Starting phenix.real_space_refine on Tue Jul 29 04:12:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xkj_22219/07_2025/6xkj_22219.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xkj_22219/07_2025/6xkj_22219.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/cci-nas-00/data/ceres_data/6xkj_22219/07_2025/6xkj_22219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xkj_22219/07_2025/6xkj_22219.map" model { file = "/net/cci-nas-00/data/ceres_data/6xkj_22219/07_2025/6xkj_22219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xkj_22219/07_2025/6xkj_22219.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= -0.000 sd= 0.003 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 32 5.16 5 C 6832 2.51 5 N 1968 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 208 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11056 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 691 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, P Time building chain proxies: 8.08, per 1000 atoms: 0.73 Number of scatterers: 11056 At special positions: 0 Unit cell: (87.3075, 87.3075, 120.567, 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 32 16.00 O 2224 8.00 N 1968 7.00 C 6832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 93.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'C' and resid 451 through 457 removed outlier: 3.951A pdb=" N LYS C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 468 through 478 Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.748A pdb=" N LYS C 509 " --> pdb=" O MET C 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 525 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.748A pdb=" N LYS A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 482 through 491 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.748A pdb=" N LYS B 509 " --> pdb=" O MET B 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 457 through 465 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 482 through 491 Processing helix chain 'D' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS D 509 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 525 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'E' and resid 457 through 465 Processing helix chain 'E' and resid 468 through 478 Processing helix chain 'E' and resid 482 through 491 Processing helix chain 'E' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS E 509 " --> pdb=" O MET E 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 525 Processing helix chain 'E' and resid 525 through 534 Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 457 through 465 Processing helix chain 'F' and resid 468 through 478 Processing helix chain 'F' and resid 482 through 491 Processing helix chain 'F' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS F 509 " --> pdb=" O MET F 505 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY F 510 " --> pdb=" O VAL F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 525 Processing helix chain 'F' and resid 525 through 534 Processing helix chain 'G' and resid 452 through 457 Processing helix chain 'G' and resid 457 through 465 Processing helix chain 'G' and resid 468 through 478 Processing helix chain 'G' and resid 482 through 491 Processing helix chain 'G' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS G 509 " --> pdb=" O MET G 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY G 510 " --> pdb=" O VAL G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 525 Processing helix chain 'G' and resid 525 through 534 Processing helix chain 'H' and resid 452 through 457 Processing helix chain 'H' and resid 457 through 465 Processing helix chain 'H' and resid 468 through 478 Processing helix chain 'H' and resid 482 through 491 Processing helix chain 'H' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS H 509 " --> pdb=" O MET H 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY H 510 " --> pdb=" O VAL H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 525 Processing helix chain 'H' and resid 525 through 534 Processing helix chain 'I' and resid 452 through 457 Processing helix chain 'I' and resid 457 through 465 Processing helix chain 'I' and resid 468 through 478 Processing helix chain 'I' and resid 482 through 491 Processing helix chain 'I' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS I 509 " --> pdb=" O MET I 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY I 510 " --> pdb=" O VAL I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 525 Processing helix chain 'I' and resid 525 through 534 Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 457 through 465 Processing helix chain 'J' and resid 468 through 478 Processing helix chain 'J' and resid 482 through 491 Processing helix chain 'J' and resid 494 through 510 removed outlier: 3.748A pdb=" N LYS J 509 " --> pdb=" O MET J 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY J 510 " --> pdb=" O VAL J 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 510 through 525 Processing helix chain 'J' and resid 525 through 534 Processing helix chain 'K' and resid 452 through 457 Processing helix chain 'K' and resid 457 through 465 Processing helix chain 'K' and resid 468 through 478 Processing helix chain 'K' and resid 482 through 491 Processing helix chain 'K' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS K 509 " --> pdb=" O MET K 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY K 510 " --> pdb=" O VAL K 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 525 Processing helix chain 'K' and resid 525 through 534 Processing helix chain 'L' and resid 452 through 457 Processing helix chain 'L' and resid 457 through 465 Processing helix chain 'L' and resid 468 through 478 Processing helix chain 'L' and resid 482 through 491 Processing helix chain 'L' and resid 494 through 510 removed outlier: 3.748A pdb=" N LYS L 509 " --> pdb=" O MET L 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY L 510 " --> pdb=" O VAL L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 525 Processing helix chain 'L' and resid 525 through 534 Processing helix chain 'M' and resid 452 through 457 Processing helix chain 'M' and resid 457 through 465 Processing helix chain 'M' and resid 468 through 478 Processing helix chain 'M' and resid 482 through 491 Processing helix chain 'M' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS M 509 " --> pdb=" O MET M 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY M 510 " --> pdb=" O VAL M 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 525 Processing helix chain 'M' and resid 525 through 534 Processing helix chain 'N' and resid 452 through 457 Processing helix chain 'N' and resid 457 through 465 Processing helix chain 'N' and resid 468 through 478 Processing helix chain 'N' and resid 482 through 491 Processing helix chain 'N' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS N 509 " --> pdb=" O MET N 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY N 510 " --> pdb=" O VAL N 506 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 525 Processing helix chain 'N' and resid 525 through 534 Processing helix chain 'O' and resid 452 through 457 Processing helix chain 'O' and resid 457 through 465 Processing helix chain 'O' and resid 468 through 478 Processing helix chain 'O' and resid 482 through 491 Processing helix chain 'O' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS O 509 " --> pdb=" O MET O 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY O 510 " --> pdb=" O VAL O 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 510 through 525 Processing helix chain 'O' and resid 525 through 534 Processing helix chain 'P' and resid 452 through 457 Processing helix chain 'P' and resid 457 through 465 Processing helix chain 'P' and resid 468 through 478 Processing helix chain 'P' and resid 482 through 491 Processing helix chain 'P' and resid 494 through 510 removed outlier: 3.747A pdb=" N LYS P 509 " --> pdb=" O MET P 505 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY P 510 " --> pdb=" O VAL P 506 " (cutoff:3.500A) Processing helix