET cc_start: 0.7561 (mmm) cc_final: 0.7055 (mpp) REVERT: A 217 LEU cc_start: 0.8350 (mt) cc_final: 0.8086 (mt) REVERT: A 218 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7680 (ttmt) REVERT: A 237 ASN cc_start: 0.7906 (t0) cc_final: 0.7689 (t0) REVERT: A 250 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7414 (mtmm) REVERT: A 292 HIS cc_start: 0.8229 (m-70) cc_final: 0.7636 (m-70) REVERT: A 319 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6604 (mt) REVERT: A 322 SER cc_start: 0.8097 (t) cc_final: 0.7714 (p) REVERT: A 335 ASN cc_start: 0.8647 (t0) cc_final: 0.8373 (t0) REVERT: A 337 GLU cc_start: 0.7263 (mp0) cc_final: 0.6650 (mp0) REVERT: A 346 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6737 (mt-10) REVERT: A 387 TYR cc_start: 0.7875 (m-10) cc_final: 0.7603 (m-10) REVERT: A 454 LYS cc_start: 0.8371 (mttm) cc_final: 0.8092 (mttm) REVERT: A 477 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 479 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7495 (ttp80) REVERT: A 481 LEU cc_start: 0.8504 (mt) cc_final: 0.8253 (mt) REVERT: A 499 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7167 (ttp80) REVERT: A 506 ASN cc_start: 0.7971 (m-40) cc_final: 0.7558 (m-40) REVERT: A 512 LEU cc_start: 0.8576 (tp) cc_final: 0.8226 (tt) REVERT: A 578 MET cc_start: 0.8137 (ttm) cc_final: 0.7904 (ttm) REVERT: A 579 MET cc_start: 0.7899 (mmm) cc_final: 0.7358 (mmm) REVERT: A 596 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7740 (tmmt) REVERT: A 597 GLN cc_start: 0.7435 (mt0) cc_final: 0.7174 (mt0) REVERT: A 611 LEU cc_start: 0.8264 (tp) cc_final: 0.7972 (tp) REVERT: A 613 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 622 LYS cc_start: 0.7876 (tttp) cc_final: 0.7539 (tttp) REVERT: A 645 LYS cc_start: 0.8949 (tptp) cc_final: 0.8338 (tptp) REVERT: A 843 TYR cc_start: 0.8645 (t80) cc_final: 0.7949 (t80) REVERT: A 848 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 849 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 852 LYS cc_start: 0.8268 (mttp) cc_final: 0.8003 (tttp) REVERT: A 862 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8397 (mmtm) REVERT: A 866 GLU cc_start: 0.7286 (tp30) cc_final: 0.7051 (tp30) REVERT: A 867 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9036 (mm) REVERT: A 868 LYS cc_start: 0.8559 (mmmm) cc_final: 0.7755 (mmmm) REVERT: A 875 ARG cc_start: 0.7658 (tpt90) cc_final: 0.7385 (tpt90) REVERT: A 880 LYS cc_start: 0.8304 (tptp) cc_final: 0.7820 (tptp) REVERT: A 881 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6974 (tm-30) REVERT: A 931 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 938 MET cc_start: 0.8516 (mmm) cc_final: 0.8237 (mmm) REVERT: B 81 ILE cc_start: 0.7912 (mt) cc_final: 0.7636 (mt) REVERT: B 84 SER cc_start: 0.8043 (t) cc_final: 0.7614 (p) REVERT: B 109 LEU cc_start: 0.7940 (mt) cc_final: 0.7641 (mt) REVERT: B 149 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7057 (tm-30) REVERT: B 199 MET cc_start: 0.7622 (mmm) cc_final: 0.6859 (tpp) REVERT: B 246 ASN cc_start: 0.8088 (m-40) cc_final: 0.7872 (m-40) REVERT: B 269 LEU cc_start: 0.7994 (tp) cc_final: 0.7690 (tp) REVERT: B 278 TRP cc_start: 0.8378 (t-100) cc_final: 0.8080 (t-100) REVERT: B 300 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: B 337 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: B 351 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8073 (tpp-160) REVERT: B 361 ASN cc_start: 0.8182 (m-40) cc_final: 0.7685 (m110) REVERT: B 384 ASP cc_start: 0.7155 (m-30) cc_final: 0.6922 (m-30) REVERT: B 387 TYR cc_start: 0.7818 (m-10) cc_final: 0.7428 (m-10) REVERT: B 390 ILE cc_start: 0.8530 (mm) cc_final: 0.8315 (mm) REVERT: B 420 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7642 (mtm-85) REVERT: B 443 GLU cc_start: 0.7719 (tp30) cc_final: 0.7109 (tp30) REVERT: B 475 GLN cc_start: 0.7470 (tp40) cc_final: 0.7189 (tp40) REVERT: B 485 ASP cc_start: 0.8460 (p0) cc_final: 0.8223 (p0) REVERT: B 499 ARG cc_start: 0.7617 (ptp90) cc_final: 0.7269 (ptp90) REVERT: B 500 ARG cc_start: 0.7843 (tpt90) cc_final: 0.7477 (tpp80) REVERT: B 509 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8260 (mm) REVERT: B 512 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8193 (tp) REVERT: B 523 TRP cc_start: 0.7612 (m100) cc_final: 0.6974 (m100) REVERT: B 527 THR cc_start: 0.8154 (p) cc_final: 0.7306 (p) REVERT: B 531 GLU cc_start: 0.6427 (mm-30) cc_final: 0.6083 (mm-30) REVERT: B 579 MET cc_start: 0.7725 (mmm) cc_final: 0.7377 (mmm) REVERT: B 581 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5873 (pp20) REVERT: B 586 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6035 (tmm) REVERT: B 588 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7922 (ttpp) REVERT: B 590 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6782 (mm-30) REVERT: B 595 TRP cc_start: 0.8018 (m100) cc_final: 0.7694 (m100) REVERT: B 613 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 645 LYS cc_start: 0.8480 (tptp) cc_final: 0.7982 (tptp) REVERT: B 825 VAL cc_start: 0.8501 (t) cc_final: 0.8271 (p) REVERT: B 826 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7585 (m110) REVERT: B 837 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: B 847 GLU cc_start: 0.7746 (tp30) cc_final: 0.7492 (tp30) REVERT: B 848 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 850 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 872 GLU cc_start: 0.7881 (tp30) cc_final: 0.7670 (tp30) REVERT: B 876 LEU cc_start: 0.8071 (mt) cc_final: 0.7817 (mt) REVERT: B 881 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 904 THR cc_start: 0.7779 (p) cc_final: 0.7387 (t) REVERT: B 907 ASN cc_start: 0.7651 (m-40) cc_final: 0.6591 (m110) REVERT: B 908 HIS cc_start: 0.7950 (m-70) cc_final: 0.7572 (m-70) REVERT: B 911 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6711 (mt-10) REVERT: B 916 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8287 (tt) REVERT: B 928 HIS cc_start: 0.7157 (t70) cc_final: 0.6848 (t70) REVERT: B 929 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7239 (mtpp) REVERT: B 941 LEU cc_start: 0.8743 (tp) cc_final: 0.8530 (tt) outliers start: 79 outliers final: 52 residues processed: 471 average time/residue: 0.2703 time to fit residues: 168.0071 Evaluate side-chains 506 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 440 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 101 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10798 Z= 0.173 Angle : 0.587 14.817 14638 Z= 0.301 Chirality : 0.040 0.283 1772 Planarity : 0.004 0.043 1796 Dihedral : 6.133 56.593 1468 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 6.53 % Allowed : 22.47 % Favored : 70.99 % 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: 2.46 (0.23), residues: 1344 helix: 1.98 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.46 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 635 HIS 0.002 0.000 HIS B 292 PHE 0.011 0.001 PHE A 455 TYR 0.011 0.001 TYR A 313 ARG 0.012 0.001 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 445 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8300 (m) cc_final: 0.7886 (m) REVERT: A 124 GLU cc_start: 0.7494 (tp30) cc_final: 0.6574 (tp30) REVERT: A 125 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 160 MET cc_start: 0.7774 (mmm) cc_final: 0.7331 (mmt) REVERT: A 186 MET cc_start: 0.6564 (mtp) cc_final: 0.6347 (mtp) REVERT: A 194 ASN cc_start: 0.8523 (p0) cc_final: 0.8241 (p0) REVERT: A 197 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7101 (mt-10) REVERT: A 199 MET cc_start: 0.7701 (mmm) cc_final: 0.7304 (mmm) REVERT: A 205 MET cc_start: 0.7510 (mmm) cc_final: 