Starting phenix.real_space_refine on Mon Mar 11 16:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc1_15959/03_2024/8bc1_15959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc1_15959/03_2024/8bc1_15959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc1_15959/03_2024/8bc1_15959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc1_15959/03_2024/8bc1_15959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc1_15959/03_2024/8bc1_15959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc1_15959/03_2024/8bc1_15959.pdb" } resolution = 2.93 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= -0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 62 5.16 5 C 5758 2.51 5 N 1366 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8684 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4339 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 6 Chain: "B" Number of atoms: 4339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4339 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.15, per 1000 atoms: 0.59 Number of scatterers: 8684 At special positions: 0 Unit cell: (123.69, 79.422, 98.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 62 16.00 O 1492 8.00 N 1366 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.612A pdb=" N TYR A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.648A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.671A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.697A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 487 removed outlier: 4.235A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 539 removed outlier: 3.924A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 639 Proline residue: A 628 - end of helix removed outlier: 3.687A pdb=" N ARG A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.659A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.416A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.553A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 276 through 281 removed outlier: 4.614A pdb=" N TYR B 280 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.647A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.672A pdb=" N LEU B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.696A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 487 removed outlier: 4.234A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 539 removed outlier: 3.923A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 639 Proline residue: B 628 - end of helix removed outlier: 3.687A pdb=" N ARG B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.660A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.417A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.552A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2590 1.35 - 1.46: 2389 1.46 - 1.58: 3853 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 8928 Sorted by residual: bond pdb=" CA VAL B 411 " pdb=" CB VAL B 411 " ideal model delta sigma weight residual 1.530 1.541 -0.010 1.05e-02 9.07e+03 9.92e-01 bond pdb=" CA VAL A 411 " pdb=" CB VAL A 411 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 8.51e-01 bond pdb=" CA ILE B 751 " pdb=" CB ILE B 751 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.43e-01 bond pdb=" CA ILE A 700 " pdb=" C ILE A 700 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.22e-02 6.72e+03 6.40e-01 bond pdb=" CA PHE A 685 " pdb=" CB PHE A 685 " ideal model delta sigma weight residual 1.532 1.544 -0.013 1.67e-02 3.59e+03 6.00e-01 ... (remaining 8923 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.06: 280 107.06 - 113.80: 4834 113.80 - 120.53: 3665 120.53 - 127.26: 3234 127.26 - 133.99: 117 Bond angle restraints: 12130 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 113.26 -2.56 1.22e+00 6.72e-01 4.40e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 113.23 -2.53 1.22e+00 6.72e-01 4.29e+00 angle pdb=" C TYR B 580 " pdb=" CA TYR B 580 " pdb=" CB TYR B 580 " ideal model delta sigma weight residual 109.22 112.23 -3.01 1.52e+00 4.33e-01 3.92e+00 