Starting phenix.real_space_refine on Fri Aug 22 23:06:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcz_15971/08_2025/8bcz_15971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcz_15971/08_2025/8bcz_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/cci-nas-00/data/ceres_data/8bcz_15971/08_2025/8bcz_15971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcz_15971/08_2025/8bcz_15971.map" model { file = "/net/cci-nas-00/data/ceres_data/8bcz_15971/08_2025/8bcz_15971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcz_15971/08_2025/8bcz_15971.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.07, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 476.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.58 Time building geometry restraints manager: 0.89 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: 0.00 - 1.45: 11609 1.45 - 2.90: 167 2.90 - 4.35: 37 4.35 - 5.79: 4 5.79 - 7.24: 1 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 3.040 nonbonded pdb=" O THR H 28 " pdb=" ND2 ASN H 32 " model vdw 2.265 3.120 nonbonded pdb=" NE2 HIS C 35 " pdb=" O TYR C 105 " model vdw 2.302 3.120 nonbonded pdb=" O SER C 52 " pdb=" NH1 ARG C 72 " model vdw 2.324 3.120 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.333 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- 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 8715 Z= 0.120 Angle : 0.490 7.243 11842 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG H 66 TYR 0.022 0.001 TYR R 495 PHE 0.014 0.001 PHE A 96 TRP 0.012 0.001 TRP E 111 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8703) covalent geometry : angle 0.48958 (11818) SS BOND : bond 0.00299 ( 12) SS BOND : angle 0.70006 ( 24) hydrogen bonds : bond 0.13455 ( 317) hydrogen bonds : angle 7.38592 ( 837) *********************** 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 to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.339 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: 0.3563 time to fit residues: 81.1823 Evaluate side-chains 154 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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** D 3 GLN D 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116126 restraints weight = 9698.645| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.15 r_work: 0.3307 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8715 Z= 0.105 Angle : 0.483 4.328 11842 Z= 0.259 Chirality : 0.043 0.139 1291 Planarity : 0.004 0.032 1514 Dihedral : 4.361 48.897 1218 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.33 % Allowed : 10.85 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1082 helix: -3.23 (0.73), residues: 27 sheet: 0.42 (0.23), residues: 465 loop : 0.55 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 24 TYR 0.022 0.001 TYR R 495 PHE 0.012 0.001 PHE A 80 TRP 0.009 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8703) covalent geometry : angle 0.48088 (11818) SS BOND : bond 0.00269 ( 12) SS BOND : angle 1.02064 ( 24) hydrogen bonds : bond 0.02584 ( 317) hydrogen bonds : angle 5.47779 ( 837) *********************** 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 185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.354 Fit side-chains REVERT: R 378 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8359 (mmtp) REVERT: H 3 GLN cc_start: 0.8244 (tt0) cc_final: 0.7402 (mm110) REVERT: H 25 SER cc_start: 0.7954 (m) cc_final: 0.7741 (t) REVERT: H 116 THR cc_start: 0.8003 (p) cc_final: 0.7654 (t) REVERT: L 7 SER cc_start: 0.8132 (m) cc_final: 0.7601 (p) REVERT: L 77 SER cc_start: 0.7352 (t) cc_final: 0.6969 (m) REVERT: L 103 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7522 (tpp80) REVERT: C 43 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8058 (ttpt) REVERT: C 65 LYS cc_start: 0.7961 (tttt) cc_final: 0.7630 (ttmt) REVERT: C 89 GLU cc_start: 0.8054 (mp0) cc_final: 0.7269 (tm-30) REVERT: C 101 SER cc_start: 0.8017 (t) cc_final: 0.7762 (m) REVERT: D 10 SER cc_start: 0.8790 (t) cc_final: 0.8241 (m) REVERT: D 45 LYS cc_start: 0.8266 (tttt) cc_final: 0.7816 (ttmm) REVERT: D 