0.7015 (mpp) REVERT: A 217 LEU cc_start: 0.8370 (mt) cc_final: 0.8108 (mt) REVERT: A 218 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7634 (ttmt) REVERT: A 237 ASN cc_start: 0.7868 (t0) cc_final: 0.7654 (t0) REVERT: A 250 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7383 (mtmm) REVERT: A 292 HIS cc_start: 0.8151 (m-70) cc_final: 0.7527 (m-70) REVERT: A 319 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6591 (mt) REVERT: A 322 SER cc_start: 0.8071 (t) cc_final: 0.7710 (p) REVERT: A 335 ASN cc_start: 0.8632 (t0) cc_final: 0.8367 (t0) REVERT: A 337 GLU cc_start: 0.7234 (mp0) cc_final: 0.6567 (mp0) REVERT: A 387 TYR cc_start: 0.7842 (m-10) cc_final: 0.7600 (m-10) REVERT: A 454 LYS cc_start: 0.8357 (mttm) cc_final: 0.8136 (mttm) REVERT: A 476 THR cc_start: 0.8321 (m) cc_final: 0.7663 (p) REVERT: A 477 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 479 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 481 LEU cc_start: 0.8483 (mt) cc_final: 0.8227 (mt) REVERT: A 491 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7394 (ttm110) REVERT: A 499 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7156 (ttp80) REVERT: A 506 ASN cc_start: 0.7984 (m-40) cc_final: 0.7588 (m-40) REVERT: A 512 LEU cc_start: 0.8519 (tp) cc_final: 0.8178 (tt) REVERT: A 578 MET cc_start: 0.8117 (ttm) cc_final: 0.7895 (ttm) REVERT: A 579 MET cc_start: 0.7876 (mmm) cc_final: 0.7342 (mmm) REVERT: A 596 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7753 (tmmt) REVERT: A 597 GLN cc_start: 0.7416 (mt0) cc_final: 0.7194 (mt0) REVERT: A 611 LEU cc_start: 0.8266 (tp) cc_final: 0.7958 (tp) REVERT: A 613 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 622 LYS cc_start: 0.7884 (tttp) cc_final: 0.7542 (tttp) REVERT: A 645 LYS cc_start: 0.8938 (tptp) cc_final: 0.8321 (tptp) REVERT: A 837 TYR cc_start: 0.8240 (t80) cc_final: 0.7886 (t80) REVERT: A 843 TYR cc_start: 0.8638 (t80) cc_final: 0.7981 (t80) REVERT: A 848 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 852 LYS cc_start: 0.8235 (mttp) cc_final: 0.8009 (tttp) REVERT: A 862 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8367 (mmtm) REVERT: A 866 GLU cc_start: 0.7272 (tp30) cc_final: 0.7039 (tp30) REVERT: A 867 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9036 (mm) REVERT: A 868 LYS cc_start: 0.8569 (mmmm) cc_final: 0.7740 (mmmm) REVERT: A 880 LYS cc_start: 0.8287 (tptp) cc_final: 0.7795 (tptp) REVERT: A 881 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6982 (tm-30) REVERT: A 910 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7857 (ttm-80) REVERT: A 931 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 938 MET cc_start: 0.8510 (mmm) cc_final: 0.8292 (mmm) REVERT: B 81 ILE cc_start: 0.7896 (mt) cc_final: 0.7608 (mt) REVERT: B 84 SER cc_start: 0.8015 (t) cc_final: 0.7594 (p) REVERT: B 109 LEU cc_start: 0.7924 (mt) cc_final: 0.7714 (mt) REVERT: B 149 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 199 MET cc_start: 0.7587 (mmm) cc_final: 0.6948 (tpt) REVERT: B 226 LEU cc_start: 0.8371 (tp) cc_final: 0.8135 (tt) REVERT: B 246 ASN cc_start: 0.8062 (m-40) cc_final: 0.7776 (m-40) REVERT: B 249 MET cc_start: 0.7449 (ttp) cc_final: 0.7035 (tmm) REVERT: B 269 LEU cc_start: 0.7968 (tp) cc_final: 0.7670 (tp) REVERT: B 278 TRP cc_start: 0.8362 (t-100) cc_final: 0.8002 (t-100) REVERT: B 300 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: B 337 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: B 351 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8075 (tpp-160) REVERT: B 366 MET cc_start: 0.8171 (tpp) cc_final: 0.7896 (tpp) REVERT: B 384 ASP cc_start: 0.7137 (m-30) cc_final: 0.6844 (m-30) REVERT: B 387 TYR cc_start: 0.7803 (m-10) cc_final: 0.7412 (m-10) REVERT: B 390 ILE cc_start: 0.8523 (mm) cc_final: 0.8301 (mm) REVERT: B 420 