Starting phenix.real_space_refine on Wed May 8 22:34:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/05_2024/8b8q_15919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/05_2024/8b8q_15919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/05_2024/8b8q_15919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/05_2024/8b8q_15919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/05_2024/8b8q_15919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/05_2024/8b8q_15919.pdb" } resolution = 2.94 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= 0.006 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 74 5.16 5 C 7480 2.51 5 N 1834 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5682 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5682 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 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: 6.24, per 1000 atoms: 0.55 Number of scatterers: 11370 At special positions: 0 Unit cell: (74.214, 113.274, 128.247, 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 74 16.00 O 1976 8.00 N 1834 7.00 C 7480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " 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=2.04 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: 4.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 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: 49 helices and 4 sheets defined 65.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.505A pdb=" N GLY A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.617A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 327 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.280A pdb=" N GLU A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 Processing helix chain 'A' and resid 447 through 484 removed outlier: 3.654A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 538 removed outlier: 3.799A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.855A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.697A pdb=" N GLU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.922A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.496A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 802 " --> pdb=" O TYR A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 796 through 802' Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.514A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.660A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 362 through 375 removed outlier: 4.264A pdb=" N GLU B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 Processing helix chain 'B' and resid 447 through 484 removed outlier: 3.788A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 538 removed outlier: 3.772A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 3.750A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.785A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 4.050A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 797 through 802 removed outlier: 3.911A pdb=" N LEU B 801 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 802 " --> pdb=" O TYR B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 802' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 removed outlier: 3.592A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.601A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 782 through 785 715 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3454 1.34 - 1.46: 2819 1.46 - 1.58: 5291 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 11674 Sorted by residual: bond pdb=" C GLU B 272 " pdb=" N TRP B 273 " ideal model delta sigma weight residual 1.332 1.312 0.021 1.40e-02 5.10e+03 2.21e+00 bond pdb=" CA PRO A 815 " pdb=" C PRO A 815 " ideal model delta sigma weight residual 1.517 1.507 0.010 6.70e-03 2.23e+04 2.18e+00 bond pdb=" C GLY B 582 " pdb=" O GLY B 582 " ideal model delta sigma weight residual 1.243 1.230 0.012 9.30e-03 1.16e+04 1.74e+00 bond pdb=" C ASN B 562 " pdb=" O ASN B 562 " ideal model delta sigma weight residual 1.235 1.251 -0.016 1.26e-02 6.30e+03 1.57e+00 bond pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 1.235 1.250 -0.014 1.26e-02 6.30e+03 1.32e+00 ... (remaining 11669 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.33: 326 106.33 - 113.25: 6144 113.25 - 120.17: 4325 120.17 - 127.09: 4889 127.09 - 134.01: 144 Bond angle restraints: 15828 Sorted by residual: angle pdb=" CA LEU A 662 " pdb=" CB LEU A 662 " pdb=" CG LEU A 662 " ideal model delta sigma weight residual 116.30 126.56 -10.26 3.50e+00 8.16e-02 8.60e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.08 -3.38 1.22e+00 6.72e-01 7.70e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.04 -3.34 1.22e+00 6.72e-01 7.50e+00 angle pdb=" CA LEU B 662 " pdb=" CB LEU B 662 " pdb=" CG LEU B 662 " ideal model delta sigma weight residual 116.30 125.35 -9.05 3.50e+00 8.16e-02 6.69e+00 angle pdb=" N ILE B 786 " pdb=" CA ILE B 786 " pdb=" C ILE B 786 " ideal model delta sigma weight residual 106.21 108.60 -2.39 1.07e+00 8.73e-01 4.99e+00 ... (remaining 15823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 6264 16.25 - 32.50: 445 32.50 - 48.75: 117 48.75 - 65.00: 36 65.00 - 81.25: 2 Dihedral angle restraints: 6864 sinusoidal: 2788 harmonic: 4076 Sorted by residual: dihedral pdb=" CA THR B 787 " pdb=" C THR B 787 " pdb=" N ASP B 788 " pdb=" CA ASP B 788 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LYS B 590 " pdb=" C LYS B 590 " pdb=" N TYR B 591 " pdb=" CA TYR B 591 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN B 362 " pdb=" C ASN B 362 " pdb=" N ILE B 363 " pdb=" CA ILE B 363 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 935 0.025 - 0.050: 471 0.050 - 0.075: 200 0.075 - 0.101: 92 0.101 - 0.126: 36 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA ILE A 762 " pdb=" N ILE A 762 " pdb=" C ILE A 762 " pdb=" CB ILE A 762 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1731 not shown) Planarity restraints: 1958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 612 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C ILE A 612 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 612 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 613 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 612 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ILE B 612 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE B 612 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 613 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 613 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C MET A 613 " -0.033 2.00e-02 2.50e+03 pdb=" O MET A 613 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 614 " 0.011 2.00e-02 2.50e+03 ... (remaining 1955 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 254 2.68 - 3.24: 11651 3.24 - 3.79: 18977 3.79 - 4.35: 23980 4.35 - 4.90: 40101 Nonbonded interactions: 94963 Sorted by model distance: nonbonded pdb=" OG SER B 782 " pdb=" O ASP B 811 " model vdw 2.126 2.440 nonbonded pdb=" OD2 ASP A 749 " pdb=" OH TYR A 776 " model vdw 2.152 2.440 nonbonded pdb=" OE1 GLU A 667 " pdb="CA CA A1002 " model vdw 2.189 2.510 nonbonded pdb=" OG SER A 782 " pdb=" O ASP A 811 " model vdw 2.196 2.440 nonbonded pdb=" OE2 GLU B 670 " pdb="CA CA B1001 " model vdw 2.229 2.510 ... (remaining 94958 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: 20.860 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: 0.000 Extract box with map and model: 23.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 32.890 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.004 0.043 11674 Z= 0.247 Angle : 0.542 10.263 15828 Z= 0.302 Chirality : 0.039 0.126 1734 Planarity : 0.004 0.043 1958 Dihedral : 12.629 81.250 4222 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 7.93 % Allowed : 7.61 % Favored : 84.47 % 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 (0.23), residues: 1346 helix: 1.68 (0.17), residues: 812 sheet: 1.14 (0.71), residues: 54 loop : -1.33 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.014 0.001 PHE A 556 TYR 0.014 0.001 TYR A 580 ARG 0.003 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 215 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 272 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 327 ASP cc_start: 0.8159 (m-30) cc_final: 0.7950 (m-30) REVERT: A 365 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7790 (t) REVERT: A 370 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7823 (mtmt) REVERT: A 472 ILE cc_start: 0.7612 (mt) cc_final: 0.7398 (pt) REVERT: A 530 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8646 (mtmt) REVERT: A 534 MET cc_start: 0.8316 (mmt) cc_final: 0.7972 (tmm) REVERT: A 588 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6255 (pp) REVERT: A 613 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7548 (mmt) REVERT: A 772 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 785 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.5425 (p0) REVERT: A 855 TYR cc_start: 0.8258 (t80) cc_final: 0.7672 (t80) REVERT: A 862 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6830 (pmtt) REVERT: B 93 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8355 (ptpt) REVERT: B 271 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7278 (mmm160) REVERT: B 290 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8382 (pptt) REVERT: B 295 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: B 352 CYS cc_start: 0.7732 (t) cc_final: 0.6759 (p) REVERT: B 365 CYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6662 (t) REVERT: B 395 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: B 409 ASP cc_start: 0.8661 (m-30) cc_final: 0.7602 (t0) REVERT: B 524 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8006 (pp) REVERT: B 534 MET cc_start: 0.7440 (mmt) cc_final: 0.6687 (ttm) REVERT: B 657 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7451 (mm-40) REVERT: B 714 MET cc_start: 0.8245 (mtm) cc_final: 0.7704 (mpm) REVERT: B 750 MET cc_start: 0.8771 (ttm) cc_final: 0.8055 (tpt) REVERT: B 773 MET cc_start: 0.8830 (mmt) cc_final: 0.8464 (tpt) REVERT: B 788 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.3723 (t0) REVERT: B 843 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8661 (mt-10) outliers start: 98 outliers final: 24 residues processed: 296 average time/residue: 1.2595 time to fit residues: 402.3271 Evaluate side-chains 170 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.0670 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN B 108 HIS B 401 GLN B 544 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11674 Z= 0.196 Angle : 0.575 9.365 15828 Z= 0.306 Chirality : 0.040 0.136 1734 Planarity : 0.004 0.040 1958 Dihedral : 8.423 59.061 1607 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 6.15 % Allowed : 14.97 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1346 helix: 1.75 (0.17), residues: 814 sheet: 0.48 (0.65), residues: 54 loop : -1.23 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.002 0.001 HIS B 129 PHE 0.018 0.001 PHE A 556 TYR 0.016 0.001 TYR A 323 ARG 0.007 0.000 ARG B 810 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 144 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: A 142 MET cc_start: 0.4813 (mmm) cc_final: 0.3510 (mtp) REVERT: A 234 ASN cc_start: 0.9362 (t0) cc_final: 0.9161 (p0) REVERT: A 272 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 365 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7818 (t) REVERT: A 370 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7910 (mtmt) REVERT: A 463 TRP cc_start: 0.7697 (t-100) cc_final: 0.7307 (t-100) REVERT: A 472 ILE cc_start: 0.7410 (mt) cc_final: 0.7189 (pt) REVERT: A 522 MET cc_start: 0.8892 (ptp) cc_final: 0.8587 (ptp) REVERT: A 534 MET cc_start: 0.8279 (mmt) cc_final: 0.7927 (tmm) REVERT: A 548 GLU cc_start: 0.8044 (pt0) cc_final: 0.7838 (pt0) REVERT: A 613 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7428 (mmt) REVERT: A 720 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: A 772 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8469 (p) REVERT: A 785 ASN cc_start: 0.5792 (OUTLIER) cc_final: 0.5561 (p0) REVERT: A 788 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.5941 (t0) REVERT: A 812 PHE cc_start: 0.8162 (m-80) cc_final: 0.7767 (m-80) REVERT: A 855 TYR cc_start: 0.8151 (t80) cc_final: 0.7740 (t80) REVERT: A 862 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6832 (pmtt) REVERT: B 73 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: B 93 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8292 (ptpt) REVERT: B 216 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7555 (mp) REVERT: B 271 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7633 (mmm160) REVERT: B 286 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8167 (p0) REVERT: B 290 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8502 (pptt) REVERT: B 352 CYS cc_start: 0.7649 (t) cc_final: 0.6693 (p) REVERT: B 365 CYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6591 (t) REVERT: B 395 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: B 409 ASP cc_start: 0.8571 (m-30) cc_final: 0.7513 (t0) REVERT: B 524 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8040 (pp) REVERT: B 534 MET cc_start: 0.7279 (mmt) cc_final: 0.6484 (ttm) REVERT: B 654 TYR cc_start: 0.7032 (t80) cc_final: 0.6766 (t80) REVERT: B 750 MET cc_start: 0.8731 (ttm) cc_final: 0.8019 (tpt) REVERT: B 773 MET cc_start: 0.8834 (mmt) cc_final: 0.8326 (tpt) REVERT: B 843 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 855 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7070 (t80) outliers start: 76 outliers final: 30 residues processed: 202 average time/residue: 0.9758 time to fit residues: 220.6050 Evaluate side-chains 166 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 117 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11674 Z= 0.448 Angle : 0.658 9.054 15828 Z= 0.358 Chirality : 0.045 0.161 1734 Planarity : 