61 ARG cc_start: 0.7892 (ptt-90) cc_final: 0.7687 (ptt-90) REVERT: D 81 GLU cc_start: 0.7683 (pm20) cc_final: 0.7465 (pm20) REVERT: F 24 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7321 (ttm-80) REVERT: A 78 ASN cc_start: 0.7266 (t0) cc_final: 0.6865 (t0) REVERT: A 104 ASP cc_start: 0.7812 (m-30) cc_final: 0.7518 (m-30) REVERT: B 45 LYS cc_start: 0.8118 (mttt) cc_final: 0.7513 (tttm) outliers start: 31 outliers final: 18 residues processed: 174 average time/residue: 0.4375 time to fit residues: 82.6810 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 L residue 10 SER Chi-restraints excluded: chain C residue 12 VAL 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 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 82 LEU 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 71 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN D 34 ASN A 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115018 restraints weight = 9598.025| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.16 r_work: 0.3289 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8715 Z= 0.126 Angle : 0.493 5.591 11842 Z= 0.262 Chirality : 0.043 0.144 1291 Planarity : 0.004 0.032 1514 Dihedral : 4.242 34.675 1214 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.54 % Allowed : 11.39 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1082 helix: -3.06 (0.85), residues: 27 sheet: 0.45 (0.23), residues: 474 loop : 0.50 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.024 0.001 TYR R 495 PHE 0.014 0.002 PHE A 96 TRP 0.010 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8703) covalent geometry : angle 0.48927 (11818) SS BOND : bond 0.00485 ( 12) SS BOND : angle 1.38245 ( 24) hydrogen bonds : bond 0.02593 ( 317) hydrogen bonds : angle 5.25642 ( 837) *********************** 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 169 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: R 467 ASP cc_start: 0.8350 (t70) cc_final: 0.7968 (t70) REVERT: H 3 GLN cc_start: 0.8215 (tt0) cc_final: 0.7442 (mm110) REVERT: H 21 SER cc_start: 0.7831 (m) cc_final: 0.7408 (p) REVERT: H 116 THR cc_start: 0.8052 (p) cc_final: 0.7642 (t) REVERT: L 7 SER cc_start: 0.8175 (m) cc_final: 0.7577 (p) REVERT: L 103 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7596 (tpp80) REVERT: C 43 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8091 (ttpt) REVERT: C 65 LYS cc_start: 0.7958 (tttt) cc_final: 0.7599 (ttmt) REVERT: C 84 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7618 (m-40) REVERT: C 89 GLU cc_start: 0.8027 (mp0) cc_final: 0.7297 (tm-30) REVERT: C 101 SER cc_start: 0.8163 (t) cc_final: 0.7807 (m) REVERT: D 10 SER cc_start: 0.8793 (t) cc_final: 0.8257 (m) REVERT: D 11 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7858 (pt) REVERT: D 42 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7307 (tttt) REVERT: D 45 LYS cc_start: 0.8279 (tttt) cc_final: 0.7810 (ttmm) REVERT: D 61 ARG cc_start: 0.7952 (ptt-90) cc_final: 0.7706 (ptt-90) REVERT: D 81 GLU cc_start: 0.7698 (pm20) cc_final: 0.7472 (pm20) REVERT: F 45 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7152 (tttt) REVERT: A 13 LYS cc_start: 0.8588 (mttt) cc_final: 0.8036 (ttpp) REVERT: A 78 ASN cc_start: 0.7323 (t0) cc_final: 0.6827 (t0) REVERT: A 104 ASP cc_start: 0.7872 (m-30) cc_final: 0.7571 (m-30) REVERT: B 45 LYS cc_start: 0.8161 (mttt) cc_final: 0.7524 (tttm) outliers start: 33 outliers final: 18 residues processed: 158 average time/residue: 0.4361 time to fit residues: 74.6241 Evaluate side-chains 153 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 60 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 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU 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 92 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 0.0040 chunk 84 optimal weight: 6.9990 chunk 39 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 1.