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7667 (mtm-85) REVERT: B 443 GLU cc_start: 0.7704 (tp30) cc_final: 0.7088 (tp30) REVERT: B 475 GLN cc_start: 0.7465 (tp40) cc_final: 0.7185 (tp40) REVERT: B 499 ARG cc_start: 0.7590 (ptp90) cc_final: 0.7245 (ptp90) REVERT: B 500 ARG cc_start: 0.7804 (tpt90) cc_final: 0.7429 (tpp80) REVERT: B 512 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 517 PHE cc_start: 0.7499 (m-10) cc_final: 0.7201 (m-80) REVERT: B 523 TRP cc_start: 0.7629 (m100) cc_final: 0.6913 (m100) REVERT: B 527 THR cc_start: 0.8092 (p) cc_final: 0.7222 (p) REVERT: B 531 GLU cc_start: 0.6426 (mm-30) cc_final: 0.6050 (mm-30) REVERT: B 579 MET cc_start: 0.7694 (mmm) cc_final: 0.7397 (mmm) REVERT: B 581 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5842 (pp20) REVERT: B 586 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6031 (tmm) REVERT: B 588 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7916 (ttpp) REVERT: B 590 GLU cc_start: 0.7704 (mm-30) cc_final: 0.6747 (mm-30) REVERT: B 595 TRP cc_start: 0.8006 (m100) cc_final: 0.7691 (m100) REVERT: B 613 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 645 LYS cc_start: 0.8445 (tptp) cc_final: 0.7971 (tptp) REVERT: B 825 VAL cc_start: 0.8510 (t) cc_final: 0.8273 (p) REVERT: B 826 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7592 (m110) REVERT: B 837 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: B 841 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8277 (ttmm) REVERT: B 847 GLU cc_start: 0.7709 (tp30) cc_final: 0.7454 (tp30) REVERT: B 848 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7773 (mt-10) REVERT: B 850 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 872 GLU cc_start: 0.7962 (tp30) cc_final: 0.7497 (tp30) REVERT: B 875 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7560 (ttt-90) REVERT: B 876 LEU cc_start: 0.8074 (mt) cc_final: 0.7859 (mt) REVERT: B 881 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7188 (mm-30) REVERT: B 904 THR cc_start: 0.7765 (p) cc_final: 0.7372 (t) REVERT: B 907 ASN cc_start: 0.7655 (m-40) cc_final: 0.6600 (m110) REVERT: B 908 HIS cc_start: 0.7940 (m-70) cc_final: 0.7548 (m-70) REVERT: B 911 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6682 (mt-10) REVERT: B 916 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8254 (tt) REVERT: B 928 HIS cc_start: 0.7162 (t70) cc_final: 0.6821 (t70) REVERT: B 929 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7189 (mtpp) REVERT: B 941 LEU cc_start: 0.8690 (tp) cc_final: 0.8485 (tt) outliers start: 75 outliers final: 52 residues processed: 471 average time/residue: 0.2741 time to fit residues: 169.7881 Evaluate side-chains 506 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 441 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10798 Z= 0.237 Angle : 0.623 15.662 14638 Z= 0.324 Chirality : 0.041 0.250 1772 Planarity : 0.004 0.039 1796 Dihedral : 6.132 59.697 1466 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 6.27 % Allowed : 23.43 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.23), residues: 1344 helix: 1.88 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.38 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 635 HIS 0.003 0.001 HIS B 292 PHE 0.023 0.001 PHE B 288 TYR 0.015 0.001 TYR B 837 ARG 0.012 0.001 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 451 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8347 (m) cc_final: 0.8022 (m) REVERT: A 112 ILE cc_start: 0.8407 (mt) cc_final: 0.8114 (mm) REVERT: A 124 GLU cc_start: 0.7531 (tp30) cc_final: 0.6613 (tp30) REVERT: A 125 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 147 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7790 (mt) REVERT: A 160 MET cc_start: 0.7680 (mmm) cc_final: 0.7291 (mmt) REVERT: A 186 MET cc_start: 0.6626 (mtp) cc_final: 0.6412 (mtp) REVERT: A 194 ASN cc_start: 0.8525 (p0) cc_final: 0.8275 (p0) REVERT: A 197 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7115 (mt-10) REVERT: A 205 MET cc_start: 0.7533 (mmm) cc_final: 0.7036 (mpp) REVERT: A 217 LEU cc_start: 0.8391 (mt) cc_final: 0.8142 (mt) REVERT: A 218 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7734 (ttmt) REVERT: A 237 ASN cc_start: 0.7919 (t0) cc_final: 0.7694 (t0) REVERT: A 250 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7437 (mtmm) REVERT: A 292 HIS cc_start: 0.8243 (m-70) cc_final: 0.7627 (m-70) REVERT: A 319 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6635 (mt) REVERT: A 322 SER cc_start: 0.8099 (t) cc_final: 0.7712 (p) REVERT: A 335 ASN cc_start: 0.8657 (t0) cc_final: 0.8368 (t0) REVERT: A 337 GLU cc_start: 0.7269 (mp0) cc_final: 0.6658 (mp0) REVERT: A 346 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6738 (mt-10) REVERT: A 387 TYR cc_start: 0.7889 (m-10) cc_final: 0.7646 (m-10) REVERT: A 401 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6639 (mtm) REVERT: A 454 LYS cc_start: 0.8367 (mttm) cc_final: 0.8162 (mttm) REVERT: A 477 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 479 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7525 (ttp80) REVERT: A 481 LEU cc_start: 0.8552 (mt) cc_final: 0.8282 (mt) REVERT: A 486 ILE cc_start: 0.8370 (mm) cc_final: 0.8138 (mt) REVERT: A 491 ARG cc_start: 0.7783 (ttm110) cc_final: 0.7535 (ttm110) REVERT: A 499 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7200 (ttp80) REVERT: A 506 ASN cc_start: 0.8009 (m-40) cc_final: 0.7630 (m-40) REVERT: A 512 LEU cc_start: 0.8539 (tp) cc_final: 0.8191 (tt) REVERT: A 578 MET cc_start: 0.8098 (ttm) cc_final: 0.7880 (ttm) REVERT: A 579 MET cc_start: 0.7874 (mmm) cc_final: 0.7357 (mmm) REVERT: A 596 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7764 (tmmt) REVERT: A 597 GLN cc_start: 0.7468 (mt0) cc_final: 0.7191 (mt0) REVERT: A 611 LEU cc_start: 0.8281 (tp) cc_final: 0.7950 (tp) REVERT: A 613 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 645 LYS cc_start: 0.8949 (tptp) cc_final: 0.8335 (tptp) REVERT: A 843 TYR cc_start: 0.8650 (t80) cc_final: 0.7982 (t80) REVERT: A 848 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 849 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 852 LYS cc_start: 0.8253 (mttp) cc_final: 0.8022 (tttp) REVERT: A 862 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8370 (mmtm) REVERT: A 866 GLU cc_start: 0.7270 (tp30) cc_final: 0.7042 (tp30) REVERT: A 867 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9051 (mm) REVERT: A 868 LYS cc_start: 0.8617 (mmmm) cc_final: 0.7797 (mmmm) REVERT: A 875 ARG cc_start: 0.7765 (tpt90) cc_final: 0.7312 (tpt170) REVERT: A 880 LYS cc_start: 0.8313 (tptp) cc_final: 0.7849 (tptp) REVERT: A 881 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7041 (tm-30) REVERT: A 931 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 938 MET cc_start: 0.8499 (mmm) cc_final: 0.8262 (mmm) REVERT: A 940 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7728 (tpp80) REVERT: B 81 ILE cc_start: 0.7917 (mt) cc_final: 0.7640 (mt) REVERT: B 84 SER cc_start: 0.8051 (t) cc_final: 0.7623 (p) REVERT: B 109 LEU cc_start: 0.7947 (mt) cc_final: 0.7653 (mt) REVERT: B 120 VAL cc_start: 0.8405 (t) cc_final: 0.8017 (p) REVERT: B 149 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 199 MET cc_start: 0.7649 (mmm) cc_final: 0.6999 (tpt) REVERT: B 246 ASN cc_start: 0.8091 (m-40) cc_final: 0.7797 (m-40) REVERT: B 249 MET cc_start: 0.7478 (ttp) cc_final: 0.7267 (ttp) REVERT: B 269 LEU cc_start: 0.7994 (tp) cc_final: 0.7702 (tp) REVERT: B 278 TRP cc_start: 0.8391 (t-100) cc_final: 0.8080 (t-100) REVERT: B 300 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: B 337 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 