chain 'P' and resid 510 through 525 Processing helix chain 'P' and resid 525 through 534 784 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3623 1.33 - 1.45: 910 1.45 - 1.57: 6523 1.57 - 1.68: 16 1.68 - 1.80: 64 Bond restraints: 11136 Sorted by residual: bond pdb=" CA GLN M 534 " pdb=" CB GLN M 534 " ideal model delta sigma weight residual 1.530 1.571 -0.041 1.69e-02 3.50e+03 5.95e+00 bond pdb=" CA GLN J 534 " pdb=" CB GLN J 534 " ideal model delta sigma weight residual 1.530 1.571 -0.041 1.69e-02 3.50e+03 5.95e+00 bond pdb=" CA GLN P 534 " pdb=" CB GLN P 534 " ideal model delta sigma weight residual 1.530 1.571 -0.041 1.69e-02 3.50e+03 5.88e+00 bond pdb=" CA GLN I 534 " pdb=" CB GLN I 534 " ideal model delta sigma weight residual 1.530 1.571 -0.041 1.69e-02 3.50e+03 5.87e+00 bond pdb=" CA GLN E 534 " pdb=" CB GLN E 534 " ideal model delta sigma weight residual 1.530 1.571 -0.041 1.69e-02 3.50e+03 5.82e+00 ... (remaining 11131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 13092 1.10 - 2.21: 1438 2.21 - 3.31: 239 3.31 - 4.41: 94 4.41 - 5.52: 49 Bond angle restraints: 14912 Sorted by residual: angle pdb=" C LEU I 461 " pdb=" N GLN I 462 " pdb=" CA GLN I 462 " ideal model delta sigma weight residual 120.31 115.88 4.43 1.52e+00 4.33e-01 8.48e+00 angle pdb=" C LEU K 461 " pdb=" N GLN K 462 " pdb=" CA GLN K 462 " ideal model delta sigma weight residual 120.31 115.93 4.38 1.52e+00 4.33e-01 8.29e+00 angle pdb=" C LEU A 461 " pdb=" N GLN A 462 " pdb=" CA GLN A 462 " ideal model delta sigma weight residual 120.31 115.94 4.37 1.52e+00 4.33e-01 8.28e+00 angle pdb=" C LEU G 461 " pdb=" N GLN G 462 " pdb=" CA GLN G 462 " ideal model delta sigma weight residual 120.31 115.94 4.37 1.52e+00 4.33e-01 8.27e+00 angle pdb=" C LEU D 461 " pdb=" N GLN D 462 " pdb=" CA GLN D 462 " ideal model delta sigma weight residual 120.31 115.94 4.37 1.52e+00 4.33e-01 8.26e+00 ... (remaining 14907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.19: 6032 14.19 - 28.38: 672 28.38 - 42.58: 304 42.58 - 56.77: 32 56.77 - 70.96: 32 Dihedral angle restraints: 7072 sinusoidal: 3072 harmonic: 4000 Sorted by residual: dihedral pdb=" CA ASP H 474 " pdb=" CB ASP H 474 " pdb=" CG ASP H 474 " pdb=" OD1 ASP H 474 " ideal model delta sinusoidal sigma weight residual -30.00 -80.29 50.29 1 2.00e+01 2.50e-03 8.67e+00 dihedral pdb=" CA ASP K 474 " pdb=" CB ASP K 474 " pdb=" CG ASP K 474 " pdb=" OD1 ASP K 474 " ideal model delta sinusoidal sigma weight residual -30.00 -80.25 50.25 1 2.00e+01 2.50e-03 8.65e+00 dihedral pdb=" CA ASP B 474 " pdb=" CB ASP B 474 " pdb=" CG ASP B 474 " pdb=" OD1 ASP B 474 " ideal model delta sinusoidal sigma weight residual -30.00 -80.24 50.24 1 2.00e+01 2.50e-03 8.65e+00 ... (remaining 7069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 678 0.027 - 0.053: 577 0.053 - 0.080: 280 0.080 - 0.106: 113 0.106 - 0.133: 32 Chirality restraints: 1680 Sorted by residual: chirality pdb=" CA GLU I 479 " pdb=" N GLU I 479 " pdb=" C GLU I 479 " pdb=" CB GLU I 479 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA GLU D 479 " pdb=" N GLU D 479 " pdb=" C GLU D 479 " pdb=" CB GLU D 479 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA GLU N 479 " pdb=" N GLU N 479 " pdb=" C GLU N 479 " pdb=" CB GLU N 479 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1677 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN L 534 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C GLN L 534 " 0.022 2.00e-02 2.50e+03 pdb=" O GLN L 534 " -0.008 2.00e-02 2.50e+03 pdb=" N GLN L 535 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 534 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C GLN H 534 " 0.022 2.00e-02 2.50e+03 pdb=" O GLN H 534 " -0.008 2.00e-02 2.50e+03 pdb=" N GLN H 535 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 534 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C GLN B 534 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 534 " 0.008 2.00e-02 2.50e+03 pdb=" N GLN B 535 " 0.007 2.00e-02 2.50e+03 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2424 2.78 - 3.31: 11712 3.31 - 3.84: 18266 3.84 - 4.37: 21191 4.37 - 4.90: 37554 Nonbonded interactions: 91147 Sorted by model distance: nonbonded pdb=" OE2 GLU E 483 " pdb=" NE2 GLN F 496 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU F 483 " pdb=" NE2 GLN G 496 " model vdw 2.263 3.120 nonbonded pdb=" OE2 GLU A 483 " pdb=" NE2 GLN B 496 " model vdw 2.267 3.120 nonbonded pdb=" NE ARG K 459 " pdb=" OD2 ASP N 477 " model vdw 2.274 3.120 nonbonded pdb=" OE2 GLU O 483 " pdb=" NE2 GLN P 496 " model vdw 2.277 3.120 ... (remaining 91142 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'P' } 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: 240.620 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 271.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.009 0.041 11136 Z= 0.396 Angle : 0.826 5.518 14912 Z= 0.485 Chirality : 0.047 0.133 1680 Planarity : 0.003 0.013 1984 Dihedral : 14.922 70.960 4448 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1328 helix: 0.60 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.81 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 458 PHE 0.007 0.002 PHE C 453 TYR 0.017 0.005 TYR A 531 ARG 0.009 0.002 ARG N 459 Details of bonding type rmsd hydrogen bonds : bond 0.14200 ( 784) hydrogen bonds : angle 6.10481 ( 2352) covalent geometry : bond 0.00893 (11136) covalent geometry : angle 0.82638 (14912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 ASN cc_start: 0.8752 (m110) cc_final: 0.8335 (m110) REVERT: A 515 ASP cc_start: 0.7947 (t0) cc_final: 0.7714 (t0) REVERT: B 473 ASP cc_start: 0.7987 (m-30) cc_final: 0.7424 (m-30) REVERT: B 474 ASP cc_start: 0.7932 (t70) cc_final: 0.7606 (t0) REVERT: B 477 ASP cc_start: 0.7817 (m-30) cc_final: 0.7522 (m-30) REVERT: B 530 SER cc_start: 0.8602 (t) cc_final: 0.8400 (m) REVERT: D 473 ASP cc_start: 0.7444 (m-30) cc_final: 0.7048 (m-30) REVERT: D 474 ASP cc_start: 0.8161 (t70) cc_final: 0.7857 (t70) REVERT: D 478 ASN cc_start: 0.8636 (m110) cc_final: 0.8370 (m110) REVERT: D 530 SER cc_start: 0.9027 (t) cc_final: 0.8743 (p) REVERT: E 462 GLN cc_start: 0.8035 (pt0) cc_final: 0.7380 (pt0) REVERT: E 469 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8257 (mmmm) REVERT: E 473 ASP cc_start: 0.7772 (m-30) cc_final: 0.7264 (m-30) REVERT: E 477 ASP cc_start: 0.7975 (m-30) cc_final: 0.7744 (m-30) REVERT: E 525 ASP cc_start: 0.8228 (t0) cc_final: 0.7838 (t0) REVERT: E 530 SER cc_start: 0.8908 (t) cc_final: 0.8562 (m) REVERT: F 477 ASP cc_start: 0.7921 (m-30) cc_final: 0.7682 (m-30) REVERT: G 462 GLN cc_start: 0.8302 (pt0) cc_final: 0.8101 (pt0) REVERT: I 462 GLN cc_start: 0.8388 (pt0) cc_final: 0.7760 (pt0) REVERT: I 491 GLN cc_start: 0.8636 (pp30) cc_final: 0.8047 (pp30) REVERT: I 495 ARG cc_start: 0.8744 (ptm-80) cc_final: 0.8272 (ttp-110) REVERT: I 530 SER cc_start: 0.9039 (t) cc_final: 0.8776 (m) REVERT: J 473 ASP cc_start: 0.7764 (m-30) cc_final: 0.7334 (m-30) REVERT: J 479 GLU cc_start: 0.7914 (mp0) cc_final: 0.7561 (mp0) REVERT: K 477 ASP cc_start: 0.7961 (m-30) cc_final: 0.7682 (m-30) REVERT: K 486 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8170 (tttm) REVERT: K 495 ARG cc_start: 0.8302 (ptm-80) cc_final: 0.8085 (ttp-110) REVERT: K 508 LYS cc_start: 0.8309 (mttp) cc_final: 0.8098 (mtpt) REVERT: K 530 SER cc_start: 0.9155 (t) cc_final: 0.8904 (p) REVERT: L 490 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7926 (mm-30) REVERT: L 530 SER cc_start: 0.9009 (t) cc_final: 0.8653 (p) REVERT: M 530 SER cc_start: 0.8980 (t) cc_final: 0.8719 (m) REVERT: N 469 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8328 (mmmm) REVERT: N 473 ASP cc_start: 0.7689 (m-30) cc_final: 0.6765 (m-30) REVERT: N 477 ASP cc_start: 0.8019 (m-30) cc_final: 0.7807 (m-30) REVERT: O 477 ASP cc_start: 0.8034 (m-30) cc_final: 0.7760 (m-30) REVERT: O 485 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7589 (mt-10) REVERT: P 485 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8091 (mt-10) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.3090 time to fit residues: 219.6933 Evaluate side-chains 479 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 484 ASN A 484 ASN G 458 HIS ** G 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 HIS I 478 ASN J 478 ASN K 476 GLN M 458 HIS O 535 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.090962 restraints weight = 16966.