Starting phenix.real_space_refine on Wed Feb 14 03:39:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/02_2024/8bcz_15971.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/02_2024/8bcz_15971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/02_2024/8bcz_15971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/02_2024/8bcz_15971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/02_2024/8bcz_15971.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/02_2024/8bcz_15971.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5376 2.51 5 N 1433 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8505 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 811 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 5.04, per 1000 atoms: 0.59 Number of scatterers: 8505 At special positions: 0 Unit cell: (91.2875, 102.972, 108.815, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1660 8.00 N 1433 7.00 C 5376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 27 sheets defined 8.5% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.644A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.057A pdb=" N TYR R 369 " --> pdb=" O TYR R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.743A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.335A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.689A pdb=" N VAL H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.653A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.928A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.670A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.571A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.776A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.569A pdb=" N LYS A 66 " --> pdb=" O PRO A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.774A pdb=" N THR A 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'R' and resid 334 through 335 removed outlier: 6.387A pdb=" N ASN R 334 " --> pdb=" O VAL R 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.641A pdb=" N MET H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.571A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.571A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.660A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.782A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.495A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.587A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.103A pdb=" N TYR E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.689A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.689A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.610A pdb=" N TRP A 38 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 52 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP A 36 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.610A pdb=" N TRP A 38 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 52 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP A 36 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.711A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 13 360 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 3.37 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: 2726 1.34 - 1.46: 2284 1.46 - 1.58: 3645 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 8703 Sorted by residual: bond pdb=" N VAL L 58 " pdb=" CA VAL L 58 " ideal model delta sigma weight residual 1.468 1.459 0.009 1.05e-02 9.07e+03 7.07e-01 bond pdb=" CB PRO R 337 " pdb=" CG PRO R 337 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.90e-01 bond pdb=" C GLN B 38 " pdb=" N LYS B 39 " ideal model delta sigma weight residual 1.331 1.350 -0.019 2.83e-02 1.25e+03 4.43e-01 bond pdb=" C LEU H 111 " pdb=" N GLY H 112 " ideal model delta sigma weight residual 1.322 1.330 -0.008 1.20e-02 6.94e+03 4.14e-01 bond pdb=" CG LEU C 51 " pdb=" CD1 LEU C 51 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.50e-01 ... (remaining 8698 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 227 107.03 - 113.77: 4681 113.77 - 120.51: 3183 120.51 - 127.25: 3633 127.25 - 133.99: 94 Bond angle restraints: 11818 Sorted by residual: angle pdb=" N ASP A 103 " pdb=" CA ASP A 103 " pdb=" C ASP A 103 " ideal model delta sigma weight residual 112.97 109.66 3.31 1.06e+00 8.90e-01 9.73e+00 angle pdb=" CA TYR R 495 " pdb=" CB TYR R 495 " pdb=" CG TYR R 495 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.98e+00 angle pdb=" C GLN B 38 " pdb=" N LYS B 39 " pdb=" CA LYS B 39 " ideal model delta sigma weight residual 120.97 128.21 -7.24 2.84e+00 1.24e-01 6.50e+00 angle pdb=" N ILE A 50 " pdb=" CA ILE A 50 " pdb=" C ILE A 50 " ideal model delta sigma weight residual 110.74 108.62 2.12 9.10e-01 1.21e+00 5.42e+00 angle pdb=" N ALA F 51 " pdb=" CA ALA F 51 " pdb=" CB ALA F 51 " ideal model delta sigma weight residual 113.65 110.64 3.01 1.47e+00 4.63e-01 4.19e+00 ... (remaining 11813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4888 17.34 - 34.68: 189 34.68 - 52.02: 33 52.02 - 69.36: 4 69.36 - 86.70: 4 Dihedral angle restraints: 5118 sinusoidal: 1963 harmonic: 3155 Sorted by residual: dihedral pdb=" CA PHE A 96 " pdb=" C PHE A 96 " pdb=" N CYS A 97 " pdb=" CA CYS A 97 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS C 35 " pdb=" C HIS C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" N GLU L 55 " pdb=" CA GLU L 55 " pdb=" CB GLU L 55 " pdb=" CG GLU L 55 " ideal model delta sinusoidal sigma weight residual -180.00 -127.98 -52.02 3 1.50e+01 4.44e-03 9.07e+00 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 812 0.031 - 0.062: 322 0.062 - 0.093: 70 0.093 - 0.124: 78 0.124 - 0.155: 9 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA ILE A 39 " pdb=" N ILE A 39 " pdb=" C ILE A 39 " pdb=" CB ILE A 39 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE F 75 " pdb=" N ILE F 75 " pdb=" C ILE F 75 " pdb=" CB ILE F 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1288 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 495 " 0.014 2.00e-02 2.50e+03 9.14e-03 1.67e+00 pdb=" CG TYR R 495 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR R 495 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 495 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 495 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 495 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 495 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 86 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO H 87 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO H 87 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO H 87 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO D 80 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.015 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 605 2.74 - 3.28: 7740 3.28 - 3.82: 14232 3.82 - 4.36: 18047 4.36 - 4.90: 31291 Nonbonded interactions: 71915 Sorted by model distance: nonbonded pdb=" OG SER R 359 " pdb=" OD1 ASN R 394 " model vdw 2.204 2.440 nonbonded pdb=" O THR H 28 " pdb=" ND2 ASN H 32 " model vdw 2.265 2.520 nonbonded pdb=" NE2 HIS C 35 " pdb=" O TYR C 105 " model vdw 2.302 2.520 nonbonded pdb=" O SER C 52 " pdb=" NH1 ARG C 72 " model vdw 2.324 2.520 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.333 2.520 ... (remaining 71910 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 'C' and (resid 2 through 25 or resid 27 through 30 or resid 32 or resid 3 \ 4 through 50 or resid 52 through 98 or resid 100 or resid 106 through 107 or res \ id 109 or resid 111 through 112 or resid 114 through 115 or resid 117 through 12 \ 1)) selection = (chain 'E' and (resid 2 through 25 or resid 27 through 30 or resid 32 or resid 3 \ 4 through 50 or resid 52 through 98 or resid 100 or resid 106 through 107 or res \ id 109 or resid 111 through 112 or resid 114 through 115 or resid 117 through 12 \ 1)) } ncs_group { reference = (chain 'D' and (resid 2 or resid 5 through 18 or resid 20 through 23 or resid 25 \ through 27 or resid 29 or resid 32 through 49 or resid 51 through 52 or resid 5 \ 4 or resid 57 through 64 or resid 66 through 72 or resid 74 through 75 or resid \ 77 through 82 or resid 84 through 90 or resid 97 through 99 or resid 101 through \ 102 or resid 106 through 107)) selection = (chain 'F' and (resid 2 or resid 5 through 18 or resid 20 through 23 or resid 25 \ through 27 or resid 29 or resid 32 through 49 or resid 51 through 52 or resid 5 \ 4 or resid 57 through 64 or resid 66 through 72 or resid 74 through 75 or resid \ 77 through 82 or resid 84 through 90 or resid 98 through 100 or resid 102 throug \ h 103 or resid 107 through 108)) selection = (chain 'L' and (resid 2 or resid 5 through 18 or resid 20 through 23 or resid 25 \ through 27 or resid 29 or resid 32 through 49 or resid 51 through 52 or resid 5 \ 4 or resid 57 through 64 or resid 66 through 72 or resid 74 through 75 or resid \ 77 through 82 or resid 84 through 90 or resid 97 through 99 or resid 101 through \ 102 or resid 106 through 107)) } 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.180 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.510 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.003 0.038 8703 Z= 0.176 Angle : 0.490 7.243 11818 Z= 0.265 Chirality : 0.042 0.155 1291 Planarity : 0.003 0.029 1514 Dihedral : 9.566 86.704 3088 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.18 % Allowed : 2.69 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.33 (0.26), residues: 1082 helix: -3.20 (0.71), residues: 26 sheet: 0.14 (0.23), residues: 475 loop : 0.65 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 111 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 96 TYR 0.022 0.001 TYR R 495 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 0.995 Fit side-chains REVERT: R 378 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8379 (mmtp) REVERT: R 493 GLN cc_start: 0.8578 (tp40) cc_final: 0.8340 (mm-40) REVERT: H 3 GLN cc_start: 0.8121 (tt0) cc_final: 0.7365 (mm-40) REVERT: H 25 SER cc_start: 0.8043 (m) cc_final: 0.7790 (t) REVERT: L 7 SER cc_start: 0.8130 (m) cc_final: 0.7852 (p) REVERT: L 77 SER cc_start: 0.7453 (t) cc_final: 0.7146 (m) REVERT: L 103 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7483 (tpp80) REVERT: C 43 LYS cc_start: 0.8266 (mmtt) cc_final: 0.8019 (ttpt) REVERT: C 65 LYS cc_start: 0.7645 (tttt) cc_final: 0.7284 (ttmt) REVERT: C 89 GLU cc_start: 0.8081 (mp0) cc_final: 0.7190 (tm-30) REVERT: C 101 SER cc_start: 0.8216 (t) cc_final: 0.7858 (m) REVERT: D 45 LYS cc_start: 0.8530 (tttt) cc_final: 0.8303 (ttmm) REVERT: F 45 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7834 (tttt) REVERT: A 83 THR cc_start: 0.8061 (p) cc_final: 0.7679 (p) REVERT: B 45 LYS cc_start: 0.8089 (mttt) cc_final: 0.7737 (tttm) outliers start: 11 outliers final: 4 residues processed: 208 average time/residue: 0.7520 time to fit residues: 171.9092 Evaluate side-chains 154 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain F residue 45 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN D 3 GLN D 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8703 Z= 0.169 Angle : 0.477 5.036 11818 Z= 0.255 Chirality : 0.043 0.138 1291 Planarity : 0.004 0.028 1514 Dihedral : 4.376 49.342 1218 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.11 % Allowed : 11.49 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.49 (0.26), residues: 1082 helix: -3.20 (0.73), residues: 27 sheet: 0.41 (0.23), residues: 463 loop : 0.60 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 PHE 0.013 0.001 PHE A 96 TYR 0.024 0.001 TYR R 495 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: R 378 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8365 (mmtp) REVERT: R 467 ASP cc_start: 0.8198 (t70) cc_final: 0.7835 (t70) REVERT: H 