351 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8051 (tpp-160) REVERT: B 361 ASN cc_start: 0.8133 (m-40) cc_final: 0.7780 (m110) REVERT: B 384 ASP cc_start: 0.7154 (m-30) cc_final: 0.6871 (m-30) REVERT: B 387 TYR cc_start: 0.7867 (m-10) cc_final: 0.7458 (m-10) REVERT: B 390 ILE cc_start: 0.8549 (mm) cc_final: 0.8327 (mm) REVERT: B 420 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: B 443 GLU cc_start: 0.7733 (tp30) cc_final: 0.7128 (tp30) REVERT: B 475 GLN cc_start: 0.7468 (tp40) cc_final: 0.7182 (tp40) REVERT: B 499 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7335 (ptp90) REVERT: B 500 ARG cc_start: 0.7870 (tpt90) cc_final: 0.7510 (tpp80) REVERT: B 512 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8192 (tp) REVERT: B 523 TRP cc_start: 0.7699 (m100) cc_final: 0.7040 (m100) REVERT: B 527 THR cc_start: 0.8141 (p) cc_final: 0.7257 (p) REVERT: B 531 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6134 (mm-30) REVERT: B 579 MET cc_start: 0.7694 (mmm) cc_final: 0.7412 (mmm) REVERT: B 586 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6038 (tmm) REVERT: B 588 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7968 (ttpp) REVERT: B 590 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6726 (mm-30) REVERT: B 595 TRP cc_start: 0.8002 (m100) cc_final: 0.7672 (m100) REVERT: B 596 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8271 (mmmt) REVERT: B 613 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 645 LYS cc_start: 0.8472 (tptp) cc_final: 0.7977 (tptp) REVERT: B 825 VAL cc_start: 0.8525 (t) cc_final: 0.8292 (p) REVERT: B 826 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7610 (m110) REVERT: B 837 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: B 847 GLU cc_start: 0.7743 (tp30) cc_final: 0.7448 (tp30) REVERT: B 848 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 872 GLU cc_start: 0.7984 (tp30) cc_final: 0.7501 (tp30) REVERT: B 875 ARG cc_start: 0.7862 (ttt-90) cc_final: 0.7578 (ttt-90) REVERT: B 876 LEU cc_start: 0.8100 (mt) cc_final: 0.7892 (mt) REVERT: B 881 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7234 (mm-30) REVERT: B 904 THR cc_start: 0.7803 (p) cc_final: 0.7502 (t) REVERT: B 907 ASN cc_start: 0.7665 (m-40) cc_final: 0.7138 (m-40) REVERT: B 911 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6859 (mt-10) REVERT: B 928 HIS cc_start: 0.7222 (t70) cc_final: 0.6876 (t70) REVERT: B 929 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7309 (mtpp) outliers start: 72 outliers final: 55 residues processed: 474 average time/residue: 0.2771 time to fit residues: 172.3904 Evaluate side-chains 511 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 444 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10798 Z= 0.190 Angle : 0.634 15.355 14638 Z= 0.322 Chirality : 0.041 0.252 1772 Planarity : 0.004 0.050 1796 Dihedral : 6.086 57.579 1466 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.49 % Allowed : 24.65 % Favored : 69.86 % 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: 2.37 (0.23), residues: 1344 helix: 1.92 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.52 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 635 HIS 0.006 0.001 HIS B 889 PHE 0.012 0.001 PHE A 598 TYR 0.013 0.001 TYR A 313 ARG 0.009 0.001 ARG A 585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 451 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8309 (m) cc_final: 0.7910 (m) REVERT: A 112 ILE cc_start: 0.8375 (mt) cc_final: 0.8082 (mm) REVERT: A 124 GLU cc_start: 0.7483 (tp30) cc_final: 0.6568 (tp30) REVERT: A 125 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 160 MET cc_start: 0.7692 (mmm) cc_final: 0.7298 (mmt) REVERT: A 186 MET cc_start: 0.6601 (mtp) cc_final: 0.6380 (mtp) REVERT: A 194 ASN cc_start: 0.8525 (p0) cc_final: 