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094196 restraints weight = 8270.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096192 restraints weight = 4533.974| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 0.034 11136 Z= 0.127 Angle : 0.520 7.455 14912 Z= 0.284 Chirality : 0.035 0.120 1680 Planarity : 0.003 0.024 1984 Dihedral : 3.307 12.691 1472 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.79 % Allowed : 9.01 % Favored : 89.20 % 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: 1.42 (0.24), residues: 1328 helix: 1.19 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 458 PHE 0.005 0.001 PHE C 453 TYR 0.007 0.001 TYR H 527 ARG 0.006 0.001 ARG N 524 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 784) hydrogen bonds : angle 4.60558 ( 2352) covalent geometry : bond 0.00277 (11136) covalent geometry : angle 0.51965 (14912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 523 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: C 473 ASP cc_start: 0.7399 (t0) cc_final: 0.7039 (t0) REVERT: C 477 ASP cc_start: 0.7921 (m-30) cc_final: 0.7689 (m-30) REVERT: C 478 ASN cc_start: 0.9056 (m-40) cc_final: 0.8816 (m-40) REVERT: C 525 ASP cc_start: 0.7798 (t0) cc_final: 0.7468 (t0) REVERT: B 473 ASP cc_start: 0.7977 (m-30) cc_final: 0.7308 (m-30) REVERT: B 474 ASP cc_start: 0.7887 (t70) cc_final: 0.7445 (t0) REVERT: B 477 ASP cc_start: 0.7741 (m-30) cc_final: 0.7362 (m-30) REVERT: B 525 ASP cc_start: 0.7998 (t0) cc_final: 0.7739 (t0) REVERT: D 473 ASP cc_start: 0.7367 (m-30) cc_final: 0.7130 (m-30) REVERT: D 474 ASP cc_start: 0.8094 (t70) cc_final: 0.7459 (t70) REVERT: D 478 ASN cc_start: 0.8560 (m110) cc_final: 0.8130 (m-40) REVERT: D 499 ASN cc_start: 0.8878 (m-40) cc_final: 0.8588 (m110) REVERT: D 523 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: D 525 ASP cc_start: 0.7905 (t0) cc_final: 0.7686 (t0) REVERT: D 530 SER cc_start: 0.8956 (t) cc_final: 0.8673 (p) REVERT: E 469 LYS cc_start: 0.8537 (mmtm) cc_final: 0.8068 (mmmm) REVERT: E 473 ASP cc_start: 0.8050 (m-30) cc_final: 0.7105 (m-30) REVERT: E 477 ASP cc_start: 0.8241 (m-30) cc_final: 0.7873 (m-30) REVERT: E 525 ASP cc_start: 0.7472 (t0) cc_final: 0.7181 (t0) REVERT: E 530 SER cc_start: 0.8818 (t) cc_final: 0.8419 (m) REVERT: F 477 ASP cc_start: 0.8006 (m-30) cc_final: 0.7668 (m-30) REVERT: G 473 ASP cc_start: 0.8218 (m-30) cc_final: 0.7608 (m-30) REVERT: G 477 ASP cc_start: 0.7834 (m-30) cc_final: 0.7561 (m-30) REVERT: G 486 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8247 (ttpp) REVERT: G 500 GLU cc_start: 0.8103 (tp30) cc_final: 0.7497 (tp30) REVERT: G 519 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7133 (ptp-110) REVERT: G 525 ASP cc_start: 0.8024 (t0) cc_final: 0.7688 (t0) REVERT: I 474 ASP cc_start: 0.7751 (t70) cc_final: 0.7450 (t0) REVERT: I 478 ASN cc_start: 0.8847 (m-40) cc_final: 0.8609 (m-40) REVERT: I 491 GLN cc_start: 0.8634 (pp30) cc_final: 0.8267 (pp30) REVERT: I 525 ASP cc_start: 0.7577 (t0) cc_final: 0.7354 (t0) REVERT: I 530 SER cc_start: 0.8953 (t) cc_final: 0.8670 (m) REVERT: J 477 ASP cc_start: 0.7936 (m-30) cc_final: 0.7572 (m-30) REVERT: J 479 GLU cc_start: 0.7855 (mp0) cc_final: 0.7509 (mp0) REVERT: K 473 ASP cc_start: 0.8174 (m-30) cc_final: 0.7590 (m-30) REVERT: K 486 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8037 (ttpp) REVERT: K 508 LYS cc_start: 0.8126 (mttp) cc_final: 0.7770 (mtpt) REVERT: K 525 ASP cc_start: 0.7664 (t0) cc_final: 0.7406 (t0) REVERT: K 530 SER cc_start: 0.9075 (t) cc_final: 0.8834 (p) REVERT: L 474 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7742 (t0) REVERT: L 530 SER cc_start: 0.8881 (t) cc_final: 0.8529 (p) REVERT: M 477 ASP cc_start: 0.8021 (m-30) cc_final: 0.7782 (m-30) REVERT: M 525 ASP cc_start: 0.7741 (t0) cc_final: 0.7448 (t0) REVERT: M 530 SER cc_start: 0.8873 (t) cc_final: 0.8519 (m) REVERT: N 469 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8188 (mmmm) REVERT: N 473 ASP cc_start: 0.7665 (m-30) cc_final: 0.6823 (m-30) REVERT: N 534 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7615 (tm-30) REVERT: O 477 ASP cc_start: 0.8300 (m-30) cc_final: 0.7983 (m-30) REVERT: O 530 SER cc_start: 0.8872 (t) cc_final: 0.8499 (p) REVERT: P 473 ASP cc_start: 0.7847 (m-30) cc_final: 0.7309 (m-30) REVERT: P 486 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8396 (ttpp) REVERT: P 490 GLU cc_start: 0.8203 (mt-10) cc_final: 0.8002 (mt-10) REVERT: P 525 ASP cc_start: 0.8020 (t0) cc_final: 0.7782 (t0) outliers start: 22 outliers final: 5 residues processed: 525 average time/residue: 0.3444 time to fit residues: 243.5328 Evaluate side-chains 487 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 480 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain F residue 490 GLU Chi-restraints excluded: chain L residue 474 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN A 478 ASN G 462 GLN G 478 ASN H 458 HIS H 499 ASN I 478 ASN J 478 ASN K 476 GLN L 476 GLN N 476 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.096018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.086945 restraints weight = 17547.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.090029 restraints weight = 8720.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.091957 restraints weight = 4894.465| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11136 Z= 0.190 Angle : 0.554 6.859 14912 Z= 0.301 Chirality : 0.038 0.157 1680 Planarity : 0.004 0.031 1984 Dihedral : 3.340 13.450 1472 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.33 % Allowed : 12.58 % Favored : 84.09 % 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: 1.41 (0.23), residues: 1328 helix: 1.18 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.08 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS P 458 PHE 0.011 0.002 PHE C 453 TYR 0.010 0.002 TYR H 527 ARG 0.005 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 784) hydrogen bonds : angle 4.48120 ( 2352) covalent geometry : bond 0.00445 (11136) covalent geometry : angle 0.55441 (14912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 492 time to evaluate : 1.238 Fit side-chains REVERT: C 473 ASP cc_start: 0.7409 (t0) cc_final: 0.7021 (t0) REVERT: C 525 ASP cc_start: 0.7895 (t0) cc_final: 0.7470 (t0) REVERT: B 473 ASP cc_start: 0.8019 (m-30) cc_final: 0.7424 (m-30) REVERT: B 474 ASP cc_start: 0.7932 (t70) cc_final: 0.7532 (t0) REVERT: B 477 ASP cc_start: 0.7682 (m-30) cc_final: 0.7384 (m-30) REVERT: B 483 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7559 (tp30) REVERT: B 525 ASP cc_start: 0.8043 (t0) cc_final: 0.7729 (t0) REVERT: D 460 GLN cc_start: 0.7731 (mm110) cc_final: 0.6854 (mp10) REVERT: D 469 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8438 (mmmm) REVERT: D 474 ASP cc_start: 0.8146 (t70) cc_final: 0.7540 (t70) REVERT: D 478 ASN cc_start: 0.8688 (m110) cc_final: 0.8276 (m-40) REVERT: D 523 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: D 525 ASP cc_start: 0.8009 (t0) cc_final: 0.7746 (t0) REVERT: D 530 SER cc_start: 0.8979 (t) cc_final: 0.8681 (p) REVERT: E 469 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8257 (mmmm) REVERT: E 473 ASP cc_start: 0.7973 (m-30) cc_final: 0.7172 (m-30) REVERT: E 477 ASP cc_start: 0.8188 (m-30) cc_final: 0.7845 (m-30) REVERT: E 525 ASP cc_start: 0.7501 (t0) cc_final: 0.7260 (t0) REVERT: E 530 SER cc_start: 0.8921 (t) cc_final: 0.8526 (m) REVERT: F 477 ASP cc_start: 0.8029 (m-30) cc_final: 0.7649 (m-30) REVERT: F 534 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7430 (tm-30) REVERT: G 462 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: G 473 ASP cc_start: 0.8235 (m-30) cc_final: 0.7848 (m-30) REVERT: G 477 ASP cc_start: 0.7890 (m-30) cc_final: 0.7656 (m-30) REVERT: G 500 GLU cc_start: 0.8017 (tp30) cc_final: 0.7326 (tp30) REVERT: I 474 ASP cc_start: 0.7861 (t70) cc_final: 0.7608 (t70) REVERT: I 491 GLN cc_start: 0.8727 (pp30) cc_final: 0.8278 (pp30) REVERT: I 495 ARG cc_start: 0.8765 (ptm-80) cc_final: 0.8395 (ttp-110) REVERT: I 530 SER cc_start: 0.9010 (t) cc_final: 0.8780 (m) REVERT: J 473 ASP cc_start: 0.7864 (m-30) cc_final: 0.7375 (m-30) REVERT: J 478 ASN cc_start: 0.8937 (m-40) cc_final: 0.8687 (m-40) REVERT: J 479 GLU cc_start: 0.7955 (mp0) cc_final: 0.7665 (mp0) REVERT: K 473 ASP cc_start: 0.8221 (m-30) cc_final: 0.7766 (m-30) REVERT: K 486 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8139 (tttm) REVERT: K 525 ASP cc_start: 0.7766 (t0) cc_final: 0.7453 (t0) REVERT: K 530 SER cc_start: 0.9156 (t) cc_final: 0.8915 (p) REVERT: L 530 SER cc_start: 0.8979 (t) cc_final: 0.8660 (p) REVERT: M 525 ASP cc_start: 0.7942 (t0) cc_final: 0.7618 (t0) REVERT: M 530 SER cc_start: 0.8935 (t) cc_final: 0.8686 (m) REVERT: M 534 GLN cc_start: 0.7877 (pp30) cc_final: 0.7478 (pp30) REVERT: N 469 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8269 (mmmm) REVERT: N 473 ASP cc_start: 0.7638 (m-30) cc_final: 0.6917 (m-30) REVERT: N 477 ASP cc_start: 0.8114 (m-30) cc_final: 0.7811 (m-30) REVERT: N 487 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7810 (mt-10) REVERT: N 523 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: N 534 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7606 (tm-30) REVERT: O 477 ASP cc_start: 0.8264 (m-30) cc_final: 0.7990 (m-30) REVERT: O 530 SER cc_start: 0.9005 (t) cc_final: 0.8629 (p) REVERT: P 473 ASP cc_start: 0.7841 (m-30) cc_final: 0.7432 (m-30) REVERT: P 477 ASP cc_start: 0.8336 (m-30) cc_final: 0.7859 (m-30) REVERT: P 479 GLU cc_start: 0.7618 (mp0) cc_final: 0.7234 (mp0) REVERT: P 525 ASP cc_start: 0.8175 (t0) cc_final: 0.7867 (t0) outliers start: 41 outliers final: 20 residues processed: 501 average time/residue: 0.2756 time to fit residues: 182.7229 Evaluate side-chains 499 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 476 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain F residue 465 MET Chi-restraints excluded: chain F residue 490 GLU Chi-restraints excluded: chain G residue 462 GLN Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain H residue 512 LEU Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain K residue 512 LEU Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 505 MET Chi-restraints excluded: chain M residue 462 GLN Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 530 SER Chi-restraints excluded: chain P residue 512 LEU Chi-restraints excluded: chain P residue 515 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 484 ASN A 478 ASN B 462 GLN F 476 GLN G 462 GLN G 478 ASN J 484 ASN K 476 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.088329 restraints weight = 17280.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.091323 restraints weight = 8545.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093275 restraints weight = 4834.262| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11136 Z= 0.145 Angle : 0.527 8.348 14912 Z= 0.287 Chirality : 0.036 0.121 1680 Planarity : 0.003 0.027 1984 Dihedral : 3.274 13.270 1472 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.08 % Allowed : 15.91 % Favored : 81.01 % 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: 1.50 (0.23), residues: 1328 helix: 1.24 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.11 (0.45), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 458 PHE 0.007 0.001 PHE C 453 TYR 0.008 0.001 TYR H 527 ARG 0.006 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 784) hydrogen bonds : angle 4.42548 ( 2352) covalent geometry : bond 0.00338 (11136) covalent geometry : angle 0.52686 (14912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 490 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: C 477 ASP cc_start: 0.8033 (m-30) cc_final: 0.7800 (m-30) REVERT: C 525 ASP cc_start: 0.7951 (t0) cc_final: 0.7438 (t0) REVERT: A 474 ASP cc_start: 0.7717 (t0) cc_final: 0.7435 (t0) REVERT: A 520 SER cc_start: 0.8882 (t) cc_final: 0.8631 (m) REVERT: B 473 ASP cc_start: 0.7948 (m-30) cc_final: 0.7276 (m-30) REVERT: B 474 ASP cc_start: 0.7910 (t70) cc_final: 0.7511 (t0) REVERT: B 477 ASP cc_start: 0.7687 (m-30) cc_final: 0.7384 (m-30) REVERT: B 525 ASP cc_start: 0.8006 (t0) cc_final: 0.7658 (t0) REVERT: D 474 ASP cc_start: 0.8151 (t70) cc_final: 0.7536 (t70) REVERT: D 478 ASN cc_start: 0.8699 (m110) cc_final: 0.8292 (m-40) REVERT: D 523 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: D 525 ASP cc_start: 0.7872 (t0) cc_final: 0.7600 (t0) REVERT: D 530 SER cc_start: 0.8954 (t) cc_final: 0.8690 (p) REVERT: E 469 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8203 (mmmm) REVERT: E 473 ASP cc_start: 0.8005 (m-30) cc_final: 0.7159 (m-30) REVERT: E 477 ASP cc_start: 0.8267 (m-30) cc_final: 0.7907 (m-30) REVERT: E 525 ASP cc_start: 0.7461 (t0) cc_final: 0.7190 (t0) REVERT: E 530 SER cc_start: 0.8868 (t) cc_final: 0.8485 (m) REVERT: F 477 ASP cc_start: 0.8076 (m-30) cc_final: 0.7698 (m-30) REVERT: F 534 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7291 (tm-30) REVERT: G 462 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: G 473 ASP cc_start: 0.8426 (m-30) cc_final: 0.7780 (m-30) REVERT: G 477 ASP cc_start: 0.7892 (m-30) cc_final: 0.7586 (m-30) REVERT: G 500 GLU cc_start: 0.8093 (tp30) cc_final: 0.7484 (tp30) REVERT: I 474 ASP cc_start: 0.7807 (t70) cc_final: 0.7552 (t70) REVERT: I 491 GLN cc_start: 0.8782 (pp30) cc_final: 0.8309 (pp30) REVERT: I 495 ARG cc_start: 0.8783 (ptm-80) cc_final: 0.8454 (ttp-110) REVERT: I 530 SER cc_start: 0.9040 (t) cc_final: 0.8768 (m) REVERT: J 473 ASP cc_start: 0.7800 (m-30) cc_final: 0.7472 (m-30) REVERT: J 477 ASP cc_start: 0.7848 (m-30) cc_final: 0.7460 (m-30) REVERT: J 478 ASN cc_start: 0.8911 (m-40) cc_final: 0.8706 (m-40) REVERT: J 479 GLU cc_start: 0.7916 (mp0) cc_final: 0.7623 (mp0) REVERT: J 486 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8434 (ttmm) REVERT: K 473 ASP cc_start: 0.8236 (m-30) cc_final: 0.7753 (m-30) REVERT: K 486 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8134 (tttm) REVERT: K 525 ASP cc_start: 0.7765 (t0) cc_final: 0.7428 (t0) REVERT: K 530 SER cc_start: 0.9188 (t) cc_final: 0.8909 (p) REVERT: L 530 SER cc_start: 0.8965 (t) cc_final: 0.8645 (p) REVERT: M 525 ASP cc_start: 0.7805 (t0) cc_final: 0.7505 (t0) REVERT: M 530 SER cc_start: 0.8926 (t) cc_final: 0.8712 (m) REVERT: M 534 GLN cc_start: 0.7843 (pp30) cc_final: 0.7520 (pp30) REVERT: N 469 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8205 (mmmm) REVERT: N 473 ASP cc_start: 0.7635 (m-30) cc_final: 0.6856 (m-30) REVERT: N 477 ASP cc_start: 0.8058 (m-30) cc_final: 0.7743 (m-30) REVERT: N 487 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7841 (mt-10) REVERT: N 534 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7647 (tm-30) REVERT: O 477 ASP cc_start: 0.8281 (m-30) cc_final: 0.8014 (m-30) REVERT: O 530 SER cc_start: 0.9002 (t) cc_final: 0.8651 (p) REVERT: P 473 ASP cc_start: 0.7885 (m-30) cc_final: 0.7446 (m-30) REVERT: P 477 ASP cc_start: 0.8431 (m-30) cc_final: 0.7767 (m-30) REVERT: P 479 GLU cc_start: 0.7647 (mp0) cc_final: 0.7246 (mp0) outliers start: 38 outliers final: 19 residues processed: 500 average time/residue: 0.2856 time to fit residues: 190.3175 Evaluate side-chains 494 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 473 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain G residue 462 GLN Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 505 MET Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain N residue 491 GLN Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain N residue 530 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 GLN G 462 GLN H 462 GLN H 476 GLN H 535 GLN J 462 GLN K 476 GLN L 476 GLN P 476 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.088369 restraints weight = 17325.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.091454 restraints weight = 8579.