3 GLN cc_start: 0.8112 (tt0) cc_final: 0.7322 (mm110) REVERT: H 21 SER cc_start: 0.7866 (m) cc_final: 0.7439 (p) REVERT: H 25 SER cc_start: 0.8024 (m) cc_final: 0.7771 (t) REVERT: H 116 THR cc_start: 0.7937 (p) cc_final: 0.7599 (t) REVERT: L 7 SER cc_start: 0.8277 (m) cc_final: 0.7803 (p) REVERT: L 77 SER cc_start: 0.7388 (t) cc_final: 0.7035 (m) REVERT: L 103 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7567 (tpp80) REVERT: C 43 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7978 (ttpt) REVERT: C 65 LYS cc_start: 0.7619 (tttt) cc_final: 0.7307 (ttmt) REVERT: C 89 GLU cc_start: 0.7989 (mp0) cc_final: 0.7277 (tm-30) REVERT: C 101 SER cc_start: 0.8132 (t) cc_final: 0.7844 (m) REVERT: D 10 SER cc_start: 0.8918 (t) cc_final: 0.8496 (m) REVERT: D 45 LYS cc_start: 0.8458 (tttt) cc_final: 0.8237 (ttmm) REVERT: F 45 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7898 (tttt) REVERT: A 78 ASN cc_start: 0.7694 (t0) cc_final: 0.7454 (t0) REVERT: B 45 LYS cc_start: 0.8158 (mttt) cc_final: 0.7844 (tttm) outliers start: 29 outliers final: 17 residues processed: 171 average time/residue: 0.8623 time to fit residues: 160.7186 Evaluate side-chains 157 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 0.0270 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8703 Z= 0.232 Angle : 0.506 5.962 11818 Z= 0.268 Chirality : 0.044 0.151 1291 Planarity : 0.004 0.038 1514 Dihedral : 4.563 50.911 1218 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.19 % Allowed : 11.92 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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 (0.26), residues: 1082 helix: -3.09 (0.85), residues: 27 sheet: 0.42 (0.23), residues: 464 loop : 0.51 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 111 HIS 0.005 0.001 HIS C 35 PHE 0.015 0.002 PHE A 96 TYR 0.026 0.002 TYR R 495 ARG 0.004 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 0.971 Fit side-chains REVERT: R 378 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8424 (mmtp) REVERT: R 467 ASP cc_start: 0.8213 (t70) cc_final: 0.7915 (t70) REVERT: H 3 GLN cc_start: 0.8116 (tt0) cc_final: 0.7363 (mm110) REVERT: H 21 SER cc_start: 0.7885 (m) cc_final: 0.7480 (p) REVERT: H 25 SER cc_start: 0.8037 (m) cc_final: 0.7790 (t) REVERT: L 7 SER cc_start: 0.8277 (m) cc_final: 0.7743 (p) REVERT: L 77 SER cc_start: 0.7449 (t) cc_final: 0.7159 (m) REVERT: L 103 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7591 (tpp80) REVERT: C 28 THR cc_start: 0.8223 (p) cc_final: 0.8020 (p) REVERT: C 43 LYS cc_start: 0.8280 (mmtt) cc_final: 0.8019 (ttpt) REVERT: C 65 LYS cc_start: 0.7687 (tttt) cc_final: 0.7317 (ttmt) REVERT: C 84 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7482 (m-40) REVERT: C 89 GLU cc_start: 0.8008 (mp0) cc_final: 0.7297 (tm-30) REVERT: C 101 SER cc_start: 0.8283 (t) cc_final: 0.7865 (m) REVERT: D 10 SER cc_start: 0.8908 (t) cc_final: 0.8490 (m) REVERT: D 42 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7598 (tttt) REVERT: D 45 LYS cc_start: 0.8455 (tttt) cc_final: 0.8222 (ttmm) REVERT: F 45 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7857 (tttt) REVERT: A 13 LYS cc_start: 0.8713 (mttt) cc_final: 0.8494 (mtpp) REVERT: A 78 ASN cc_start: 0.7668 (t0) cc_final: 0.7390 (t0) REVERT: B 45 LYS cc_start: 0.8190 (mttt) cc_final: 0.7834 (tttm) outliers start: 39 outliers final: 24 residues processed: 170 average time/residue: 0.8626 time to fit residues: 159.8635 Evaluate side-chains 161 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 14 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8703 Z= 0.172 Angle : 0.473 6.143 11818 Z= 0.252 Chirality : 0.043 0.145 1291 Planarity : 0.004 0.028 1514 Dihedral : 4.459 51.315 1218 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.65 % Allowed : 13.10 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.52 (0.26), residues: 1082 helix: -3.08 (0.82), residues: 27 sheet: 