0.005 0.044 1958 Dihedral : 8.167 59.968 1587 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 8.01 % Allowed : 13.92 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1346 helix: 1.35 (0.17), residues: 814 sheet: -0.35 (0.59), residues: 54 loop : -1.50 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 463 HIS 0.005 0.001 HIS B 129 PHE 0.019 0.002 PHE A 556 TYR 0.020 0.002 TYR B 757 ARG 0.008 0.001 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 128 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: A 365 CYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 370 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7939 (mtmt) REVERT: A 530 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8670 (mtpt) REVERT: A 548 GLU cc_start: 0.8142 (pt0) cc_final: 0.7919 (pt0) REVERT: A 554 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7032 (ttmm) REVERT: A 613 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.6390 (mpt) REVERT: A 855 TYR cc_start: 0.8230 (t80) cc_final: 0.7796 (t80) REVERT: A 862 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6598 (pmtt) REVERT: B 73 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: B 93 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8309 (ptmm) REVERT: B 286 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8329 (t0) REVERT: B 290 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8391 (pptt) REVERT: B 352 CYS cc_start: 0.7928 (t) cc_final: 0.7322 (p) REVERT: B 365 CYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6834 (t) REVERT: B 395 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: B 409 ASP cc_start: 0.8741 (m-30) cc_final: 0.7590 (t0) REVERT: B 524 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8102 (pp) REVERT: B 530 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7653 (tmtt) REVERT: B 534 MET cc_start: 0.7529 (mmt) cc_final: 0.6742 (ttm) REVERT: B 654 TYR cc_start: 0.7241 (t80) cc_final: 0.7040 (t80) REVERT: B 730 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7653 (mp-120) REVERT: B 750 MET cc_start: 0.8819 (ttm) cc_final: 0.8131 (tpt) REVERT: B 843 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8716 (mt-10) REVERT: B 855 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7219 (t80) outliers start: 99 outliers final: 41 residues processed: 214 average time/residue: 0.9547 time to fit residues: 226.5788 Evaluate side-chains 176 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 120 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 GLN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11674 Z= 0.206 Angle : 0.573 9.494 15828 Z= 0.306 Chirality : 0.041 0.201 1734 Planarity : 0.004 0.041 1958 Dihedral : 7.892 58.876 1583 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.83 % Allowed : 16.91 % Favored : 77.27 % 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: 0.68 (0.22), residues: 1346 helix: 1.51 (0.17), residues: 816 sheet: -0.49 (0.57), residues: 64 loop : -1.33 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 463 HIS 0.002 0.001 HIS A 249 PHE 0.020 0.001 PHE A 556 TYR 0.018 0.001 TYR A 528 ARG 0.005 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 139 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: A 365 CYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7687 (t) REVERT: A 370 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7980 (mtmt) REVERT: A 405 GLU cc_start: 0.8489 (tt0) cc_final: 0.7793 (tp30) REVERT: A 524 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7663 (pp) REVERT: A 530 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8634 (mtpt) REVERT: A 548 GLU cc_start: 0.8162 (pt0) cc_final: 0.7955 (pt0) REVERT: A 613 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7479 (mmt) REVERT: A 785 ASN cc_start: 0.6057 (OUTLIER) cc_final: 0.5603 (p0) REVERT: A 788 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6044 (t0) REVERT: A 855 TYR cc_start: 0.8176 (t80) cc_final: 0.7764 (t80) REVERT: B 93 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8278 (ptmm) REVERT: B 286 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8122 (p0) REVERT: B 290 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8477 (pptt) REVERT: B 322 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7835 (tm) REVERT: B 329 ASP cc_start: 0.8294 (p0) cc_final: 0.8002 (p0) REVERT: B 352 CYS cc_start: 0.7860 (t) cc_final: 0.6966 (p) REVERT: B 363 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.6895 (mp) REVERT: B 365 CYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6507 (t) REVERT: B 395 GLU cc_start: 0.8650 (mp0) cc_final: 0.8289 (mp0) REVERT: B 409 ASP cc_start: 0.8660 (m-30) cc_final: 