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.093412 restraints weight = 4789.447| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11136 Z= 0.135 Angle : 0.519 7.038 14912 Z= 0.284 Chirality : 0.035 0.142 1680 Planarity : 0.003 0.032 1984 Dihedral : 3.251 13.404 1472 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.33 % Allowed : 16.64 % Favored : 80.03 % 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: 1.72 (0.22), residues: 1328 helix: 1.37 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.51 (0.41), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 458 PHE 0.007 0.001 PHE C 453 TYR 0.007 0.001 TYR H 527 ARG 0.006 0.000 ARG N 524 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 784) hydrogen bonds : angle 4.41120 ( 2352) covalent geometry : bond 0.00316 (11136) covalent geometry : angle 0.51912 (14912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 482 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 525 ASP cc_start: 0.7799 (t0) cc_final: 0.7331 (t0) REVERT: B 473 ASP cc_start: 0.7985 (m-30) cc_final: 0.7325 (m-30) REVERT: B 474 ASP cc_start: 0.7868 (t70) cc_final: 0.7353 (t0) REVERT: B 477 ASP cc_start: 0.7678 (m-30) cc_final: 0.7424 (m-30) REVERT: B 478 ASN cc_start: 0.8484 (m-40) cc_final: 0.7830 (m110) REVERT: B 525 ASP cc_start: 0.7841 (t0) cc_final: 0.7560 (t0) REVERT: D 474 ASP cc_start: 0.8073 (t70) cc_final: 0.7526 (t70) REVERT: D 478 ASN cc_start: 0.8665 (m110) cc_final: 0.8318 (m-40) REVERT: D 523 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: D 530 SER cc_start: 0.8981 (t) cc_final: 0.8736 (p) REVERT: E 469 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8257 (mmmm) REVERT: E 473 ASP cc_start: 0.7972 (m-30) cc_final: 0.7063 (m-30) REVERT: E 477 ASP cc_start: 0.8282 (m-30) cc_final: 0.7921 (m-30) REVERT: E 525 ASP cc_start: 0.7283 (t0) cc_final: 0.7074 (t0) REVERT: E 530 SER cc_start: 0.8897 (t) cc_final: 0.8612 (m) REVERT: F 477 ASP cc_start: 0.8038 (m-30) cc_final: 0.7679 (m-30) REVERT: F 534 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7255 (tm-30) REVERT: G 462 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: G 473 ASP cc_start: 0.8371 (m-30) cc_final: 0.7679 (m-30) REVERT: G 477 ASP cc_start: 0.7919 (m-30) cc_final: 0.7685 (m-30) REVERT: G 500 GLU cc_start: 0.7917 (tp30) cc_final: 0.7375 (tp30) REVERT: I 474 ASP cc_start: 0.7680 (t70) cc_final: 0.7326 (t70) REVERT: I 478 ASN cc_start: 0.8817 (m110) cc_final: 0.8572 (m110) REVERT: I 491 GLN cc_start: 0.8766 (pp30) cc_final: 0.8271 (pp30) REVERT: I 495 ARG cc_start: 0.8812 (ptm-80) cc_final: 0.8484 (ttp-110) REVERT: I 530 SER cc_start: 0.9042 (t) cc_final: 0.8809 (m) REVERT: J 473 ASP cc_start: 0.7724 (m-30) cc_final: 0.7203 (m-30) REVERT: J 477 ASP cc_start: 0.7916 (m-30) cc_final: 0.7525 (m-30) REVERT: J 478 ASN cc_start: 0.8893 (m-40) cc_final: 0.8638 (m-40) REVERT: J 479 GLU cc_start: 0.7918 (mp0) cc_final: 0.7654 (mp0) REVERT: K 473 ASP cc_start: 0.8142 (m-30) cc_final: 0.7676 (m-30) REVERT: K 486 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8173 (tttm) REVERT: K 505 MET cc_start: 0.8177 (mtp) cc_final: 0.7843 (mtp) REVERT: K 525 ASP cc_start: 0.7642 (t0) cc_final: 0.7354 (t0) REVERT: K 530 SER cc_start: 0.9193 (t) cc_final: 0.8962 (p) REVERT: L 479 GLU cc_start: 0.7738 (mp0) cc_final: 0.7529 (mp0) REVERT: L 530 SER cc_start: 0.9010 (t) cc_final: 0.8750 (p) REVERT: M 477 ASP cc_start: 0.7926 (m-30) cc_final: 0.7627 (m-30) REVERT: M 525 ASP cc_start: 0.7761 (t0) cc_final: 0.7461 (t0) REVERT: M 534 GLN cc_start: 0.7670 (pp30) cc_final: 0.7402 (pp30) REVERT: N 469 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8232 (mmmm) REVERT: N 473 ASP cc_start: 0.7497 (m-30) cc_final: 0.6715 (m-30) REVERT: N 474 ASP cc_start: 0.7200 (t0) cc_final: 0.6846 (t0) REVERT: N 477 ASP cc_start: 0.8023 (m-30) cc_final: 0.7788 (m-30) REVERT: N 478 ASN cc_start: 0.8774 (m-40) cc_final: 0.8426 (m110) REVERT: N 487 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7844 (mt-10) REVERT: N 534 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7532 (tm-30) REVERT: O 474 ASP cc_start: 0.7423 (t0) cc_final: 0.7037 (t0) REVERT: O 477 ASP cc_start: 0.8329 (m-30) cc_final: 0.8089 (m-30) REVERT: O 520 SER cc_start: 0.8844 (t) cc_final: 0.8553 (m) REVERT: O 530 SER cc_start: 0.9052 (t) cc_final: 0.8755 (p) REVERT: P 473 ASP cc_start: 0.7951 (m-30) cc_final: 0.7422 (m-30) REVERT: P 477 ASP cc_start: 0.8419 (m-30) cc_final: 0.7733 (m-30) REVERT: P 479 GLU cc_start: 0.7570 (mp0) cc_final: 0.7235 (mp0) REVERT: P 525 ASP cc_start: 0.8063 (t0) cc_final: 0.7790 (t0) outliers start: 41 outliers final: 23 residues processed: 498 average time/residue: 0.3118 time to fit residues: 206.9296 Evaluate side-chains 494 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 469 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 490 GLU Chi-restraints excluded: chain G residue 462 GLN Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain K residue 522 SER Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 505 MET Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain M residue 462 GLN Chi-restraints excluded: chain N residue 491 GLN Chi-restraints excluded: chain O residue 523 GLU Chi-restraints excluded: chain P residue 482 THR Chi-restraints excluded: chain P residue 515 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 8.9990 chunk 100 optimal weight: 0.0070 chunk 40 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 GLN F 476 GLN H 462 GLN H 476 GLN I 534 GLN K 476 GLN L 535 GLN P 476 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.089610 restraints weight = 17267.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092877 restraints weight = 8255.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094925 restraints weight = 4504.434| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11136 Z= 0.126 Angle : 0.524 7.079 14912 Z= 0.288 Chirality : 0.035 0.129 1680 Planarity : 0.003 0.028 1984 Dihedral : 3.229 13.669 1472 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.25 % Allowed : 17.53 % Favored : 79.22 % 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: 1.78 (0.22), residues: 1328 helix: 1.41 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.50 (0.41), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 458 PHE 0.006 0.001 PHE I 453 TYR 0.007 0.001 TYR H 527 ARG 0.007 0.000 ARG I 533 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 784) hydrogen bonds : angle 4.40159 ( 2352) covalent geometry : bond 0.00290 (11136) covalent geometry : angle 0.52408 (14912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 477 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: C 520 SER cc_start: 0.8604 (t) cc_final: 0.8273 (m) REVERT: A 474 ASP cc_start: 0.7751 (t0) cc_final: 0.7502 (t0) REVERT: B 473 ASP cc_start: 0.8010 (m-30) cc_final: 0.7361 (m-30) REVERT: B 474 ASP cc_start: 0.7941 (t70) cc_final: 0.7505 (t0) REVERT: B 477 ASP cc_start: 0.7693 (m-30) cc_final: 0.7459 (m-30) REVERT: B 525 ASP cc_start: 0.7894 (t0) cc_final: 0.7524 (t0) REVERT: B 534 GLN cc_start: 0.7356 (mp10) cc_final: 0.7128 (mp10) REVERT: D 474 ASP cc_start: 0.8162 (t70) cc_final: 0.7529 (t70) REVERT: D 478 ASN cc_start: 0.8688 (m110) cc_final: 0.8257 (m-40) REVERT: D 500 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7356 (mm-30) REVERT: D 523 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: D 530 SER cc_start: 0.8852 (t) cc_final: 0.8607 (p) REVERT: E 469 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8200 (mmmm) REVERT: E 473 ASP cc_start: 0.7887 (m-30) cc_final: 0.7097 (m-30) REVERT: E 477 ASP cc_start: 0.8285 (m-30) cc_final: 0.7914 (m-30) REVERT: E 525 ASP cc_start: 0.7338 (t0) cc_final: 0.7038 (t0) REVERT: E 530 SER cc_start: 0.8762 (t) cc_final: 0.8412 (m) REVERT: F 477 ASP cc_start: 0.8103 (m-30) cc_final: 0.7670 (m-30) REVERT: F 520 SER cc_start: 0.8744 (t) cc_final: 0.8324 (m) REVERT: F 534 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7326 (tm-30) REVERT: G 462 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: G 473 ASP cc_start: 0.8457 (m-30) cc_final: 0.7751 (m-30) REVERT: G 477 ASP cc_start: 0.8011 (m-30) cc_final: 0.7702 (m-30) REVERT: G 