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113053 restraints weight = 9837.958| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.19 r_work: 0.3254 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8715 Z= 0.172 Angle : 0.533 7.047 11842 Z= 0.281 Chirality : 0.044 0.164 1291 Planarity : 0.004 0.042 1514 Dihedral : 4.359 35.441 1212 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.08 % Allowed : 11.60 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.26), residues: 1082 helix: -2.72 (1.02), residues: 21 sheet: 0.52 (0.23), residues: 461 loop : 0.45 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 3 TYR 0.027 0.002 TYR R 495 PHE 0.015 0.002 PHE A 96 TRP 0.011 0.002 TRP E 111 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8703) covalent geometry : angle 0.52946 (11818) SS BOND : bond 0.00597 ( 12) SS BOND : angle 1.52241 ( 24) hydrogen bonds : bond 0.02711 ( 317) hydrogen bonds : angle 5.41722 ( 837) *********************** 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 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: R 467 ASP cc_start: 0.8352 (t70) cc_final: 0.7999 (t70) REVERT: H 3 GLN cc_start: 0.8275 (tt0) cc_final: 0.7454 (mm110) REVERT: H 21 SER cc_start: 0.7837 (m) cc_final: 0.7392 (p) REVERT: L 7 SER cc_start: 0.8187 (m) cc_final: 0.7598 (p) REVERT: L 77 SER cc_start: 0.7462 (t) cc_final: 0.7144 (m) REVERT: L 103 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7583 (tpp80) REVERT: C 43 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8153 (ttpt) REVERT: C 65 LYS cc_start: 0.8009 (tttt) cc_final: 0.7640 (ttmt) REVERT: C 89 GLU cc_start: 0.8106 (mp0) cc_final: 0.7311 (tm-30) REVERT: D 10 SER cc_start: 0.8770 (t) cc_final: 0.8216 (m) REVERT: D 42 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7345 (tttt) REVERT: D 45 LYS cc_start: 0.8266 (tttt) cc_final: 0.7795 (ttmm) REVERT: F 45 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7189 (tttt) REVERT: A 13 LYS cc_start: 0.8605 (mttt) cc_final: 0.8029 (ttpp) REVERT: A 78 ASN cc_start: 0.7400 (t0) cc_final: 0.6758 (t0) REVERT: B 45 LYS cc_start: 0.8167 (mttt) cc_final: 0.7497 (tttm) outliers start: 38 outliers final: 27 residues processed: 159 average time/residue: 0.4296 time to fit residues: 74.0616 Evaluate side-chains 156 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 60 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 31 THR 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 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 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113376 restraints weight = 9783.683| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.19 r_work: 0.3272 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8715 Z= 0.152 Angle : 0.517 6.997 11842 Z= 0.272 Chirality : 0.044 0.145 1291 Planarity : 0.004 0.037 1514 Dihedral : 4.351 35.573 1212 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.44 % Allowed : 13.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.26), residues: 1082 helix: -2.88 (0.92), residues: 21 sheet: 0.52 (0.23), residues: 461 loop : 0.39 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 61 TYR 0.025 0.002 TYR R 495 PHE 0.013 0.002 PHE A 96 TRP 0.011 0.002 TRP A 49 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8703) covalent geometry : angle 0.51360 (11818) SS BOND : bond 0.00428 ( 12) SS BOND : angle 1.44351 ( 24) hydrogen bonds : bond 0.02601 ( 317) hydrogen bonds : angle 5.30903 ( 837) *********************** 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 to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: R 467 ASP cc_start: 0.8364 (t70) cc_final: 0.7998 (t70) REVERT: H 3 GLN cc_start: 0.8175 (tt0) cc_final: 0.7437 (mm110) REVERT: H 21 SER cc_start: 0.7846 (m) cc_final: 0.7409 (p) REVERT: H 116 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7646 (t) REVERT: L 7 SER cc_start: 0.8181 (m) cc_final: 0.7587 (p) REVERT: L 77 SER cc_start: 0.7521 (t) cc_final: 0.7202 (m) REVERT: L 103 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7583 (tpp80) REVERT: C 43 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8139 (ttpt) REVERT: C 65 LYS cc_start: 0.8027 (tttt) cc_final: 0.7674 (ttmt) REVERT: C 89 GLU cc_start: 0.8081 (mp0) cc_final: 0.7317 (tm-30) REVERT: D 10 SER cc_start: 0.8768 (t) cc_final: 0.8229 (m) REVERT: D 42 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7411 (tttt) REVERT: D 45 LYS cc_start: 0.8272 (tttt) cc_final: 0.7809 (ttmm) REVERT: E 102 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7750 (ptmt) REVERT: F 45 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7173 (tttt) REVERT: A 13 LYS cc_start: 0.8577 (mttt) cc_final: 0.7983 (ttpp) REVERT: A 78 ASN cc_start: 0.7416 (t0) cc_final: 0.6805 (t0) REVERT: B 45 LYS cc_start: 0.8188 (mttt) cc_final: 0.7510 (tttm) outliers start: 32 outliers final: 24 residues processed: 156 average time/residue: 0.4341 time to fit residues: 73.7014 Evaluate side-chains 154 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 60 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 31 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 7 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 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 15 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 360 ASN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115750 restraints weight = 9593.393| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.18 r_work: 0.3305 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8715 Z= 0.105 Angle : 0.483 8.368 11842 Z= 0.253 Chirality : 0.043 0.137 1291 Planarity : 0.003 0.027 1514 Dihedral : 4.143 35.027 1212 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.54 % Allowed : 13.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1082 helix: -2.90 (0.87), residues: 21 sheet: 0.63 (0.23), residues: 466 loop : 0.45 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 3 TYR 0.020 0.001 TYR R 495 PHE 0.011 0.001 PHE A 80 TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8703) covalent geometry : angle 0.48114 (11818) SS BOND : bond 0.00373 ( 12) SS BOND : angle 1.12549 ( 24) hydrogen bonds : bond 0.02390 ( 317) hydrogen bonds : angle 5.02909 ( 837) *********************** 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 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.300 Fit side-chains REVERT: H 3 GLN cc_start: 0.8128 (tt0) cc_final: 0.7390 (mm110) REVERT: H 116 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7598 (t) REVERT: L 4 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.6793 (mtp) REVERT: L 7 SER cc_start: 0.8134 (m) cc_final: 0.7526 (p) REVERT: L 103 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7669 (tpp80) REVERT: C 43 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8048 (ttpt) REVERT: C 65 LYS cc_start: 0.7986 (tttt) cc_final: 0.7638 (ttmt) REVERT: C 89 GLU cc_start: 0.7997 (mp0) cc_final: 0.7297 (tm-30) REVERT: D 10 SER cc_start: 0.8739 (t) cc_final: 0.8223 (m) REVERT: D 42 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7389 (tttt) REVERT: D 45 LYS cc_start: 0.8241 (tttt) cc_final: 0.7750 (ttmm) REVERT: E 102 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7732 (ptmt) REVERT: F 24 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.6568 (ttp80) REVERT: F 45 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7123 (tttt) REVERT: F 70 ASP cc_start: 0.6407 (m-30) cc_final: 0.6168 (m-30) REVERT: A 13 LYS cc_start: 0.8549 (mttt) cc_final: 0.7916 (ttpp) REVERT: A 78 ASN cc_start: 0.7353 (t0) cc_final: 0.6855 (t0) REVERT: B 45 LYS cc_start: 0.8152 (mttt) cc_final: 0.7461 (tttm) outliers start: 33 outliers final: 23 residues processed: 146 average time/residue: 0.3952 time to fit residues: 62.6547 Evaluate side-chains 146 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 60 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 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 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 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 3 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** D 3 GLN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115125 restraints weight = 9803.011| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.20 r_work: 0.3300 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8715 Z= 0.121 Angle : 0.496 7.274 