0.7437 (t0) REVERT: B 524 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8046 (pp) REVERT: B 530 LYS cc_start: 0.8361 (mmtm) cc_final: 0.7543 (tmtt) REVERT: B 534 MET cc_start: 0.7473 (mmt) cc_final: 0.6679 (ttm) REVERT: B 555 MET cc_start: 0.8793 (mmm) cc_final: 0.8586 (mmt) REVERT: B 580 TYR cc_start: 0.8047 (p90) cc_final: 0.7811 (p90) REVERT: B 654 TYR cc_start: 0.7289 (t80) cc_final: 0.6842 (t80) REVERT: B 657 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7273 (mt0) REVERT: B 730 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8000 (mp-120) REVERT: B 750 MET cc_start: 0.8783 (ttm) cc_final: 0.8088 (tpt) REVERT: B 843 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8681 (mt-10) REVERT: B 855 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7140 (t80) outliers start: 72 outliers final: 34 residues processed: 197 average time/residue: 0.9291 time to fit residues: 203.4802 Evaluate side-chains 175 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11674 Z= 0.389 Angle : 0.634 9.360 15828 Z= 0.341 Chirality : 0.044 0.147 1734 Planarity : 0.005 0.044 1958 Dihedral : 7.420 57.359 1568 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 7.04 % Allowed : 16.50 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1346 helix: 1.42 (0.17), residues: 804 sheet: 0.25 (0.63), residues: 44 loop : -1.58 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 463 HIS 0.004 0.001 HIS A 844 PHE 0.038 0.002 PHE A 558 TYR 0.020 0.002 TYR A 528 ARG 0.004 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 127 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 290 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8508 (tmmt) REVERT: A 365 CYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7781 (t) REVERT: A 370 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7885 (mtmt) REVERT: A 530 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8650 (mtpt) REVERT: A 548 GLU cc_start: 0.8171 (pt0) cc_final: 0.7951 (pt0) REVERT: A 554 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7072 (ttmm) REVERT: A 613 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7538 (mmt) REVERT: A 788 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.6205 (t0) REVERT: A 855 TYR cc_start: 0.8193 (t80) cc_final: 0.7779 (t80) REVERT: B 53 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: B 93 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8284 (ptmm) REVERT: B 216 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7743 (mp) REVERT: B 271 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6553 (tpm-80) REVERT: B 286 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8086 (p0) REVERT: B 290 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8444 (pptt) REVERT: B 329 ASP cc_start: 0.8344 (p0) cc_final: 0.8073 (p0) REVERT: B 352 CYS cc_start: 0.7938 (t) cc_final: 0.7085 (p) REVERT: B 365 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6723 (t) REVERT: B 369 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7210 (mtmt) REVERT: B 409 ASP cc_start: 0.8723 (m-30) cc_final: 0.7454 (t0) REVERT: B 524 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8200 (pp) REVERT: B 530 LYS cc_start: 0.8408 (mmtm) cc_final: 0.7694 (tmtt) REVERT: B 534 MET cc_start: 0.7567 (mmt) cc_final: 0.6832 (ttm) REVERT: B 654 TYR cc_start: 0.7439 (t80) cc_final: 0.7193 (t80) REVERT: B 730 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8742 (mp10) REVERT: B 750 MET cc_start: 0.8805 (ttm) cc_final: 0.8101 (tpt) REVERT: B 855 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7200 (t80) outliers start: 87 outliers final: 46 residues processed: 203 average time/residue: 0.9795 time to fit residues: 221.1884 Evaluate side-chains 189 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 125 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.0470 chunk 128 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11674 Z= 0.195 Angle : 0.590 12.715 15828 Z= 0.311 Chirality : 0.041 0.155 1734 Planarity : 0.004 0.041 1958 Dihedral : 7.207 57.853 1567 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.66 % Allowed : 18.53 % Favored : 75.81 % 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: 0.72 (0.22), residues: 1346 helix: 1.60 (0.18), residues: 804 sheet: -0.54 (0.57), residues: 64 loop : -1.35 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 463 HIS 0.011 0.001 HIS A 518 PHE 0.033 0.001 PHE A 558 TYR 0.018 0.001 TYR B 325 ARG 0.004 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 137 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 102 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7559 (pp20) REVERT: A 142 MET