angle pdb=" C TYR A 580 " pdb=" CA TYR A 580 " pdb=" CB TYR A 580 " ideal model delta sigma weight residual 109.22 112.20 -2.98 1.52e+00 4.33e-01 3.85e+00 angle pdb=" CA PRO B 763 " pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 117.93 120.18 -2.25 1.20e+00 6.94e-01 3.51e+00 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 4748 12.66 - 25.33: 336 25.33 - 37.99: 96 37.99 - 50.65: 32 50.65 - 63.31: 8 Dihedral angle restraints: 5220 sinusoidal: 2106 harmonic: 3114 Sorted by residual: dihedral pdb=" CA VAL A 625 " pdb=" C VAL A 625 " pdb=" N LEU A 626 " pdb=" CA LEU A 626 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA VAL B 625 " pdb=" C VAL B 625 " pdb=" N LEU B 626 " pdb=" CA LEU B 626 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N GLU B 395 " pdb=" CA GLU B 395 " pdb=" CB GLU B 395 " pdb=" CG GLU B 395 " ideal model delta sinusoidal sigma weight residual -60.00 -117.63 57.63 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 812 0.025 - 0.050: 276 0.050 - 0.075: 173 0.075 - 0.100: 63 0.100 - 0.125: 8 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO A 689 " pdb=" N PRO A 689 " pdb=" C PRO A 689 " pdb=" CB PRO A 689 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 1329 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 700 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ILE A 700 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 700 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG A 701 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 697 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C ILE B 697 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 697 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 698 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 697 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ILE A 697 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 697 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 698 " -0.008 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2201 2.79 - 3.32: 9052 3.32 - 3.85: 14674 3.85 - 4.37: 16711 4.37 - 4.90: 28388 Nonbonded interactions: 71026 Sorted by model distance: nonbonded pdb=" O LEU B 626 " pdb=" N VAL B 630 " model vdw 2.265 2.520 nonbonded pdb=" O LEU A 626 " pdb=" N VAL A 630 " model vdw 2.265 2.520 nonbonded pdb=" O THR B 364 " pdb=" OG SER B 367 " model vdw 2.273 2.440 nonbonded pdb=" O THR A 364 " pdb=" OG SER A 367 " model vdw 2.273 2.440 nonbonded pdb=" O SER A 376 " pdb=" OG1 THR A 379 " model vdw 2.281 2.440 ... (remaining 71021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 4.180 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.590 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 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 : 0.002 0.018 8928 Z= 0.122 Angle : 0.458 5.542 12130 Z= 0.261 Chirality : 0.036 0.125 1332 Planarity : 0.004 0.032 1486 Dihedral : 10.381 63.314 3196 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.43 % Allowed : 5.25 % Favored : 91.33 % 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: 1.53 (0.26), residues: 1026 helix: 1.62 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.011 0.001 PHE B 393 TYR 0.011 0.001 TYR A 580 ARG 0.002 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8370 (mt) cc_final: 0.8006 (tp) REVERT: A 381 ILE cc_start: 0.6080 (mt) cc_final: 0.5828 (mt) REVERT: A 386 MET cc_start: 0.5095 (mmp) cc_final: 0.4500 (mmp) REVERT: A 530 LYS cc_start: 0.6932 (mmtm) cc_final: 0.6593 (mmmm) REVERT: A 595 GLU cc_start: 0.5110 (mp0) cc_final: 0.3651 (tm-30) REVERT: A 613 MET cc_start: 0.6979 (mtp) cc_final: 0.6312 (mtp) REVERT: A 638 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7104 (tmmt) REVERT: A 813 ARG cc_start: 0.4596 (mtt90) cc_final: 0.3334 (ppt170) REVERT: B 285 LEU cc_start: 0.8377 (mt) cc_final: 0.8019 (tp) REVERT: B 381 ILE cc_start: 0.6065 (mt) cc_final: 0.5805 (mt) REVERT: B 386 MET cc_start: 0.5120 (mmp) cc_final: 0.4486 (mmp) REVERT: B 507 MET cc_start: 0.5033 (ttm) cc_final: 0.4176 (tpp) REVERT: B 530 LYS cc_start: 0.6927 (mmtm) cc_final: 0.6587 (mmmm) REVERT: B 595 GLU cc_start: 0.5123 (mp0) cc_final: 0.3668 (tm-30) REVERT: B 613 MET cc_start: 0.6980 (mtp) cc_final: 0.6311 (mtp) REVERT: B 638 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7140 (tmmt) REVERT: B 813 ARG cc_start: 0.4723 (mtt90) cc_final: 0.3329 (ppt170) outliers start: 32 outliers final: 3 residues processed: 280 average time/residue: 0.8595 time to fit residues: 261.3138 Evaluate side-chains 170 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 730 GLN A 814 ASN A 830 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 730 GLN B 814 ASN B 830 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8928 Z= 0.255 Angle : 0.639 10.516 12130 Z= 0.332 Chirality : 0.042 0.156 1332 Planarity : 0.005 0.046 1486 Dihedral : 4.290 42.374 1172 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.53 % Allowed : 15.31 % Favored : 81.16 % 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 (0.26), residues: 1026 helix: 1.59 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 408 HIS 0.022 0.003 HIS A 844 PHE 0.014 0.001 PHE B 558 TYR 0.015 0.001 TYR A 668 ARG 0.005 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.4856 (mm-30) cc_final: 0.4471 (mp0) REVERT: A 381 ILE cc_start: 0.6090 (mt) cc_final: 0.5829 (mt) REVERT: A 553 MET cc_start: 0.6619 (tmt) cc_final: 0.6216 (tmm) REVERT: A 595 GLU cc_start: 0.5283 (mp0) cc_final: 0.3870 (tm-30) REVERT: A 608 GLN cc_start: 0.6129 (tp40) cc_final: 0.5531 (tt0) REVERT: A 611 ILE cc_start: 0.7748 (mm) cc_final: 0.7524 (mm) REVERT: A 613 MET cc_start: 0.7015 (mtp) cc_final: 0.6219 (ttm) REVERT: A 638 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.6973 (tmmt) REVERT: A 813 ARG cc_start: 0.4956 (mtt90) cc_final: 0.3464 (ppt170) REVERT: B 294 GLU cc_start: 0.4862 (mm-30) cc_final: 0.4474 (mp0) REVERT: B 348 MET cc_start: 0.5502 (mmm) cc_final: 0.5211 (mmt) REVERT: B 381 ILE cc_start: 0.6083 (mt) cc_final: 0.5807 (mt) REVERT: B 386 MET cc_start: 0.5463 (mmp) cc_final: 0.5260 (mmm) REVERT: B 553 MET cc_start: 0.6604 (tmt) cc_final: 0.6193 (tmm) REVERT: B 595 GLU cc_start: 0.5517 (mp0) cc_final: 0.3923 (tm-30) REVERT: B 608 GLN cc_start: 0.6147 (tp40) cc_final: 0.5526 (tt0) REVERT: B 613 MET cc_start: 0.7019 (mtp) cc_final: 0.6236 (ttm) REVERT: B 638 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.6973 (tmmt) REVERT: B 813 ARG cc_start: 0.4966 (mtt90) cc_final: 0.3431 (ppt170) REVERT: B 840 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.5421 (tt) outliers start: 33 outliers final: 11 residues processed: 209 average time/residue: 0.9971 time to fit residues: 224.8516 Evaluate side-chains 162 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8928 Z= 0.230 Angle : 0.645 9.598 12130 Z= 0.324 Chirality : 0.042 0.161 1332 Planarity : 0.005 0.048 1486 Dihedral : 4.458 42.053 1172 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.28 % Allowed : 17.99 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1026 helix: 1.43 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.56 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 408 HIS 0.013 0.002 HIS A 844 PHE 0.026 0.002 PHE A 558 TYR 0.015 0.001 TYR B 528 ARG 0.006 0.001 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 0.865 Fit side-chains REVERT: A 294 GLU cc_start: 0.4965 (mm-30) cc_final: 0.4472 (mp0) REVERT: A 553 MET cc_start: 0.6683 (tmt) cc_final: 0.6159 (tmm) REVERT: A 595 GLU cc_start: 0.5342 (mp0) cc_final: 0.3775 (tm-30) REVERT: A 608 GLN cc_start: 0.6126 (tp40) cc_final: 0.5546 (tt0) REVERT: A 613 MET cc_start: 0.7002 (mtp) cc_final: 0.6357 (mtp) REVERT: A 638 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.6985 (tmmt) REVERT: A 813 ARG cc_start: 0.5169 (mtt90) cc_final: 0.3570 (ppt170) REVERT: B 294 GLU cc_start: 0.4978 (mm-30) cc_final: 0.4479 (mp0) REVERT: B 386 MET cc_start: 0.5608 (mmp) cc_final: 0.5254 (mmm) REVERT: B 553 MET cc_start: 0.6666 (tmt) cc_final: 0.6145 (tmm) REVERT: B 595 GLU cc_start: 0.5364 (mp0) cc_final: 0.3760 (tm-30) REVERT: B 608 GLN cc_start: 0.6097 (tp40) cc_final: 0.5534 (tt0) REVERT: B 611 ILE cc_start: 0.7844 (mm) cc_final: 0.7632 (mm) REVERT: B 613 MET cc_start: 0.7004 (mtp) cc_final: 0.6358 (mtp) REVERT: B 638 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.6986 (tmmt) REVERT: B 699 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: B 813 ARG cc_start: 0.5098 (mtt90) cc_final: 0.3490 (ppt170) outliers start: 40 outliers final: 20 residues processed: 198 average time/residue: 0.9095 time to fit residues: 195.5257 Evaluate side-chains 171 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 GLN B 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8928 Z= 0.198 Angle : 0.652 12.541 12130 Z= 0.319 Chirality : 0.040 0.147 1332 Planarity : 0.005 0.050 1486 Dihedral : 4.380 42.721 1170 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.93 % Allowed : 18.63 % Favored : 76.45 % 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: 1.25 (0.25), residues: 1026 helix: 1.41 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.61 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 408 HIS 0.007 0.001 HIS A 844 PHE 0.027 0.001 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.008 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.5063 (mm-30) cc_final: 0.4771 (mm-30) REVERT: A 553 MET cc_start: 0.6680 (tmt) cc_final: 0.6152 (tmm) REVERT: A 595 GLU cc_start: 0.5134 (mp0) cc_final: 0.3484 (tm-30) REVERT: A 604 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6710 (mt-10) REVERT: A 608 GLN cc_start: 0.6420 (tp40) cc_final: 0.5706 (tt0) REVERT: A 613 MET cc_start: 0.7134 (mtp) cc_final: 0.6623 (mtp) REVERT: A 638 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.6973 (tmmt) REVERT: A 813 ARG cc_start: 0.5153 (mtt90) cc_final: 0.3523 (ppt170) REVERT: B 294 GLU cc_start: 0.5076 (mm-30) cc_final: 0.4822 (mm-30) REVERT: B 348 MET cc_start: 0.4767 (mmp) cc_final: 0.4263 (mmt) REVERT: B 386 MET cc_start: 0.5540 (mmp) cc_final: 0.5142 (mmm) REVERT: B 553 MET cc_start: 0.6677 (tmt) cc_final: 0.6363 (tmt) REVERT: B 595 GLU cc_start: 0.5397 (mp0) cc_final: 0.3615 (tm-30) REVERT: B 604 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6776 (mt-10) REVERT: B 608 GLN cc_start: 0.6068 (tp40) cc_final: 0.5518 (tt0) REVERT: B 613 MET cc_start: 0.7128 (mtp) cc_final: 0.6612 (mtp) REVERT: B 638 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.6974 (tmmt) REVERT: B 813 ARG cc_start: 0.5093 (mtt90) cc_final: 0.3453 (ppt170) outliers start: 46 outliers final: 14 residues processed: 209 average time/residue: 0.8124 time to fit residues: 185.7231 Evaluate side-chains 164 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 85 optimal weight: 0.0000 chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8928 Z= 0.208 Angle : 0.679 12.216 12130 Z= 0.330 Chirality : 0.041 0.148 1332 Planarity : 0.005 0.050 1486 Dihedral : 4.356 41.530 1170 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.82 % Allowed : 19.16 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1026 helix: 1.36 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.59 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 408 HIS 0.005 0.001 HIS B 844 PHE 0.030 0.001 PHE A 558 TYR 0.016 0.001 TYR A 528 ARG 0.003 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 168 time to evaluate : 1.004 Fit side-chains REVERT: A 289 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6752 (ttt90) REVERT: A 294 GLU cc_start: 0.5108 (mm-30) cc_final: 0.4683 (mp0) REVERT: A 553 MET cc_start: 0.6702 (tmt) cc_final: 0.6183 (tmm) REVERT: A 595 GLU cc_start: 0.4916 (mp0) cc_final: 0.3474 (tm-30) REVERT: A 604 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6820 (mt-10) REVERT: A 608 GLN cc_start: 0.6436 (tp40) cc_final: 0.5728 (tt0) REVERT: A 613 MET cc_start: 0.7186 (mtp) cc_final: 0.6677 (mtp) REVERT: A 638 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.6971 (tmmt) REVERT: A 813 ARG cc_start: 0.5239 (mtt90) cc_final: 0.3609 (ppt170) REVERT: B 289 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6762 (ttt90) REVERT: B 294 GLU cc_start: 0.5117 (mm-30) cc_final: 0.4688 (mp0) REVERT: B 386 MET cc_start: 0.5584 (mmp) cc_final: 0.5270 (mmm) REVERT: B 553 MET cc_start: 0.6690 (tmt) cc_final: 0.6150 (tmm) REVERT: B 595 GLU cc_start: 0.5351 (mp0) cc_final: 0.3596 (tm-30) REVERT: B 604 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6953 (mt-10) REVERT: B 608 GLN cc_start: 0.6082 (tp40) cc_final: 0.5546 (tt0) REVERT: B 613 MET cc_start: 0.7140 (mtp) cc_final: 0.6648 (mtp) REVERT: B 638 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.6971 (tmmt) REVERT: B 813 ARG cc_start: 0.5142 (mtt90) cc_final: 0.3471 (ppt170) outliers start: 45 outliers final: 17 residues processed: 200 average time/residue: 0.9024 time to fit residues: 195.9220 Evaluate side-chains 172 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN B 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8928 Z= 0.262 Angle : 0.711 13.970 12130 Z= 0.350 Chirality : 0.043 0.189 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.512 39.146 1170 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.25 % Allowed : 19.91 % Favored : 74.84 % 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: 0.97 (0.26), residues: 1026 helix: 1.26 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 408 HIS 0.005 0.001 HIS A 844 PHE 0.032 0.002 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.006 0.001 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 168 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.5250 (mm-30) cc_final: 0.4646 (mp0) REVERT: A 553 MET cc_start: 0.6768 (tmt) cc_final: 0.6236 (tmm) REVERT: A 595 GLU cc_start: 0.4766 (mp0) cc_final: 0.3537 (tm-30) REVERT: A 608 GLN cc_start: 0.6142 (tp40) cc_final: 0.5613 (tt0) REVERT: A 613 MET cc_start: 0.7027 (mtp) cc_final: 0.6383 (mtp) REVERT: A 638 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.6897 (tmmt) REVERT: A 813 ARG cc_start: 0.5598 (mtt90) cc_final: 0.3829 (ppt170) REVERT: B 294 GLU cc_start: 0.5268 (mm-30) cc_final: 0.4683 (mp0) REVERT: B 386 MET cc_start: 0.5669 (mmp) cc_final: 0.5260 (mmm) REVERT: B 553 MET cc_start: 0.6770 (tmt) cc_final: 0.6217 (tmm) REVERT: B 592 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.5321 (tmm-80) REVERT: B 595 GLU cc_start: 0.4988 (mp0) cc_final: 0.3315 (tm-30) REVERT: B 604 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7084 (mt-10) REVERT: B 608 GLN cc_start: 0.6157 (tp40) cc_final: 0.5641 (tt0) REVERT: B 613 MET cc_start: 0.7009 (mtp) cc_final: 0.6357 (mtp) REVERT: B 638 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7004 (tmmt) REVERT: B 813 ARG cc_start: 0.5345 (mtt90) cc_final: 0.3548 (ppt170) REVERT: B 842 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7403 (mpp) outliers start: 49 outliers final: 22 residues processed: 200 average time/residue: 0.8765 time to fit residues: 190.6607 Evaluate side-chains 179 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8928 Z= 0.230 Angle : 0.716 14.400 12130 Z= 0.349 Chirality : 0.043 0.165 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.534 41.577 1170 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.96 % Allowed : 22.38 % Favored : 73.66 % 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: 0.94 (0.26), residues: 1026 helix: 1.24 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 408 HIS 0.003 0.001 HIS B 844 PHE 0.033 0.001 PHE A 558 TYR 0.016 0.001 TYR A 528 ARG 0.005 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 0.975 Fit side-chains REVERT: A 553 MET cc_start: 0.6771 (tmt) cc_final: 0.6230 (tmm) REVERT: A 595 GLU cc_start: 0.4708 (mp0) cc_final: 0.3355 (tm-30) REVERT: A 604 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6907 (mt-10) REVERT: A 608 GLN cc_start: 0.6483 (tp40) cc_final: 0.5804 (tt0) REVERT: A 613 MET cc_start: 0.6938 (mtp) cc_final: 0.6301 (mtp) REVERT: A 638 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7023 (tmmt) REVERT: A 813 ARG cc_start: 0.5427 (mtt90) cc_final: 