0.8273 (p0) REVERT: A 197 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7083 (mt-10) REVERT: A 217 LEU cc_start: 0.8376 (mt) cc_final: 0.8110 (mt) REVERT: A 218 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7704 (ttmt) REVERT: A 237 ASN cc_start: 0.7880 (t0) cc_final: 0.7653 (t0) REVERT: A 250 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7385 (mtmm) REVERT: A 292 HIS cc_start: 0.8220 (m-70) cc_final: 0.7579 (m-70) REVERT: A 319 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6585 (mt) REVERT: A 322 SER cc_start: 0.8081 (t) cc_final: 0.7724 (p) REVERT: A 335 ASN cc_start: 0.8641 (t0) cc_final: 0.8364 (t0) REVERT: A 337 GLU cc_start: 0.7206 (mp0) cc_final: 0.6563 (mp0) REVERT: A 387 TYR cc_start: 0.7854 (m-10) cc_final: 0.7628 (m-10) REVERT: A 401 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6574 (mtm) REVERT: A 454 LYS cc_start: 0.8362 (mttm) cc_final: 0.8154 (mttm) REVERT: A 476 THR cc_start: 0.8339 (m) cc_final: 0.7729 (p) REVERT: A 477 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8219 (tt) REVERT: A 479 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7516 (ttp80) REVERT: A 481 LEU cc_start: 0.8510 (mt) cc_final: 0.8244 (mt) REVERT: A 486 ILE cc_start: 0.8353 (mm) cc_final: 0.8096 (mt) REVERT: A 491 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7474 (ttm110) REVERT: A 499 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7172 (ttp80) REVERT: A 506 ASN cc_start: 0.8000 (m-40) cc_final: 0.7597 (m-40) REVERT: A 512 LEU cc_start: 0.8494 (tp) cc_final: 0.8160 (tt) REVERT: A 578 MET cc_start: 0.8123 (ttm) cc_final: 0.7882 (ttm) REVERT: A 579 MET cc_start: 0.7876 (mmm) cc_final: 0.7348 (mmm) REVERT: A 596 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7797 (tmmt) REVERT: A 597 GLN cc_start: 0.7411 (mt0) cc_final: 0.7170 (mt0) REVERT: A 611 LEU cc_start: 0.8256 (tp) cc_final: 0.7955 (tp) REVERT: A 613 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 645 LYS cc_start: 0.8937 (tptp) cc_final: 0.8296 (tptp) REVERT: A 826 ASN cc_start: 0.7378 (t0) cc_final: 0.7024 (t0) REVERT: A 837 TYR cc_start: 0.8259 (t80) cc_final: 0.7935 (t80) REVERT: A 843 TYR cc_start: 0.8635 (t80) cc_final: 0.8010 (t80) REVERT: A 848 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 849 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 852 LYS cc_start: 0.8222 (mttp) cc_final: 0.7970 (tttp) REVERT: A 862 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8336 (mmtm) REVERT: A 866 GLU cc_start: 0.7311 (tp30) cc_final: 0.7058 (tp30) REVERT: A 867 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9050 (mm) REVERT: A 868 LYS cc_start: 0.8595 (mmmm) cc_final: 0.7769 (mmmm) REVERT: A 875 ARG cc_start: 0.7740 (tpt90) cc_final: 0.7304 (tpt170) REVERT: A 880 LYS cc_start: 0.8296 (tptp) cc_final: 0.7806 (tptp) REVERT: A 881 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7022 (tm-30) REVERT: A 931 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 938 MET cc_start: 0.8537 (mmm) cc_final: 0.8294 (mmm) REVERT: A 940 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7701 (tpp80) REVERT: B 81 ILE cc_start: 0.7905 (mt) cc_final: 0.7640 (mt) REVERT: B 84 SER cc_start: 0.8028 (t) cc_final: 0.7597 (p) REVERT: B 109 LEU cc_start: 0.7928 (mt) cc_final: 0.7696 (mt) REVERT: B 120 VAL cc_start: 0.8391 (t) cc_final: 0.8004 (p) REVERT: B 125 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6984 (tp30) REVERT: B 149 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 199 MET cc_start: 0.7597 (mmm) cc_final: 0.6967 (tpt) REVERT: B 246 ASN cc_start: 0.8055 (m-40) cc_final: 0.7761 (m-40) REVERT: B 269 LEU cc_start: 0.7937 (tp) cc_final: 0.7650 (tp) REVERT: B 278 TRP cc_start: 0.8369 (t-100) cc_final: 0.8038 (t-100) REVERT: B 300 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: B 337 