11842 Z= 0.260 Chirality : 0.043 0.139 1291 Planarity : 0.004 0.030 1514 Dihedral : 4.190 35.304 1212 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.65 % Allowed : 14.07 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.26), residues: 1082 helix: -3.02 (0.84), residues: 21 sheet: 0.67 (0.24), residues: 465 loop : 0.47 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 3 TYR 0.022 0.001 TYR R 495 PHE 0.013 0.001 PHE A 96 TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8703) covalent geometry : angle 0.49420 (11818) SS BOND : bond 0.00340 ( 12) SS BOND : angle 1.07957 ( 24) hydrogen bonds : bond 0.02519 ( 317) hydrogen bonds : angle 5.05286 ( 837) *********************** 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 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.243 Fit side-chains REVERT: R 406 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7847 (mp0) REVERT: R 467 ASP cc_start: 0.8397 (t70) cc_final: 0.8079 (t70) REVERT: H 3 GLN cc_start: 0.8135 (tt0) cc_final: 0.7388 (mm110) REVERT: L 7 SER cc_start: 0.8142 (m) cc_final: 0.7525 (p) REVERT: L 103 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7659 (tpp80) REVERT: C 43 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8070 (ttpt) REVERT: C 65 LYS cc_start: 0.8007 (tttt) cc_final: 0.7599 (ttmt) REVERT: C 89 GLU cc_start: 0.7981 (mp0) cc_final: 0.7249 (tm-30) REVERT: D 10 SER cc_start: 0.8722 (t) cc_final: 0.8202 (m) REVERT: D 42 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7413 (tttt) REVERT: D 45 LYS cc_start: 0.8250 (tttt) cc_final: 0.7756 (ttmm) REVERT: E 102 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7755 (ptmt) REVERT: F 24 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.6557 (ttp80) REVERT: F 45 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7131 (tttt) REVERT: F 70 ASP cc_start: 0.6468 (m-30) cc_final: 0.6239 (m-30) REVERT: A 13 LYS cc_start: 0.8506 (mttt) cc_final: 0.7869 (ttpp) REVERT: A 78 ASN cc_start: 0.7375 (t0) cc_final: 0.6838 (t0) REVERT: B 45 LYS cc_start: 0.8154 (mttt) cc_final: 0.7454 (tttm) outliers start: 34 outliers final: 25 residues processed: 147 average time/residue: 0.3784 time to fit residues: 60.4193 Evaluate side-chains 147 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 75 SER 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 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 12 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.0030 chunk 70 optimal weight: 7.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- 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** D 3 GLN D 24 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113058 restraints weight = 9727.789| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.19 r_work: 0.3265 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8715 Z= 0.163 Angle : 0.534 7.057 11842 Z= 0.278 Chirality : 0.044 0.145 1291 Planarity : 0.004 0.041 1514 Dihedral : 4.401 35.969 1212 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.76 % Allowed : 13.86 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1082 helix: -3.15 (0.82), residues: 21 sheet: 0.67 (0.23), residues: 462 loop : 0.39 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 3 TYR 0.025 0.002 TYR R 495 PHE 0.015 0.002 PHE A 96 TRP 0.010 0.002 TRP A 49 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8703) covalent geometry : angle 0.53212 (11818) SS BOND : bond 0.00369 ( 12) SS BOND : angle 1.21324 ( 24) hydrogen bonds : bond 0.02639 ( 317) hydrogen bonds : angle 5.26682 ( 837) *********************** 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 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.285 Fit side-chains REVERT: R 406 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7910 (mp0) REVERT: R 467 ASP cc_start: 0.8403 (t70) cc_final: 0.8031 (t70) REVERT: H 3 GLN cc_start: 0.8167 (tt0) cc_final: 0.7399 (mm110) REVERT: H 21 SER cc_start: 0.7786 (m) cc_final: 0.7336 (p) REVERT: L 7 SER cc_start: 0.8167 (m) cc_final: 0.7541 (p) REVERT: L 103 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7668 (tpp80) REVERT: C 43 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8105 (ttpt) REVERT: C 65 LYS cc_start: 0.7982 (tttt) cc_final: 0.7634 (ttmt) REVERT: C 89 GLU cc_start: 0.8057 (mp0) cc_final: 0.7306 (tm-30) REVERT: D 10 SER cc_start: 0.8748 (t) cc_final: 0.8203 (m) REVERT: D 42 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7420 (tttt) REVERT: D 45 LYS cc_start: 0.8260 (tttt) cc_final: 0.7770 (ttmm) REVERT: E 102 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7714 (ptmt) REVERT: F 24 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.6593 (ttp80) REVERT: F 45 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7090 (tttt) REVERT: F 70 ASP cc_start: 0.6520 (m-30) cc_final: 0.6285 (m-30) REVERT: A 13 LYS cc_start: 0.8516 (mttt) cc_final: 0.7943 (mtpp) REVERT: A 78 ASN cc_start: 0.7422 (t0) cc_final: 0.6773 (t0) REVERT: B 45 LYS cc_start: 0.8171 (mttt) cc_final: 0.7456 (tttm) outliers start: 35 outliers final: 26 residues processed: 149 average time/residue: 0.3703 time to fit residues: 60.2004 Evaluate side-chains 153 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 75 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 0.5980 chunk 77 optimal weight: 0.0270 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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** D 3 GLN 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 = 0.150392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115586 restraints weight = 9670.336| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.19 r_work: 0.3300 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8715 Z= 0.112 Angle : 0.495 6.886 11842 Z= 0.260 Chirality : 0.043 0.138 1291 Planarity : 0.003 0.035 1514 Dihedral : 4.246 35.409 1212 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.22 % Allowed : 14.61 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1082 helix: -3.09 (0.82), residues: 21 sheet: 0.74 (0.24), residues: 462 loop : 0.45 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 3 TYR 0.021 0.001 TYR R 495 PHE 0.011 0.001 PHE A 80 TRP 0.010 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8703) covalent geometry : angle 0.49243 (11818) SS BOND : bond 0.00415 ( 12) SS BOND : angle 1.21186 ( 24) hydrogen bonds : bond 0.02446 ( 317) hydrogen bonds : angle 5.05430 ( 837) *********************** 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 149 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: R 406 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7816 (mp0) REVERT: R 467 ASP cc_start: 0.8413 (t70) cc_final: 0.8070 (t70) REVERT: H 3 GLN cc_start: 0.8149 (tt0) cc_final: 0.7393 (mm110) REVERT: H 116 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7605 (t) REVERT: L 7 SER cc_start: 0.8165 (m) cc_final: 0.7539 (p) REVERT: L 103 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7789 (tpp80) REVERT: C 43 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8065 (ttpt) REVERT: C 65 LYS cc_start: 0.7999 (tttt) cc_final: 0.7598 (ttmt) REVERT: C 83 MET cc_start: 0.8031 (mtm) cc_final: 0.7747 (mtp) REVERT: C 89 GLU cc_start: 0.8003 (mp0) cc_final: 0.7268 (tm-30) REVERT: D 10 SER cc_start: 0.8727 (t) cc_final: 0.8195 (m) REVERT: D 42 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7423 (tttt) REVERT: D 45 LYS cc_start: 0.8233 (tttt) cc_final: 0.7737 (ttmm) REVERT: E 102 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7753 (ptmt) REVERT: F 45 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7106 (tttt) REVERT: A 13 LYS cc_start: 0.8492 (mttt) cc_final: 0.7922 (mtpp) REVERT: A 78 ASN cc_start: 0.7387 (t0) cc_final: 0.6864 (t0) REVERT: B 45 LYS cc_start: 0.8155 (mttt) cc_final: 0.7449 (tttm) outliers start: 30 outliers final: 24 residues processed: 139 average time/residue: 0.4313 time to fit residues: 65.2457 Evaluate side-chains 142 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 75 SER 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 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 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 75 optimal weight: 0.0670 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115047 restraints weight = 9746.809| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.16 r_work: 0.3303 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8715 Z= 0.119 Angle : 0.502 6.771 11842 Z= 0.262 Chirality : 0.043 0.139 1291 Planarity : 0.004 0.037 1514 Dihedral : 4.241 35.343 1212 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.11 % Allowed : 14.