500 GLU cc_start: 0.7887 (tp30) cc_final: 0.7261 (tp30) REVERT: G 523 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: I 474 ASP cc_start: 0.7833 (t70) cc_final: 0.7392 (t70) REVERT: I 478 ASN cc_start: 0.8805 (m110) cc_final: 0.8551 (m110) REVERT: I 491 GLN cc_start: 0.8799 (pp30) cc_final: 0.8309 (pp30) REVERT: I 495 ARG cc_start: 0.8714 (ptm-80) cc_final: 0.8437 (ttp-110) REVERT: I 530 SER cc_start: 0.8876 (t) cc_final: 0.8641 (m) REVERT: J 473 ASP cc_start: 0.7722 (m-30) cc_final: 0.7155 (m-30) REVERT: J 477 ASP cc_start: 0.7987 (m-30) cc_final: 0.7529 (m-30) REVERT: J 478 ASN cc_start: 0.8937 (m-40) cc_final: 0.8671 (m-40) REVERT: J 479 GLU cc_start: 0.7917 (mp0) cc_final: 0.7566 (mp0) REVERT: J 486 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8315 (ttmm) REVERT: K 473 ASP cc_start: 0.8280 (m-30) cc_final: 0.7812 (m-30) REVERT: K 505 MET cc_start: 0.8225 (mtp) cc_final: 0.7860 (mtp) REVERT: K 525 ASP cc_start: 0.7659 (t0) cc_final: 0.7301 (t0) REVERT: K 530 SER cc_start: 0.9132 (t) cc_final: 0.8874 (p) REVERT: L 479 GLU cc_start: 0.7811 (mp0) cc_final: 0.7544 (mp0) REVERT: L 530 SER cc_start: 0.8931 (t) cc_final: 0.8615 (p) REVERT: M 525 ASP cc_start: 0.7774 (t0) cc_final: 0.7413 (t0) REVERT: M 534 GLN cc_start: 0.7804 (pp30) cc_final: 0.7566 (pp30) REVERT: N 469 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8154 (mmmm) REVERT: N 473 ASP cc_start: 0.7602 (m-30) cc_final: 0.6765 (m-30) REVERT: N 477 ASP cc_start: 0.8125 (m-30) cc_final: 0.7804 (m-30) REVERT: N 487 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7856 (mt-10) REVERT: N 534 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7664 (tm-30) REVERT: O 477 ASP cc_start: 0.8385 (m-30) cc_final: 0.8125 (m-30) REVERT: O 530 SER cc_start: 0.8995 (t) cc_final: 0.8641 (p) REVERT: P 473 ASP cc_start: 0.7988 (m-30) cc_final: 0.7450 (m-30) REVERT: P 477 ASP cc_start: 0.8488 (m-30) cc_final: 0.7737 (m-30) REVERT: P 479 GLU cc_start: 0.7672 (mp0) cc_final: 0.7246 (mp0) REVERT: P 525 ASP cc_start: 0.8037 (t0) cc_final: 0.7666 (t0) outliers start: 40 outliers final: 22 residues processed: 491 average time/residue: 0.2734 time to fit residues: 179.1447 Evaluate side-chains 491 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 466 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain G residue 462 GLN Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 525 ASP Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 522 SER Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain M residue 462 GLN Chi-restraints excluded: chain N residue 462 GLN Chi-restraints excluded: chain N residue 491 GLN Chi-restraints excluded: chain O residue 523 GLU Chi-restraints excluded: chain P residue 482 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 104 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 98 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 GLN G 462 GLN G 478 ASN ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 534 GLN K 476 GLN P 458 HIS P 476 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.086649 restraints weight = 17600.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.089722 restraints weight = 8765.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.091658 restraints weight = 4918.622| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11136 Z= 0.184 Angle : 0.584 8.342 14912 Z= 0.320 Chirality : 0.038 0.150 1680 Planarity : 0.004 0.036 1984 Dihedral : 3.389 14.034 1472 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.98 % Allowed : 17.37 % Favored : 78.65 % 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: 1.64 (0.22), residues: 1328 helix: 1.30 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.37 (0.43), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 458 PHE 0.010 0.002 PHE C 453 TYR 0.009 0.002 TYR I 527 ARG 0.007 0.001 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 784) hydrogen bonds : angle 4.44342 ( 2352) covalent geometry : bond 0.00435 (11136) covalent geometry : angle 0.58409 (14912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 478 time to evaluate : 1.382 Fit side-chains REVERT: C 486 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8827 (ttmm) REVERT: C 520 SER cc_start: 0.8642 (t) cc_final: 0.8422 (m) REVERT: B 473 ASP cc_start: 0.8045 (m-30) cc_final: 0.7458 (m-30) REVERT: B 474 ASP cc_start: 0.7882 (t70) cc_final: 0.7452 (t0) REVERT: B 525 ASP cc_start: 0.7894 (t0) cc_final: 0.7583 (t0) REVERT: D 460 GLN cc_start: 0.7676 (mm110) cc_final: 0.6888 (mp10) REVERT: D 462 GLN cc_start: 0.8710 (tt0) cc_final: 0.8461 (tt0) REVERT: D 478 ASN cc_start: 0.8653 (m110) cc_final: 0.8302 (m-40) REVERT: D 530 SER cc_start: 0.9000 (t) cc_final: 0.8767 (p) REVERT: E 469 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8294 (mmmm) REVERT: E 473 ASP cc_start: 0.7878 (m-30) cc_final: 0.7097 (m-30) REVERT: E 477 ASP cc_start: 0.8274 (m-30) cc_final: 0.7915 (m-30) REVERT: E 525 ASP cc_start: 0.7370 (t0) cc_final: 0.7164 (t0) REVERT: E 530 SER cc_start: 0.8949 (t) cc_final: 0.8642 (m) REVERT: F 477 ASP cc_start: 0.8010 (m-30) cc_final: 0.7627 (m-30) REVERT: F 520 SER cc_start: 0.8774 (t) cc_final: 0.8368 (m) REVERT: F 534 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7115 (pp30) REVERT: G 473 ASP cc_start: 0.8385 (m-30) cc_final: 0.7698 (m-30) REVERT: G 477 ASP cc_start: 0.7977 (m-30) cc_final: 0.7701 (m-30) REVERT: I 474 ASP cc_start: 0.7681 (t70) cc_final: 0.7305 (t70) REVERT: I 478 ASN cc_start: 0.8777 (m110) cc_final: 0.8550 (m110) REVERT: I 491 GLN cc_start: 0.8738 (pp30) cc_final: 0.8230 (pp30) REVERT: I 495 ARG cc_start: 0.8857 (ptm-80) cc_final: 0.8531 (ttp-110) REVERT: J 473 ASP cc_start: 0.7710 (m-30) cc_final: 0.7256 (m-30) REVERT: J 477 ASP cc_start: 0.7870 (m-30) cc_final: 0.7481 (m-30) REVERT: J 478 ASN cc_start: 0.8925 (m-40) cc_final: 0.8667 (m-40) REVERT: J 479 GLU cc_start: 0.7915 (mp0) cc_final: 0.7625 (mp0) REVERT: J 486 LYS cc_start: 0.8631 (ttpp) cc_final: 0.8429 (ttmm) REVERT: K 469 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8250 (mmtp) REVERT: K 473 ASP cc_start: 0.8207 (m-30) cc_final: 0.7692 (m-30) REVERT: K 505 MET cc_start: 0.8239 (mtp) cc_final: 0.7914 (mtp) REVERT: K 525 ASP cc_start: 0.7702 (t0) cc_final: 0.7394 (t0) REVERT: K 530 SER cc_start: 0.9206 (t) cc_final: 0.8964 (p) REVERT: L 479 GLU cc_start: 0.7760 (mp0) cc_final: 0.7536 (mp0) REVERT: L 530 SER cc_start: 0.9087 (t) cc_final: 0.8757 (p) REVERT: M 525 ASP cc_start: 0.7813 (t0) cc_final: 0.7555 (t0) REVERT: M 534 GLN cc_start: 0.7707 (pp30) cc_final: 0.7506 (pp30) REVERT: N 469 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8240 (mmmm) REVERT: N 473 ASP cc_start: 0.7507 (m-30) cc_final: 0.6729 (m-30) REVERT: N 477 ASP cc_start: 0.8061 (m-30) cc_final: 0.7811 (m-30) REVERT: N 478 ASN cc_start: 0.8879 (m-40) cc_final: 0.8572 (m110) REVERT: N 487 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7844 (mt-10) REVERT: O 477 ASP cc_start: 0.8379 (m-30) cc_final: 0.8126 (m-30) REVERT: O 530 SER cc_start: 0.9087 (t) cc_final: 0.8785 (p) REVERT: P 473 ASP cc_start: 0.7969 (m-30) cc_final: 0.7427 (m-30) REVERT: P 477 ASP cc_start: 0.8421 (m-30) cc_final: 0.7732 (m-30) REVERT: P 479 GLU cc_start: 0.7603 (mp0) cc_final: 0.7258 (mp0) REVERT: P 525 ASP cc_start: 0.8081 (t0) cc_final: 0.7881 (t0) outliers start: 49 outliers final: 32 residues processed: 499 average time/residue: 0.2767 time to fit residues: 182.2214 Evaluate side-chains 496 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 464 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 465 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 525 ASP Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain H residue 512 LEU Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 534 GLN Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 522 SER Chi-restraints excluded: chain L residue 473 ASP Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 505 MET Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain M residue 462 GLN Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain N residue 462 GLN Chi-restraints excluded: chain N residue 491 GLN Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain P residue 482 THR Chi-restraints excluded: chain P residue 515 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 GLN I 534 GLN K 476 GLN P 476 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.088096 restraints weight = 17449.