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: B 351 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8148 (tpp-160) REVERT: B 387 TYR cc_start: 0.7841 (m-10) cc_final: 0.7440 (m-10) REVERT: B 390 ILE cc_start: 0.8536 (mm) cc_final: 0.8327 (mm) REVERT: B 420 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7756 (mtm-85) REVERT: B 443 GLU cc_start: 0.7721 (tp30) cc_final: 0.7430 (tm-30) REVERT: B 475 GLN cc_start: 0.7506 (tp40) cc_final: 0.7231 (tp40) REVERT: B 499 ARG cc_start: 0.7613 (ptp90) cc_final: 0.7261 (ptp90) REVERT: B 500 ARG cc_start: 0.7808 (tpt90) cc_final: 0.7442 (tpp80) REVERT: B 509 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8312 (mm) REVERT: B 512 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 523 TRP cc_start: 0.7631 (m100) cc_final: 0.6885 (m100) REVERT: B 527 THR cc_start: 0.8071 (p) cc_final: 0.7154 (p) REVERT: B 531 GLU cc_start: 0.6411 (mm-30) cc_final: 0.6033 (mm-30) REVERT: B 579 MET cc_start: 0.7685 (mmm) cc_final: 0.7425 (mmm) REVERT: B 581 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5842 (pp20) REVERT: B 586 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6003 (tmm) REVERT: B 588 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7945 (ttpp) REVERT: B 590 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6676 (mm-30) REVERT: B 595 TRP cc_start: 0.7983 (m100) cc_final: 0.7665 (m100) REVERT: B 613 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7151 (tm-30) REVERT: B 645 LYS cc_start: 0.8447 (tptp) cc_final: 0.7958 (tptp) REVERT: B 825 VAL cc_start: 0.8504 (t) cc_final: 0.8273 (p) REVERT: B 826 ASN cc_start: 0.7928 (t0) cc_final: 0.7568 (m110) REVERT: B 837 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: B 847 GLU cc_start: 0.7658 (tp30) cc_final: 0.7362 (tp30) REVERT: B 848 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 872 GLU cc_start: 0.7961 (tp30) cc_final: 0.7097 (tp30) REVERT: B 876 LEU cc_start: 0.8094 (mt) cc_final: 0.7643 (mt) REVERT: B 881 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 903 ARG cc_start: 0.7085 (mtm180) cc_final: 0.6426 (mtm180) REVERT: B 904 THR cc_start: 0.7809 (p) cc_final: 0.7486 (t) REVERT: B 907 ASN cc_start: 0.7645 (m-40) cc_final: 0.7135 (m-40) REVERT: B 911 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6790 (mt-10) REVERT: B 916 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8256 (tt) REVERT: B 924 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7661 (pp20) REVERT: B 928 HIS cc_start: 0.7203 (t70) cc_final: 0.6843 (t70) REVERT: B 929 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7243 (mtpp) outliers start: 63 outliers final: 47 residues processed: 472 average time/residue: 0.2834 time to fit residues: 175.9848 Evaluate side-chains 509 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 449 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 292 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109960 restraints weight = 19752.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113279 restraints weight = 9358.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115368 restraints weight = 5486.710| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10798 Z= 0.214 Angle : 0.646 15.618 14638 Z= 0.329 Chirality : 0.041 0.248 1772 Planarity : 0.005 0.119 1796 Dihedral : 6.089 58.743 1466 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.84 % Allowed : 24.74 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.23), residues: 1344 helix: 1.88 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.35 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 635 HIS 0.014 0.001 HIS A 157 PHE 0.024 0.001 PHE B 288 TYR 0.014 0.001 TYR B 837 ARG 0.013 0.001 ARG A 609 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.89 seconds wall clock time: 57 minutes 10.95 seconds (3430.95 seconds total)