0.46 (0.23), residues: 472 loop : 0.60 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE A 96 TYR 0.022 0.001 TYR R 495 ARG 0.006 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: R 378 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8404 (mmtp) REVERT: R 467 ASP cc_start: 0.8197 (t70) cc_final: 0.7889 (t70) REVERT: H 3 GLN cc_start: 0.8100 (tt0) cc_final: 0.7350 (mm110) REVERT: H 21 SER cc_start: 0.7880 (m) cc_final: 0.7443 (p) REVERT: H 25 SER cc_start: 0.7961 (m) cc_final: 0.7751 (t) REVERT: L 7 SER cc_start: 0.8293 (m) cc_final: 0.7743 (p) REVERT: L 55 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: L 77 SER cc_start: 0.7448 (t) cc_final: 0.7157 (m) REVERT: L 103 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7573 (tpp80) REVERT: C 19 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6782 (mmm160) REVERT: C 43 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7981 (ttpt) REVERT: C 65 LYS cc_start: 0.7654 (tttt) cc_final: 0.7271 (ttmt) REVERT: C 89 GLU cc_start: 0.7971 (mp0) cc_final: 0.7285 (tm-30) REVERT: C 101 SER cc_start: 0.8248 (t) cc_final: 0.7838 (m) REVERT: D 10 SER cc_start: 0.8920 (t) cc_final: 0.8511 (m) REVERT: D 42 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7588 (tttt) REVERT: D 45 LYS cc_start: 0.8438 (tttt) cc_final: 0.8225 (ttmm) REVERT: F 45 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7920 (tttt) REVERT: A 13 LYS cc_start: 0.8642 (mttt) cc_final: 0.8425 (mtpp) REVERT: A 78 ASN cc_start: 0.7645 (t0) cc_final: 0.7421 (t0) REVERT: B 45 LYS cc_start: 0.8196 (mttt) cc_final: 0.7841 (tttm) outliers start: 34 outliers final: 21 residues processed: 159 average time/residue: 0.8761 time to fit residues: 151.7933 Evaluate side-chains 157 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8703 Z= 0.151 Angle : 0.457 5.654 11818 Z= 0.243 Chirality : 0.042 0.138 1291 Planarity : 0.003 0.025 1514 Dihedral : 4.328 50.788 1217 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.65 % Allowed : 13.43 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.63 (0.26), residues: 1082 helix: -3.18 (0.73), residues: 27 sheet: 0.59 (0.23), residues: 465 loop : 0.61 (0.28), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 PHE 0.011 0.001 PHE A 80 TYR 0.020 0.001 TYR R 495 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: R 378 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8288 (mmtp) REVERT: R 467 ASP cc_start: 0.8201 (t70) cc_final: 0.7917 (t70) REVERT: H 3 GLN cc_start: 0.8038 (tt0) cc_final: 0.7311 (mm110) REVERT: L 7 SER cc_start: 0.8268 (m) cc_final: 0.7732 (p) REVERT: L 55 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: L 77 SER cc_start: 0.7453 (t) cc_final: 0.7155 (m) REVERT: L 103 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7553 (tpp80) REVERT: C 19 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6749 (mmm160) REVERT: C 43 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7987 (ttpt) REVERT: C 65 LYS cc_start: 0.7670 (tttt) cc_final: 0.7336 (ttmt) REVERT: C 84 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7771 (m-40) REVERT: C 89 GLU cc_start: 0.7906 (mp0) cc_final: 0.7272 (tm-30) REVERT: C 101 SER cc_start: 0.8111 (t) cc_final: 0.7796 (m) REVERT: D 10 SER cc_start: 0.8893 (t) cc_final: 0.8512 (m) REVERT: D 42 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7637 (tttt) REVERT: D 45 LYS cc_start: 0.8434 (tttt) cc_final: 0.8215 (ttmm) REVERT: F 45 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7923 (tttt) REVERT: A 13 LYS cc_start: 0.8632 (mttt) cc_final: 0.8415 (mtpp) REVERT: A 104 ASP cc_start: 0.8117 (m-30) cc_final: 0.7873 (m-30) REVERT: B 45 LYS cc_start: 0.8182 (mttt) cc_final: 0.7843 (tttm) outliers start: 34 outliers final: 22 residues processed: 155 average time/residue: 0.8971 time to fit residues: 151.1381 Evaluate side-chains 153 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.0570 chunk 8 