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.091015 restraints weight = 8596.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092966 restraints weight = 4913.445| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11136 Z= 0.149 Angle : 0.579 8.180 14912 Z= 0.319 Chirality : 0.037 0.142 1680 Planarity : 0.004 0.035 1984 Dihedral : 3.396 13.929 1472 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.25 % Allowed : 18.91 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1328 helix: 1.30 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.43 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 458 PHE 0.007 0.001 PHE C 453 TYR 0.010 0.001 TYR H 527 ARG 0.007 0.001 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 784) hydrogen bonds : angle 4.48791 ( 2352) covalent geometry : bond 0.00349 (11136) covalent geometry : angle 0.57946 (14912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 472 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 473 ASP cc_start: 0.7895 (m-30) cc_final: 0.7393 (m-30) REVERT: B 474 ASP cc_start: 0.7779 (t70) cc_final: 0.7163 (t0) REVERT: B 520 SER cc_start: 0.8582 (t) cc_final: 0.8341 (t) REVERT: B 525 ASP cc_start: 0.7815 (t0) cc_final: 0.7486 (t0) REVERT: D 478 ASN cc_start: 0.8659 (m110) cc_final: 0.8293 (m-40) REVERT: D 530 SER cc_start: 0.8949 (t) cc_final: 0.8722 (p) REVERT: E 469 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8269 (mmmm) REVERT: E 473 ASP cc_start: 0.7903 (m-30) cc_final: 0.7088 (m-30) REVERT: E 477 ASP cc_start: 0.8277 (m-30) cc_final: 0.7905 (m-30) REVERT: E 530 SER cc_start: 0.8951 (t) cc_final: 0.8635 (m) REVERT: F 477 ASP cc_start: 0.7986 (m-30) cc_final: 0.7582 (m-30) REVERT: F 520 SER cc_start: 0.8809 (t) cc_final: 0.8414 (m) REVERT: F 534 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7066 (pp30) REVERT: G 473 ASP cc_start: 0.8335 (m-30) cc_final: 0.7720 (m-30) REVERT: G 477 ASP cc_start: 0.7962 (m-30) cc_final: 0.7748 (m-30) REVERT: I 474 ASP cc_start: 0.7635 (t70) cc_final: 0.7247 (t70) REVERT: I 478 ASN cc_start: 0.8739 (m110) cc_final: 0.8485 (m110) REVERT: I 491 GLN cc_start: 0.8727 (pp30) cc_final: 0.8227 (pp30) REVERT: I 495 ARG cc_start: 0.8825 (ptm-80) cc_final: 0.8493 (ttp-110) REVERT: J 473 ASP cc_start: 0.7593 (m-30) cc_final: 0.7103 (m-30) REVERT: J 477 ASP cc_start: 0.7892 (m-30) cc_final: 0.7394 (m-30) REVERT: J 478 ASN cc_start: 0.8927 (m-40) cc_final: 0.8687 (m-40) REVERT: J 479 GLU cc_start: 0.7893 (mp0) cc_final: 0.7611 (mp0) REVERT: J 486 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8326 (ttmm) REVERT: K 473 ASP cc_start: 0.8143 (m-30) cc_final: 0.7722 (m-30) REVERT: K 493 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8521 (mmmt) REVERT: K 505 MET cc_start: 0.8185 (mtp) cc_final: 0.7861 (mtp) REVERT: K 525 ASP cc_start: 0.7549 (t0) cc_final: 0.7292 (t0) REVERT: K 530 SER cc_start: 0.9191 (t) cc_final: 0.8953 (p) REVERT: L 479 GLU cc_start: 0.7743 (mp0) cc_final: 0.7531 (mp0) REVERT: L 530 SER cc_start: 0.9082 (t) cc_final: 0.8781 (p) REVERT: M 525 ASP cc_start: 0.7747 (t0) cc_final: 0.7454 (t0) REVERT: N 469 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8216 (mmmm) REVERT: N 473 ASP cc_start: 0.7485 (m-30) cc_final: 0.6686 (m-30) REVERT: N 477 ASP cc_start: 0.8085 (m-30) cc_final: 0.7840 (m-30) REVERT: N 478 ASN cc_start: 0.8864 (m-40) cc_final: 0.8567 (m110) REVERT: N 487 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7883 (mt-10) REVERT: O 477 ASP cc_start: 0.8443 (m-30) cc_final: 0.8173 (m-30) REVERT: O 520 SER cc_start: 0.8834 (t) cc_final: 0.8609 (m) REVERT: O 530 SER cc_start: 0.9062 (t) cc_final: 0.8764 (p) REVERT: P 473 ASP cc_start: 0.7948 (m-30) cc_final: 0.7405 (m-30) REVERT: P 477 ASP cc_start: 0.8452 (m-30) cc_final: 0.7744 (m-30) REVERT: P 479 GLU cc_start: 0.7569 (mp0) cc_final: 0.7206 (mp0) REVERT: P 523 GLU cc_start: 0.8075 (pp20) cc_final: 0.7832 (pp20) outliers start: 40 outliers final: 35 residues processed: 487 average time/residue: 0.3211 time to fit residues: 210.2505 Evaluate side-chains 497 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 462 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 491 GLN Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 525 ASP Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain H residue 512 LEU Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 534 GLN Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 522 SER Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 505 MET Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain M residue 462 GLN Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain N residue 462 GLN Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 491 GLN Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain O residue 496 GLN Chi-restraints excluded: chain O residue 523 GLU Chi-restraints excluded: chain P residue 515 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 GLN ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 GLN I 534 GLN K 476 GLN P 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.090030 restraints weight = 17453.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093068 restraints weight = 8522.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094955 restraints weight = 4724.853| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11136 Z= 0.163 Angle : 0.637 9.434 14912 Z= 0.350 Chirality : 0.038 0.189 1680 Planarity : 0.004 0.034 1984 Dihedral : 3.478 14.083 1472 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.33 % Allowed : 19.24 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1328 helix: 1.24 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.36 (0.43), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 458 PHE 0.009 0.001 PHE N 453 TYR 0.009 0.001 TYR E 527 ARG 0.008 0.001 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 784) hydrogen bonds : angle 4.53870 ( 2352) covalent geometry : bond 0.00383 (11136) covalent geometry : angle 0.63665 (14912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 476 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 473 ASP cc_start: 0.7794 (m-30) cc_final: 0.7397 (m-30) REVERT: B 474 ASP cc_start: 0.7838 (t70) cc_final: 0.7199 (t0) REVERT: B 478 ASN cc_start: 0.8379 (m-40) cc_final: 0.7785 (m110) REVERT: B 520 SER cc_start: 0.8615 (t) cc_final: 0.8357 (t) REVERT: B 525 ASP cc_start: 0.7877 (t0) cc_final: 0.7481 (t0) REVERT: D 530 SER cc_start: 0.8929 (t) cc_final: 0.8662 (p) REVERT: E 469 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8264 (mmmm) REVERT: E 473 ASP cc_start: 0.7880 (m-30) cc_final: 0.7359 (m-30) REVERT: E 530 SER cc_start: 0.8865 (t) cc_final: 0.8521 (m) REVERT: F 477 ASP cc_start: 0.8030 (m-30) cc_final: 0.7602 (m-30) REVERT: F 520 SER cc_start: 0.8773 (t) cc_final: 0.8387 (m) REVERT: F 534 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7238 (pp30) REVERT: G 473 ASP cc_start: 0.8442 (m-30) cc_final: 0.7773 (m-30) REVERT: G 477 ASP cc_start: 0.8019 (m-30) cc_final: 0.7762 (m-30) REVERT: G 523 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6172 (mp0) REVERT: I 474 ASP cc_start: 0.7708 (t70) cc_final: 0.7466 (t70) REVERT: I 491 GLN cc_start: 0.8782 (pp30) cc_final: 0.8272 (pp30) REVERT: I 495 ARG cc_start: 0.8815 (ptm-80) cc_final: 0.8494 (ttp-110) REVERT: J 473 ASP cc_start: 0.7652 (m-30) cc_final: 0.7077 (m-30) REVERT: J 477 ASP cc_start: 0.7915 (m-30) cc_final: 0.7374 (m-30) REVERT: J 478 ASN cc_start: 0.8965 (m-40) cc_final: 0.8701 (m-40) REVERT: J 479 GLU cc_start: 0.7970 (mp0) cc_final: 0.7615 (mp0) REVERT: K 473 ASP cc_start: 0.8245 (m-30) cc_final: 0.7810 (m-30) REVERT: K 493 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8560 (mmmt) REVERT: K 505 MET cc_start: 0.8261 (mtp) cc_final: 0.7912 (mtp) REVERT: K 525 ASP