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1082 helix: -3.09 (0.82), residues: 21 sheet: 0.73 (0.24), residues: 462 loop : 0.46 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 3 TYR 0.022 0.001 TYR R 495 PHE 0.012 0.001 PHE A 96 TRP 0.010 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8703) covalent geometry : angle 0.49923 (11818) SS BOND : bond 0.00367 ( 12) SS BOND : angle 1.20067 ( 24) hydrogen bonds : bond 0.02461 ( 317) hydrogen bonds : angle 5.03450 ( 837) ********************** 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 144 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.359 Fit side-chains REVERT: R 406 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7907 (mp0) REVERT: R 467 ASP cc_start: 0.8404 (t70) cc_final: 0.8064 (t70) REVERT: H 3 GLN cc_start: 0.8143 (tt0) cc_final: 0.7441 (mm110) REVERT: H 116 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7638 (t) REVERT: L 7 SER cc_start: 0.8193 (m) cc_final: 0.7571 (p) REVERT: L 103 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7826 (tpp80) REVERT: C 43 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8108 (ttpt) REVERT: C 65 LYS cc_start: 0.8033 (tttt) cc_final: 0.7644 (ttmt) REVERT: C 83 MET cc_start: 0.8077 (mtm) cc_final: 0.7801 (mtp) REVERT: C 89 GLU cc_start: 0.7978 (mp0) cc_final: 0.7307 (tm-30) REVERT: D 10 SER cc_start: 0.8751 (t) cc_final: 0.8225 (m) REVERT: D 42 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7445 (tttt) REVERT: D 45 LYS cc_start: 0.8268 (tttt) cc_final: 0.7800 (ttmm) REVERT: E 102 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7795 (ptmt) REVERT: F 24 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.6575 (ttp80) REVERT: F 45 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7144 (tttt) REVERT: F 70 ASP cc_start: 0.6498 (m-30) cc_final: 0.6284 (m-30) REVERT: A 13 LYS cc_start: 0.8523 (mttt) cc_final: 0.7964 (mtpp) REVERT: A 78 ASN cc_start: 0.7415 (t0) cc_final: 0.6892 (t0) REVERT: B 45 LYS cc_start: 0.8179 (mttt) cc_final: 0.7504 (tttm) outliers start: 29 outliers final: 26 residues processed: 133 average time/residue: 0.4447 time to fit residues: 64.3952 Evaluate side-chains 143 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 443 SER 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 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 75 SER 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 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 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 chunk 68 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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** D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117980 restraints weight = 9665.668| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.18 r_work: 0.3334 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8715 Z= 0.091 Angle : 0.471 6.665 11842 Z= 0.248 Chirality : 0.042 0.133 1291 Planarity : 0.003 0.036 1514 Dihedral : 4.056 34.700 1212 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.69 % Allowed : 15.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.26), residues: 1082 helix: -3.04 (0.83), residues: 21 sheet: 0.78 (0.24), residues: 459 loop : 0.52 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 3 TYR 0.018 0.001 TYR R 495 PHE 0.011 0.001 PHE A 80 TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8703) covalent geometry : angle 0.46936 (11818) SS BOND : bond 0.00314 ( 12) SS BOND : angle 1.08450 ( 24) hydrogen bonds : bond 0.02294 ( 317) hydrogen bonds : angle 4.81082 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.81 seconds wall clock time: 57 minutes 6.79 seconds (3426.79 seconds total)