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8703 Z= 0.143 Angle : 0.462 7.553 11818 Z= 0.243 Chirality : 0.042 0.137 1291 Planarity : 0.003 0.029 1514 Dihedral : 4.283 50.448 1217 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.87 % Allowed : 13.64 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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 (0.26), residues: 1082 helix: -3.24 (0.69), residues: 27 sheet: 0.62 (0.23), residues: 466 loop : 0.65 (0.28), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.011 0.001 PHE A 80 TYR 0.019 0.001 TYR R 495 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 0.989 Fit side-chains REVERT: R 378 LYS cc_start: 0.8612 (mmmm) cc_final: 0.8277 (mmtp) REVERT: R 467 ASP cc_start: 0.8199 (t70) cc_final: 0.7917 (t70) REVERT: H 3 GLN cc_start: 0.8031 (tt0) cc_final: 0.7320 (mm110) REVERT: L 7 SER cc_start: 0.8301 (m) cc_final: 0.7727 (p) REVERT: L 77 SER cc_start: 0.7444 (t) cc_final: 0.7147 (m) REVERT: L 103 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7729 (tpp80) REVERT: C 43 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7987 (ttpt) REVERT: C 65 LYS cc_start: 0.7671 (tttt) cc_final: 0.7347 (ttmt) REVERT: C 83 MET cc_start: 0.7917 (mtm) cc_final: 0.7637 (mtp) REVERT: C 84 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: C 89 GLU cc_start: 0.7845 (mp0) cc_final: 0.7247 (tm-30) REVERT: C 101 SER cc_start: 0.8167 (t) cc_final: 0.7808 (m) REVERT: D 10 SER cc_start: 0.8885 (t) cc_final: 0.8508 (m) REVERT: D 42 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7614 (tttt) REVERT: D 45 LYS cc_start: 0.8442 (tttt) cc_final: 0.8224 (ttmm) REVERT: F 45 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7923 (tttt) REVERT: A 13 LYS cc_start: 0.8613 (mttt) cc_final: 0.8396 (mtpp) REVERT: A 104 ASP cc_start: 0.8096 (m-30) cc_final: 0.7846 (m-30) REVERT: B 28 ASP cc_start: 0.8489 (t0) cc_final: 0.8285 (t70) REVERT: B 45 LYS cc_start: 0.8171 (mttt) cc_final: 0.7842 (tttm) outliers start: 36 outliers final: 25 residues processed: 154 average time/residue: 0.8899 time to fit residues: 149.1724 Evaluate side-chains 155 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8703 Z= 0.216 Angle : 0.500 7.149 11818 Z= 0.262 Chirality : 0.043 0.139 1291 Planarity : 0.004 0.036 1514 Dihedral : 4.470 51.338 1217 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.08 % Allowed : 13.43 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.57 (0.26), residues: 1082 helix: -3.37 (0.65), residues: 27 sheet: 0.60 (0.24), residues: 462 loop : 0.53 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.002 PHE A 96 TYR 0.024 0.001 TYR R 495 ARG 0.008 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 0.996 Fit side-chains REVERT: R 378 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8439 (mmtp) REVERT: R 467 ASP cc_start: 0.8205 (t70) cc_final: 0.7931 (t70) REVERT: H 3 GLN cc_start: 0.8052 (tt0) cc_final: 0.7330 (mm110) REVERT: L 4 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7055 (mtp) REVERT: L 7 SER cc_start: 0.8285 (m) cc_final: 0.7735 (p) REVERT: L 77 SER cc_start: 0.7472 (t) cc_final: 0.7197 (m) REVERT: L 103 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7725 (tpp80) REVERT: C 43 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7996 (ttpt) REVERT: C 65 LYS cc_start: 0.7681 (tttt) cc_final: 0.7340 (ttmt) REVERT: C 83 MET cc_start: 0.7909 (mtm) cc_final: 0.7497 (mtp) REVERT: C 84 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7561 (m-40) REVERT: C 89 GLU cc_start: 0.7895 (mp0) cc_final: 0.7312 (tm-30) REVERT: D 10 SER cc_start: 0.8890 (t) cc_final: 0.8523 (m) REVERT: D 42 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7606 (tttt) REVERT: D 45 LYS cc_start: 0.8448 (tttt) cc_final: 0.8231 (ttmm) REVERT: F 45 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7905 (tttt) REVERT: A 13 LYS cc_start: 0.8611 (mttt) cc_final: 0.8392 (mtpp) REVERT: A 104 ASP cc_start: 0.8083 (m-30) cc_final: 0.7842 (m-30) REVERT: B 45 LYS cc_start: 0.8191 (mttt) cc_final: 0.7841 (tttm) outliers start: 38 outliers final: 28 residues processed: 153 average time/residue: 0.8656 time to fit residues: 144.5383 Evaluate side-chains 159 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.0020 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 354 ASN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8703 Z= 0.349 Angle : 0.581 7.612 11818 Z= 0.303 Chirality : 0.046 0.147 1291 Planarity : 0.004 0.053 1514 Dihedral : 4.868 53.812 1217 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.19 % Allowed : 13.21 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.49 (0.26), residues: 1082 helix: -3.30 (0.78), residues: 21 sheet: 0.61 (0.23), residues: 453 loop : 0.37 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 49 HIS 0.005 0.002 HIS E 35 PHE 0.018 0.002 PHE A 96 TYR 0.030 0.002 TYR R 495 ARG 0.006 0.000 ARG L 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 0.981 Fit side-chains REVERT: R 378 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8467 (mmtp) REVERT: R 467 ASP cc_start: 0.8221 (t70) cc_final: 0.7959 (t70) REVERT: H 3 GLN cc_start: 0.8072 (tt0) cc_final: 0.7330 (mm110) REVERT: H 21 SER cc_start: 0.7921 (m) cc_final: 0.7432 (p) REVERT: L 4 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7065 (mtp) REVERT: L 7 SER cc_start: 0.8330 (m) cc_final: 0.7772 (p) REVERT: L 77 SER cc_start: 0.7577 (t) cc_final: 0.7341 (m) REVERT: L 103 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7788 (tpp80) REVERT: C 43 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8073 (ttpt) REVERT: C 65 LYS cc_start: 0.7724 (tttt) cc_final: 0.7332 (ttmt) REVERT: C 83 MET cc_start: 0.7864 (mtm) cc_final: 0.7558 (mtp) REVERT: C 84 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7976 (m-40) REVERT: C 89 GLU cc_start: 0.7995 (mp0) cc_final: 0.7404 (tm-30) REVERT: D 10 SER cc_start: 0.8904 (t) cc_final: 0.8507 (m) REVERT: D 42 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7562 (pttt) REVERT: D 45 LYS cc_start: 0.8462 (tttt) cc_final: 0.8236 (ttmm) REVERT: F 24 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7856 (ttm-80) REVERT: F 45 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7845 (tttt) REVERT: A 13 LYS cc_start: 0.8638 (mttt) cc_final: 0.8412 (mtpp) REVERT: B 45 LYS cc_start: 0.8204 (mttt) cc_final: 0.7818 (tttm) outliers start: 39 outliers final: 32 residues processed: 158 average time/residue: 0.8858 time to fit residues: 152.7564 Evaluate side-chains 168 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8703 Z= 0.223 Angle : 0.526 7.024 11818 Z= 0.276 Chirality : 0.043 0.140 1291 Planarity : 0.004 0.043 1514 Dihedral : 4.704 53.909 1217 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.65 % Allowed : 14.29 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.52 (0.26), residues: 1082 helix: -3.32 (0.75), residues: 21 sheet: 0.64 (0.23), residues: 452 loop : 0.39 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 49 HIS 0.005 0.001 HIS C 35 PHE 0.014 0.001 PHE A 96 TYR 0.024 0.001 TYR R 495 ARG 0.009 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 0.936 Fit side-chains REVERT: R 378 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8435 (mmtp) REVERT: R 406 GLU cc_start: 0.8331 (mp0) cc_final: 0.8121 (mp0) REVERT: R 467 ASP cc_start: 0.8204 (t70) cc_final: 0.7963 (t70) REVERT: H 3 GLN cc_start: 0.8026 (tt0) cc_final: 0.7325 (mm110) REVERT: H 21 SER cc_start: 0.7876 (m) cc_final: 0.7443 (p) REVERT: L 4 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7109 (mtp) REVERT: L 7 SER cc_start: 0.8332 (m) cc_final: 0.7771 (p) REVERT: L 77 SER cc_start: 0.7519 (t) cc_final: 0.7276 (m) REVERT: L 103 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7686 (tpp80) REVERT: C 43 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8084 (ttpt) REVERT: C 65 LYS cc_start: 0.7706 (tttt) cc_final: 0.7351 (ttmt) REVERT: C 83 MET cc_start: 0.7835 (mtm) cc_final: 0.7571 (mtp) REVERT: C 84 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7827 (m-40) REVERT: C 89 GLU cc_start: 0.7929 (mp0) cc_final: 0.7402 (tm-30) REVERT: D 10 SER cc_start: 0.8878 (t) cc_final: 0.8511 (m) REVERT: D 42 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7566 (pttt) REVERT: D 45 LYS cc_start: 0.8439 (tttt) cc_final: 0.8218 (ttmm) REVERT: F 24 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7817 (ttm-80) REVERT: F 45 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7873 (tttt) REVERT: A 13 LYS cc_start: 0.8610 (mttt) cc_final: 0.8392 (mtpp) REVERT: B 45 LYS cc_start: 0.8204 (mttt) cc_final: 0.7817 (tttm) outliers start: 34 outliers final: 27 residues processed: 151 average time/residue: 0.8672 time to fit residues: 143.1502 Evaluate side-chains 157 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 69 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8703 Z= 0.148 Angle : 0.481 6.660 11818 Z= 0.254 Chirality : 0.042 0.138 1291 Planarity : 0.004 0.042 1514 Dihedral : 4.466 52.673 1217 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.90 % Allowed : 15.04 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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 (0.26), residues: 1082 helix: -3.15 (0.80), residues: 21 sheet: 0.70 (0.24), residues: 459 loop : 0.53 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE A 80 TYR 0.019 0.001 TYR R 495 ARG 0.009 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.041 Fit side-chains REVERT: R 378 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8292 (mmtp) REVERT: R 467 ASP cc_start: 0.8196 (t70) cc_final: 0.7875 (t70) REVERT: H 3 GLN cc_start: 0.7996 (tt0) cc_final: 0.7325 (mm110) REVERT: L 4 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7140 (mtp) REVERT: L 7 SER cc_start: 0.8314 (m) cc_final: 0.7753 (p) REVERT: L 103 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7717 (tpp80) REVERT: C 43 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7992 (ttpt) REVERT: C 65 LYS cc_start: 0.7660 (tttt) cc_final: 0.7332 (ttmt) REVERT: C 83 MET cc_start: 0.7758 (mtm) cc_final: 0.7329 (mtp) REVERT: C 84 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7340 (m-40) REVERT: C 89 GLU cc_start: 0.7811 (mp0) cc_final: 0.7375 (tm-30) REVERT: D 3 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7835 (mp10) REVERT: D 10 SER cc_start: 0.8837 (t) cc_final: 0.8482 (m) REVERT: D 42 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7566 (pttt) REVERT: D 45 LYS cc_start: 0.8426 (tttt) cc_final: 0.8211 (ttmm) REVERT: F 45 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7901 (tttt) REVERT: A 13 LYS cc_start: 0.8583 (mttt) cc_final: 0.8369 (mtpp) REVERT: A 104 ASP cc_start: 0.8063 (m-30) cc_final: 0.7815 (m-30) REVERT: B 45 LYS cc_start: 0.8191 (mttt) cc_final: 0.7832 (tttm) outliers start: 27 outliers final: 19 residues processed: 144 average time/residue: 0.8784 time to fit residues: 137.7148 Evaluate side-chains 145 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115463 restraints weight = 9665.242| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.18 r_work: 0.3298 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8703 Z= 0.182 Angle : 0.495 6.579 11818 Z= 0.260 Chirality : 0.043 0.137 1291 Planarity : 0.004 0.043 1514 Dihedral : 4.412 52.544 1216 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.58 % Allowed : 15.68 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.67 (0.26), residues: 1082 helix: -3.17 (0.80), residues: 21 sheet: 0.72 (0.24), residues: 455 loop : 0.51 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE A 80 TYR 0.021 0.001 TYR R 495 ARG 0.009 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3657.41 seconds wall clock time: 66 minutes 16.42 seconds (3976.42 seconds total)