0.3816 (ppt170) REVERT: B 294 GLU cc_start: 0.5606 (mm-30) cc_final: 0.5313 (mm-30) REVERT: B 386 MET cc_start: 0.5429 (mmp) cc_final: 0.5101 (mmm) REVERT: B 553 MET cc_start: 0.6757 (tmt) cc_final: 0.6194 (tmm) REVERT: B 595 GLU cc_start: 0.4951 (mp0) cc_final: 0.3494 (tm-30) REVERT: B 604 GLU cc_start: 0.7266 (tm-30) cc_final: 0.7053 (mt-10) REVERT: B 608 GLN cc_start: 0.6726 (tp40) cc_final: 0.5800 (tt0) REVERT: B 613 MET cc_start: 0.6937 (mtp) cc_final: 0.6294 (mtp) REVERT: B 638 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7025 (tmmt) REVERT: B 813 ARG cc_start: 0.5368 (mtt90) cc_final: 0.3621 (ppt170) outliers start: 37 outliers final: 17 residues processed: 183 average time/residue: 0.8461 time to fit residues: 169.6994 Evaluate side-chains 170 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 0.0370 chunk 96 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8928 Z= 0.213 Angle : 0.721 14.809 12130 Z= 0.357 Chirality : 0.044 0.322 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.749 44.888 1168 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.10 % Allowed : 23.23 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.87 (0.26), residues: 1026 helix: 1.13 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 408 HIS 0.003 0.001 HIS B 844 PHE 0.034 0.001 PHE A 558 TYR 0.016 0.001 TYR A 528 ARG 0.005 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8651 (mm) cc_final: 0.8438 (pt) REVERT: A 553 MET cc_start: 0.6759 (tmt) cc_final: 0.6213 (tmm) REVERT: A 595 GLU cc_start: 0.4480 (mp0) cc_final: 0.3235 (tm-30) REVERT: A 608 GLN cc_start: 0.6716 (tp40) cc_final: 0.5795 (tt0) REVERT: A 613 MET cc_start: 0.6955 (mtp) cc_final: 0.6293 (mtp) REVERT: A 638 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.6979 (tmmt) REVERT: A 671 MET cc_start: 0.7609 (mmt) cc_final: 0.7351 (mmp) REVERT: A 813 ARG cc_start: 0.5340 (mtt90) cc_final: 0.3788 (ppt170) REVERT: B 386 MET cc_start: 0.5414 (mmp) cc_final: 0.5041 (mmm) REVERT: B 408 TRP cc_start: 0.7057 (m-10) cc_final: 0.6754 (m100) REVERT: B 553 MET cc_start: 0.6750 (tmt) cc_final: 0.6185 (tmm) REVERT: B 592 ARG cc_start: 0.5677 (OUTLIER) cc_final: 0.5437 (tmm-80) REVERT: B 595 GLU cc_start: 0.4986 (mp0) cc_final: 0.3928 (mt-10) REVERT: B 608 GLN cc_start: 0.6728 (tp40) cc_final: 0.5818 (tt0) REVERT: B 613 MET cc_start: 0.6943 (mtp) cc_final: 0.6264 (mtp) REVERT: B 638 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7015 (tmmt) REVERT: B 671 MET cc_start: 0.7620 (mmt) cc_final: 0.7400 (mmp) REVERT: B 813 ARG cc_start: 0.5345 (mtt90) cc_final: 0.3601 (ppt170) outliers start: 29 outliers final: 14 residues processed: 182 average time/residue: 0.8215 time to fit residues: 163.7580 Evaluate side-chains 166 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8928 Z= 0.238 Angle : 0.741 14.999 12130 Z= 0.365 Chirality : 0.045 0.227 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.750 43.441 1168 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.57 % Allowed : 24.73 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.78 (0.26), residues: 1026 helix: 1.13 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -0.96 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 408 HIS 0.003 0.001 HIS B 844 PHE 0.035 0.002 PHE A 558 TYR 0.016 0.001 TYR A 528 ARG 0.004 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.034 Fit side-chains REVERT: A 408 TRP cc_start: 0.6961 (m-10) cc_final: 0.6714 (m100) REVERT: A 468 ILE cc_start: 0.8660 (mm) cc_final: 0.8453 (pt) REVERT: A 553 MET cc_start: 0.6719 (tmt) cc_final: 0.6226 (tmm) REVERT: A 595 GLU cc_start: 0.4446 (mp0) cc_final: 0.3167 (tm-30) REVERT: A 608 GLN cc_start: 0.6653 (tp40) cc_final: 0.5882 (tt0) REVERT: A 613 MET cc_start: 0.6826 (mtp) cc_final: 0.6333 (mtp) REVERT: A 638 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.6989 (tmmt) REVERT: A 671 MET cc_start: 0.7686 (mmt) cc_final: 0.7452 (mmp) REVERT: A 810 ARG cc_start: 0.1728 (mmm160) cc_final: 0.1493 (mpp-170) REVERT: A 813 ARG cc_start: 0.5413 (mtt90) cc_final: 0.3721 (ppt170) REVERT: B 386 MET cc_start: 0.5178 (mmp) cc_final: 0.4945 (mmm) REVERT: B 408 TRP cc_start: 0.7002 (m-10) cc_final: 0.6796 (m100) REVERT: B 553 MET cc_start: 0.6747 (tmt) cc_final: 0.6185 (tmm) REVERT: B 555 MET cc_start: 0.7440 (mmm) cc_final: 0.7030 (tpt) REVERT: B 595 GLU cc_start: 0.4463 (mp0) cc_final: 0.3465 (mt-10) REVERT: B 608 GLN cc_start: 0.6658 (tp40) cc_final: 0.5874 (tt0) REVERT: B 613 MET cc_start: 0.6941 (mtp) cc_final: 0.6286 (mtp) REVERT: B 638 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.6995 (tmmt) REVERT: B 813 ARG cc_start: 0.5233 (mtt90) cc_final: 0.3537 (ppt170) outliers start: 24 outliers final: 14 residues processed: 165 average time/residue: 0.7901 time to fit residues: 143.2629 Evaluate side-chains 158 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5467 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8928 Z= 0.241 Angle : 0.748 15.941 12130 Z= 0.370 Chirality : 0.045 0.221 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.766 41.862 1168 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.25 % Allowed : 25.37 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.73 (0.26), residues: 1026 helix: 1.06 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 408 HIS 0.002 0.000 HIS A 844 PHE 0.037 0.002 PHE A 558 TYR 0.015 0.001 TYR A 528 ARG 0.005 0.000 ARG B 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6654 (ttt90) REVERT: A 468 ILE cc_start: 0.8722 (mm) cc_final: 0.8520 (pt) REVERT: A 553 MET cc_start: 0.6723 (tmt) cc_final: 0.6239 (tmm) REVERT: A 595 GLU cc_start: 0.4082 (mp0) cc_final: 0.2842 (tm-30) REVERT: A 608 GLN cc_start: 0.6600 (tp40) cc_final: 0.5912 (tt0) REVERT: A 613 MET cc_start: 0.6852 (mtp) cc_final: 0.6406 (ttm) REVERT: A 638 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.6988 (tmmt) REVERT: A 671 MET cc_start: 0.7675 (mmt) cc_final: 0.7235 (mmp) REVERT: A 810 ARG cc_start: 0.2043 (mmm160) cc_final: 0.1630 (mtm110) REVERT: A 813 ARG cc_start: 0.5652 (mtt90) cc_final: 0.3801 (ppt170) REVERT: A 842 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: B 289 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6708 (ttt90) REVERT: B 386 MET cc_start: 0.5361 (mmp) cc_final: 0.5133 (mmm) REVERT: B 553 MET cc_start: 0.6768 (tmt) cc_final: 0.6211 (tmm) REVERT: B 555 MET cc_start: 0.7438 (mmm) cc_final: 0.6999 (tpt) REVERT: B 595 GLU cc_start: 0.3942 (mp0) cc_final: 0.3193 (mt-10) REVERT: B 608 GLN cc_start: 0.6615 (tp40) cc_final: 0.5900 (tt0) REVERT: B 613 MET cc_start: 0.6838 (mtp) cc_final: 0.6436 (ttm) REVERT: B 638 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6988 (tmmt) REVERT: B 813 ARG cc_start: 0.5289 (mtt90) cc_final: 0.3491 (ppt170) outliers start: 21 outliers final: 14 residues processed: 166 average time/residue: 0.8575 time to fit residues: 155.1939 Evaluate side-chains 166 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 34 optimal weight: 0.0060 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 720 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.272261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.248086 restraints weight = 14152.888| |-----------------------------------------------------------------------------| r_work (start): 0.5037 rms_B_bonded: 2.88 r_work: 0.4954 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8928 Z= 0.215 Angle : 0.737 15.504 12130 Z= 0.363 Chirality : 0.044 0.209 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.709 41.503 1168 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.57 % Allowed : 25.70 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.74 (0.26), residues: 1026 helix: 1.06 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.88 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 408 HIS 0.002 0.000 HIS A 844 PHE 0.034 0.001 PHE A 558 TYR 0.015 0.001 TYR B 528 ARG 0.005 0.000 ARG B 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.47 seconds wall clock time: 61 minutes 14.58 seconds (3674.58 seconds total)