cc_start: 0.7752 (t0) cc_final: 0.7442 (t0) REVERT: K 530 SER cc_start: 0.9164 (t) cc_final: 0.8893 (p) REVERT: L 479 GLU cc_start: 0.7813 (mp0) cc_final: 0.7557 (mp0) REVERT: L 530 SER cc_start: 0.9071 (t) cc_final: 0.8718 (p) REVERT: M 479 GLU cc_start: 0.7310 (mp0) cc_final: 0.7083 (mp0) REVERT: M 525 ASP cc_start: 0.7791 (t0) cc_final: 0.7433 (t0) REVERT: N 469 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8191 (mmmm) REVERT: N 473 ASP cc_start: 0.7534 (m-30) cc_final: 0.6712 (m-30) REVERT: N 477 ASP cc_start: 0.8151 (m-30) cc_final: 0.7839 (m-30) REVERT: N 478 ASN cc_start: 0.8895 (m-40) cc_final: 0.8596 (m110) REVERT: N 487 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7896 (mt-10) REVERT: O 477 ASP cc_start: 0.8450 (m-30) cc_final: 0.8158 (m-30) REVERT: O 530 SER cc_start: 0.9038 (t) cc_final: 0.8698 (p) REVERT: P 473 ASP cc_start: 0.7981 (m-30) cc_final: 0.7489 (m-30) REVERT: P 477 ASP cc_start: 0.8467 (m-30) cc_final: 0.7719 (m-30) REVERT: P 479 GLU cc_start: 0.7664 (mp0) cc_final: 0.7241 (mp0) REVERT: P 523 GLU cc_start: 0.8071 (pp20) cc_final: 0.7560 (pp20) REVERT: P 524 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.8032 (mpt180) outliers start: 41 outliers final: 37 residues processed: 490 average time/residue: 0.2932 time to fit residues: 191.3271 Evaluate side-chains 504 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 466 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 491 GLN Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 525 ASP Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain H residue 512 LEU Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 534 GLN Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 522 SER Chi-restraints excluded: chain L residue 473 ASP Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain M residue 462 GLN Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain N residue 462 GLN Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 491 GLN Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain O residue 496 GLN Chi-restraints excluded: chain O residue 523 GLU Chi-restraints excluded: chain P residue 515 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 GLN I 534 GLN K 476 GLN P 476 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.091139 restraints weight = 17067.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094209 restraints weight = 8377.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.096131 restraints weight = 4633.455| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11136 Z= 0.135 Angle : 0.618 9.037 14912 Z= 0.342 Chirality : 0.036 0.171 1680 Planarity : 0.004 0.034 1984 Dihedral : 3.425 14.835 1472 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.92 % Allowed : 20.70 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1328 helix: 1.24 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 458 PHE 0.005 0.001 PHE I 453 TYR 0.009 0.001 TYR H 527 ARG 0.009 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 784) hydrogen bonds : angle 4.57477 ( 2352) covalent geometry : bond 0.00304 (11136) covalent geometry : angle 0.61849 (14912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 483 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: B 474 ASP cc_start: 0.7711 (t70) cc_final: 0.7063 (t0) REVERT: B 478 ASN cc_start: 0.8341 (m-40) cc_final: 0.7684 (m110) REVERT: B 520 SER cc_start: 0.8672 (t) cc_final: 0.8415 (t) REVERT: B 525 ASP cc_start: 0.7778 (t0) cc_final: 0.7470 (t0) REVERT: D 530 SER cc_start: 0.8966 (t) cc_final: 0.8721 (p) REVERT: E 469 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8137 (mmmm) REVERT: E 473 ASP cc_start: 0.7953 (m-30) cc_final: 0.7370 (m-30) REVERT: E 530 SER cc_start: 0.8853 (t) cc_final: 0.8521 (m) REVERT: F 477 ASP cc_start: 0.8044 (m-30) cc_final: 0.7638 (m-30) REVERT: F 520 SER cc_start: 0.8805 (t) cc_final: 0.8513 (t) REVERT: F 534 GLN cc_start: 0.7429 (tm-30) cc_final: 0.7118 (pp30) REVERT: G 473 ASP cc_start: 0.8310 (m-30) cc_final: 0.7711 (m-30) REVERT: G 477 ASP cc_start: 0.7999 (m-30) cc_final: 0.7797 (m-30) REVERT: G 523 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: I 474 ASP cc_start: 0.7601 (t70) cc_final: 0.7373 (t70) REVERT: I 491 GLN cc_start: 0.8733 (pp30) cc_final: 0.8232 (pp30) REVERT: J 456 GLU cc_start: 0.8054 (pm20) cc_final: 0.7778 (pm20) REVERT: J 473 ASP cc_start: 0.7522 (m-30) cc_final: 0.7041 (m-30) REVERT: J 477 ASP cc_start: 0.7905 (m-30) cc_final: 0.7392 (m-30) REVERT: J 478 ASN cc_start: 0.8918 (m-40) cc_final: 0.8674 (m-40) REVERT: J 479 GLU cc_start: 0.7875 (mp0) cc_final: 0.7602 (mp0) REVERT: J 486 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8310 (ttmm) REVERT: K 473 ASP cc_start: 0.8129 (m-30) cc_final: 0.7719 (m-30) REVERT: K 493 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8568 (mmmt) REVERT: K 505 MET cc_start: 0.8182 (mtp) cc_final: 0.7862 (mtp) REVERT: K 525 ASP cc_start: 0.7454 (t0) cc_final: 0.7188 (t0) REVERT: K 530 SER cc_start: 0.9176 (t) cc_final: 0.8919 (p) REVERT: L 530 SER cc_start: 0.9088 (t) cc_final: 0.8777 (p) REVERT: N 469 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8210 (mmmm) REVERT: N 473 ASP cc_start: 0.7442 (m-30) cc_final: 0.6626 (m-30) REVERT: N 477 ASP cc_start: 0.8114 (m-30) cc_final: 0.7872 (m-30) REVERT: N 478 ASN cc_start: 0.8831 (m-40) cc_final: 0.8547 (m110) REVERT: N 487 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7739 (mt-10) REVERT: O 477 ASP cc_start: 0.8458 (m-30) cc_final: 0.8185 (m-30) REVERT: O 530 SER cc_start: 0.9030 (t) cc_final: 0.8749 (p) REVERT: P 473 ASP cc_start: 0.7851 (m-30) cc_final: 0.7394 (m-30) REVERT: P 477 ASP cc_start: 0.8459 (m-30) cc_final: 0.7752 (m-30) REVERT: P 479 GLU cc_start: 0.7560 (mp0) cc_final: 0.7201 (mp0) REVERT: P 523 GLU cc_start: 0.7959 (pp20) cc_final: 0.7482 (pp20) outliers start: 36 outliers final: 29 residues processed: 494 average time/residue: 0.2741 time to fit residues: 180.8040 Evaluate side-chains 506 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 476 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 491 GLN Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 525 ASP Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain H residue 512 LEU Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 534 GLN Chi-restraints excluded: chain K residue 462 GLN Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 522 SER Chi-restraints excluded: chain L residue 491 GLN Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain M residue 462 GLN Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain N residue 462 GLN Chi-restraints excluded: chain N residue 491 GLN Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain O residue 456 GLU Chi-restraints excluded: chain O residue 496 GLN Chi-restraints excluded: chain O residue 523 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 462 GLN D 478 ASN ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 499 ASN I 534 GLN K 458 HIS L 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.090424 restraints weight = 17036.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.093426 restraints weight = 8410.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.095334 restraints weight = 4677.026| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11136 Z= 0.144 Angle : 0.638 10.116 14912 Z= 0.352 Chirality : 0.037 0.166 1680 Planarity : 0.004 0.034 1984 Dihedral : 3.489 15.709 1472 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.68 % Allowed : 21.10 % Favored : 76.22 % 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: 1.47 (0.22), residues: 1328 helix: 1.19 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.44 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 458 PHE 0.006 0.001 PHE I 453 TYR 0.008 0.001 TYR F 527 ARG 0.008 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 784) hydrogen bonds : angle 4.61283 ( 2352) covalent geometry : bond 0.00330 (11136) covalent geometry : angle 0.63832 (14912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5739.02 seconds wall clock time: 102 minutes 18.09 seconds (6138.09 seconds total)