cc_start: 0.5103 (mmm) cc_final: 0.3725 (mtp) REVERT: A 365 CYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7708 (t) REVERT: A 370 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (mtmt) REVERT: A 548 GLU cc_start: 0.8128 (pt0) cc_final: 0.7884 (pt0) REVERT: A 613 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7506 (mmt) REVERT: A 785 ASN cc_start: 0.6230 (OUTLIER) cc_final: 0.5903 (p0) REVERT: A 788 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6227 (t0) REVERT: B 53 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: B 93 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8304 (ptpt) REVERT: B 142 MET cc_start: 0.6443 (mtm) cc_final: 0.6121 (ptp) REVERT: B 216 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7812 (mp) REVERT: B 286 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8108 (p0) REVERT: B 290 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8492 (pptt) REVERT: B 322 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7860 (tm) REVERT: B 352 CYS cc_start: 0.7861 (t) cc_final: 0.7013 (p) REVERT: B 363 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.6868 (mp) REVERT: B 365 CYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6384 (t) REVERT: B 386 MET cc_start: 0.9170 (tpt) cc_final: 0.8817 (tpt) REVERT: B 395 GLU cc_start: 0.8681 (mp0) cc_final: 0.8315 (mp0) REVERT: B 409 ASP cc_start: 0.8634 (m-30) cc_final: 0.7328 (t0) REVERT: B 524 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8132 (pp) REVERT: B 530 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7572 (tmtt) REVERT: B 534 MET cc_start: 0.7530 (mmt) cc_final: 0.6742 (ttm) REVERT: B 730 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8772 (mp10) REVERT: B 750 MET cc_start: 0.8782 (ttm) cc_final: 0.8047 (tpt) REVERT: B 788 ASP cc_start: 0.5824 (OUTLIER) cc_final: 0.5013 (OUTLIER) REVERT: B 827 TYR cc_start: 0.7364 (t80) cc_final: 0.6525 (m-80) REVERT: B 855 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7068 (t80) outliers start: 70 outliers final: 30 residues processed: 196 average time/residue: 0.9858 time to fit residues: 215.6401 Evaluate side-chains 169 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 122 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 0.0030 chunk 82 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11674 Z= 0.211 Angle : 0.594 11.035 15828 Z= 0.312 Chirality : 0.041 0.190 1734 Planarity : 0.004 0.041 1958 Dihedral : 7.121 58.523 1567 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.42 % Allowed : 18.69 % Favored : 75.89 % 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: 0.78 (0.22), residues: 1346 helix: 1.66 (0.18), residues: 804 sheet: -0.66 (0.56), residues: 64 loop : -1.32 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 463 HIS 0.014 0.001 HIS A 518 PHE 0.022 0.001 PHE B 558 TYR 0.032 0.001 TYR B 77 ARG 0.003 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 132 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: A 365 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7722 (t) REVERT: A 370 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7876 (mtmt) REVERT: A 548 GLU cc_start: 0.8141 (pt0) cc_final: 0.7887 (pt0) REVERT: A 785 ASN cc_start: 0.6243 (OUTLIER) cc_final: 0.5892 (p0) REVERT: A 788 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6343 (t0) REVERT: A 812 PHE cc_start: 0.8048 (m-80) cc_final: 0.7520 (m-80) REVERT: B 93 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8310 (ptpt) REVERT: B 142 MET cc_start: 0.6305 (mtm) cc_final: 0.6016 (ptp) REVERT: B 271 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6597 (tpm-80) REVERT: B 286 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8115 (p0) REVERT: B 290 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8484 (pptt) REVERT: B 322 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7863 (tm) REVERT: B 352 CYS cc_start: 0.7868 (t) cc_final: 0.7041 (p) REVERT: B 363 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7028 (pt) REVERT: B 365 CYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6475 (t) REVERT: B 395 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: B 409 ASP cc_start: 0.8621 (m-30) cc_final: 0.7323 (t0) REVERT: B 524 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 534 MET cc_start: 0.7519 (mmt) cc_final: 0.6783 (ttm) REVERT: B 654 TYR cc_start: 0.7279 (t80) cc_final: 0.6817 (t80) REVERT: B 750 MET cc_start: 0.8791 (ttm) cc_final: 0.8073 (tpt) REVERT: B 788 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5264 (t0) REVERT: B 827 TYR cc_start: 0.7133 (t80) cc_final: 0.6503 (m-80) REVERT: B 855 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7047 (t80) outliers start: 67 outliers final: 30 residues processed: 186 average time/residue: 0.9103 time to fit residues: 188.6763 Evaluate side-chains 167 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 121 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 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 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11674 Z= 0.262 Angle : 0.620 10.760 15828 Z= 0.327 Chirality : 0.042 0.236 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.849 56.501 1562 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.85 % Allowed : 19.66 % Favored : 75.49 % 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: 0.70 (0.22), residues: 1346 helix: 1.58 (0.17), residues: 818 sheet: 0.03 (0.63), residues: 44 loop : -1.49 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 463 HIS 0.019 0.001 HIS A 518 PHE 0.024 0.002 PHE B 558 TYR 0.028 0.001 TYR B 77 ARG 0.004 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 121 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: A 142 MET cc_start: 0.5086 (mmm) cc_final: 0.3802 (mtm) REVERT: A 365 CYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7746 (t) REVERT: A 370 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (mtmt) REVERT: A 529 GLU cc_start: 0.8400 (tt0) cc_final: 0.8198 (pt0) REVERT: A 548 GLU cc_start: 0.8168 (pt0) cc_final: 0.7912 (pt0) REVERT: A 785 ASN cc_start: 0.6135 (OUTLIER) cc_final: 0.5728 (p0) REVERT: A 788 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6330 (t0) REVERT: B 93 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8305 (ptpt) REVERT: B 142 MET cc_start: 0.6194 (mtm) cc_final: 0.5940 (ptp) REVERT: B 271 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6623 (tpm-80) REVERT: B 286 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8112 (p0) REVERT: B 290 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8465 (pptt) REVERT: B 322 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7877 (tm) REVERT: B 352 CYS cc_start: 0.7926 (t) cc_final: 0.7111 (p) REVERT: B 363 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7193 (mp) REVERT: B 365 CYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6547 (t) REVERT: B 386 MET cc_start: 0.9155 (tpt) cc_final: 0.8847 (tpt) REVERT: B 395 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: B 409 ASP cc_start: 0.8652 (m-30) cc_final: 0.7342 (t0) REVERT: B 528 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: B 534 MET cc_start: 0.7522 (mmt) cc_final: 0.6809 (ttm) REVERT: B 654 TYR cc_start: 0.7385 (t80) cc_final: 0.7140 (t80) REVERT: B 750 MET cc_start: 0.8795 (ttm) cc_final: 0.8072 (tpt) REVERT: B 788 ASP cc_start: 0.5847 (OUTLIER) cc_final: 0.5451 (t0) REVERT: B 827 TYR cc_start: 0.7187 (t80) cc_final: 0.6572 (m-80) REVERT: B 855 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7086 (t80) outliers start: 60 outliers final: 30 residues processed: 171 average time/residue: 0.9321 time to fit residues: 177.3390 Evaluate side-chains 162 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.0670 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 131 optimal weight: 0.0770 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11674 Z= 0.185 Angle : 0.610 12.842 15828 Z= 0.319 Chirality : 0.041 0.176 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.589 55.620 1560 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.45 % Allowed : 20.39 % Favored : 75.16 % 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: 0.78 (0.22), residues: 1346 helix: 1.63 (0.17), residues: 818 sheet: 0.17 (0.66), residues: 44 loop : -1.42 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 463 HIS 0.024 0.001 HIS A 518 PHE 0.021 0.001 PHE B 558 TYR 0.027 0.001 TYR B 77 ARG 0.007 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 135 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: A 365 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7721 (t) REVERT: A 370 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7814 (mtmt) REVERT: A 534 MET cc_start: 0.7813 (tpp) cc_final: 0.7071 (tmm) REVERT: A 548 GLU cc_start: 0.8177 (pt0) cc_final: 0.7917 (pt0) REVERT: A 558 PHE cc_start: 0.7665 (m-80) cc_final: 0.6990 (t80) REVERT: A 788 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6258 (t0) REVERT: B 93 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8302 (ptpt) REVERT: B 142 MET cc_start: 0.6139 (mtm) cc_final: 0.5913 (ptp) REVERT: B 271 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6580 (tpm-80) REVERT: B 286 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8126 (p0) REVERT: B 290 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8448 (pptt) REVERT: B 322 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7887 (tm) REVERT: B 352 CYS cc_start: 0.7886 (t) cc_final: 0.7054 (p) REVERT: B 365 CYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6321 (t) REVERT: B 386 MET cc_start: 0.9133 (tpt) cc_final: 0.8852 (tpt) REVERT: B 395 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 409 ASP cc_start: 0.8586 (m-30) cc_final: 0.7330 (t0) REVERT: B 463 TRP cc_start: 0.7720 (m-90) cc_final: 0.7520 (m-90) REVERT: B 534 MET cc_start: 0.7511 (mmt) cc_final: 0.6768 (ttm) REVERT: B 750 MET cc_start: 0.8761 (ttm) cc_final: 0.8031 (tpt) REVERT: B 827 TYR cc_start: 0.7156 (t80) cc_final: 0.6519 (m-80) REVERT: B 855 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 867 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8650 (mmtt) outliers start: 55 outliers final: 30 residues processed: 180 average time/residue: 0.8849 time to fit residues: 177.9772 Evaluate side-chains 164 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 126 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11674 Z= 0.212 Angle : 0.627 12.268 15828 Z= 0.332 Chirality : 0.042 0.222 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.311 56.226 1556 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.96 % Allowed : 21.44 % Favored : 74.60 % 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: 0.80 (0.22), residues: 1346 helix: 1.67 (0.17), residues: 814 sheet: 0.11 (0.67), residues: 44 loop : -1.44 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 463 HIS 0.029 0.001 HIS A 518 PHE 0.018 0.001 PHE A 556 TYR 0.019 0.001 TYR B 325 ARG 0.008 0.000 ARG A 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 123 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: A 365 CYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7719 (t) REVERT: A 370 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7845 (mtmt) REVERT: A 381 ILE cc_start: 0.8983 (mt) cc_final: 0.8732 (mt) REVERT: A 529 GLU cc_start: 0.7885 (pt0) cc_final: 0.7500 (pm20) REVERT: A 534 MET cc_start: 0.7686 (tpp) cc_final: 0.6986 (tmm) REVERT: A 548 GLU cc_start: 0.8184 (pt0) cc_final: 0.7923 (pt0) REVERT: A 788 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6266 (t0) REVERT: B 93 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8285 (ptpt) REVERT: B 142 MET cc_start: 0.6070 (mtm) cc_final: 0.5860 (ptp) REVERT: B 271 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6602 (tpm-80) REVERT: B 286 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8125 (p0) REVERT: B 290 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8462 (pptt) REVERT: B 322 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7884 (tm) REVERT: B 352 CYS cc_start: 0.7912 (t) cc_final: 0.7082 (p) REVERT: B 363 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7011 (pt) REVERT: B 365 CYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6426 (t) REVERT: B 386 MET cc_start: 0.9142 (tpt) cc_final: 0.8853 (tpt) REVERT: B 395 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: B 409 ASP cc_start: 0.8569 (m-30) cc_final: 0.7339 (t0) REVERT: B 528 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: B 534 MET cc_start: 0.7513 (mmt) cc_final: 0.6799 (ttm) REVERT: B 654 TYR cc_start: 0.7242 (t80) cc_final: 0.7013 (t80) REVERT: B 750 MET cc_start: 0.8773 (ttm) cc_final: 0.8046 (tpt) REVERT: B 827 TYR cc_start: 0.7152 (t80) cc_final: 0.6511 (m-80) REVERT: B 855 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 867 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8642 (mmtt) outliers start: 49 outliers final: 29 residues processed: 162 average time/residue: 0.9501 time to fit residues: 172.3981 Evaluate side-chains 163 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS B 68 GLN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.140090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103011 restraints weight = 20757.819| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.82 r_work: 0.3338 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11674 Z= 0.377 Angle : 0.697 12.542 15828 Z= 0.373 Chirality : 0.045 0.221 1734 Planarity : 0.005 0.061 1958 Dihedral : 6.568 58.433 1556 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.13 % Allowed : 21.36 % Favored : 74.51 % 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: 0.43 (0.22), residues: 1346 helix: 1.36 (0.17), residues: 820 sheet: -0.38 (0.63), residues: 44 loop : -1.57 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP B 463 HIS 0.027 0.002 HIS A 518 PHE 0.023 0.002 PHE B 558 TYR 0.020 0.002 TYR B 325 ARG 0.004 0.000 ARG A 478 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: