Starting phenix.real_space_refine on Thu Mar 13 01:23:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcz_15971/03_2025/8bcz_15971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcz_15971/03_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_15971/03_2025/8bcz_15971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcz_15971/03_2025/8bcz_15971.map" model { file = "/net/cci-nas-00/data/ceres_data/8bcz_15971/03_2025/8bcz_15971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcz_15971/03_2025/8bcz_15971.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5376 2.51 5 N 1433 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8505 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 811 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 7.32, per 1000 atoms: 0.86 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 27 sheets defined 8.5% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.644A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.057A pdb=" N TYR R 369 " --> pdb=" O TYR R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.743A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.335A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.689A pdb=" N VAL H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.653A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.928A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.670A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.571A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.776A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.569A pdb=" N LYS A 66 " --> pdb=" O PRO A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.774A pdb=" N THR A 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'R' and resid 334 through 335 removed outlier: 6.387A pdb=" N ASN R 334 " --> pdb=" O VAL R 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.641A pdb=" N MET H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.571A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.571A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.660A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.782A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.495A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.587A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.103A pdb=" N TYR E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.689A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.689A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.610A pdb=" N TRP A 38 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 52 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP A 36 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.610A pdb=" N TRP A 38 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 52 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP A 36 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.711A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 13 360 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.52 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: 36.660 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.370 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8703 Z= 0.176 Angle : 0.490 7.243 11818 Z= 0.265 Chirality : 0.042 0.155 1291 Planarity : 0.003 0.029 1514 Dihedral : 9.566 86.704 3088 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.18 % Allowed : 2.69 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1082 helix: -3.20 (0.71), residues: 26 sheet: 0.14 (0.23), residues: 475 loop : 0.65 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 111 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 96 TYR 0.022 0.001 TYR R 495 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.992 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: 0.7901 time to fit residues: 180.5174 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 : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain F residue 45 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.149614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114577 restraints weight = 9586.308| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.21 r_work: 0.3291 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8703 Z= 0.181 Angle : 0.491 4.868 11818 Z= 0.264 Chirality : 0.043 0.139 1291 Planarity : 0.004 0.029 1514 Dihedral : 4.426 49.468 1218 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.65 % Allowed : 10.63 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1082 helix: -3.25 (0.73), residues: 27 sheet: 0.41 (0.23), residues: 464 loop : 0.54 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 PHE 0.013 0.001 PHE A 96 TYR 0.024 0.001 TYR R 495 ARG 0.007 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.901 Fit side-chains REVERT: R 378 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8356 (mmtp) REVERT: H 3 GLN cc_start: 0.8248 (tt0) cc_final: 0.7388 (mm110) REVERT: H 21 SER cc_start: 0.7808 (m) cc_final: 0.7359 (p) REVERT: H 25 SER cc_start: 0.7964 (m) cc_final: 0.7740 (t) REVERT: H 116 THR cc_start: 0.8010 (p) cc_final: 0.7650 (t) REVERT: L 7 SER cc_start: 0.8147 (m) cc_final: 0.7610 (p) REVERT: L 77 SER cc_start: 0.7332 (t) cc_final: 0.6944 (m) REVERT: L 103 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7525 (tpp80) REVERT: C 43 LYS cc_start: 0.8385 (mmtt) cc_final: 0.8042 (ttpt) REVERT: C 65 LYS cc_start: 0.7941 (tttt) cc_final: 0.7604 (ttmt) REVERT: C 89 GLU cc_start: 0.8076 (mp0) cc_final: 0.7265 (tm-30) REVERT: C 101 SER cc_start: 0.8078 (t) cc_final: 0.7786 (m) REVERT: D 10 SER cc_start: 0.8775 (t) cc_final: 0.8220 (m) REVERT: D 45 LYS cc_start: 0.8268 (tttt) cc_final: 0.7813 (ttmm) REVERT: D 61 ARG cc_start: 0.7895 (ptt-90) cc_final: 0.7672 (ptt-90) REVERT: F 24 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7347 (ttm-80) REVERT: F 45 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7170 (tttt) REVERT: A 78 ASN cc_start: 0.7271 (t0) cc_final: 0.6857 (t0) REVERT: B 45 LYS cc_start: 0.8150 (mttt) cc_final: 0.7513 (tttm) outliers start: 34 outliers final: 18 residues processed: 174 average time/residue: 1.0613 time to fit residues: 201.8868 Evaluate side-chains 161 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.148769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114435 restraints weight = 9774.854| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.16 r_work: 0.3291 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8703 Z= 0.194 Angle : 0.487 5.634 11818 Z= 0.260 Chirality : 0.043 0.153 1291 Planarity : 0.004 0.030 1514 Dihedral : 4.471 50.205 1218 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.87 % Allowed : 11.60 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1082 helix: -3.07 (0.85), residues: 27 sheet: 0.46 (0.23), residues: 471 loop : 0.49 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.013 0.001 PHE A 96 TYR 0.023 0.001 TYR R 495 ARG 0.004 0.000 ARG L 3 *********************** 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 172 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.974 Fit side-chains REVERT: R 378 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8203 (mmtp) REVERT: R 467 ASP cc_start: 0.8343 (t70) cc_final: 0.7955 (t70) REVERT: R 498 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: H 3 GLN cc_start: 0.8201 (tt0) cc_final: 0.7398 (mm110) REVERT: H 21 SER cc_start: 0.7783 (m) cc_final: 0.7344 (p) REVERT: H 25 SER cc_start: 0.7904 (m) cc_final: 0.7696 (t) REVERT: H 88 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: H 116 THR cc_start: 0.8007 (p) cc_final: 0.7608 (t) REVERT: L 7 SER cc_start: 0.8154 (m) cc_final: 0.7562 (p) REVERT: L 103 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7560 (tpp80) REVERT: C 28 THR cc_start: 0.8136 (p) cc_final: 0.7936 (p) REVERT: C 43 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8034 (ttpt) REVERT: C 65 LYS cc_start: 0.7926 (tttt) cc_final: 0.7549 (ttmt) REVERT: C 84 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7538 (m-40) REVERT: C 89 GLU cc_start: 0.8018 (mp0) cc_final: 0.7246 (tm-30) REVERT: C 101 SER cc_start: 0.8142 (t) cc_final: 0.7783 (m) REVERT: D 10 SER cc_start: 0.8772 (t) cc_final: 0.8222 (m) REVERT: D 11 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7808 (pt) REVERT: D 42 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7283 (tttt) REVERT: D 45 LYS cc_start: 0.8237 (tttt) cc_final: 0.7748 (ttmm) REVERT: D 61 ARG cc_start: 0.7881 (ptt-90) cc_final: 0.7638 (ptt-90) REVERT: D 81 GLU cc_start: 0.7691 (pm20) cc_final: 0.7452 (pm20) REVERT: F 24 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7246 (ttm110) REVERT: F 45 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7042 (tttt) REVERT: A 13 LYS cc_start: 0.8570 (mttt) cc_final: 0.8020 (ttpp) REVERT: A 78 ASN cc_start: 0.7273 (t0) cc_final: 0.6797 (t0) REVERT: B 45 LYS cc_start: 0.8137 (mttt) cc_final: 0.7468 (tttm) outliers start: 36 outliers final: 19 residues processed: 161 average time/residue: 0.9749 time to fit residues: 170.0699 Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 498 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 GLU 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 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 100 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.146137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110605 restraints weight = 9758.878| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.21 r_work: 0.3234 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8703 Z= 0.311 Angle : 0.547 7.125 11818 Z= 0.288 Chirality : 0.045 0.164 1291 Planarity : 0.004 0.048 1514 Dihedral : 4.717 53.000 1216 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.19 % Allowed : 11.92 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1082 helix: -2.71 (1.05), residues: 21 sheet: 0.47 (0.23), residues: 461 loop : 0.38 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 111 HIS 0.005 0.002 HIS C 35 PHE 0.016 0.002 PHE A 96 TYR 0.029 0.002 TYR R 495 ARG 0.004 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: R 378 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8430 (mmtp) REVERT: R 467 ASP cc_start: 0.8361 (t70) cc_final: 0.8008 (t70) REVERT: H 3 GLN cc_start: 0.8214 (tt0) cc_final: 0.7441 (mm110) REVERT: H 21 SER cc_start: 0.7897 (m) cc_final: 0.7423 (p) REVERT: H 25 SER cc_start: 0.8000 (m) cc_final: 0.7771 (t) REVERT: L 7 SER cc_start: 0.8213 (m) cc_final: 0.7620 (p) REVERT: L 77 SER cc_start: 0.7462 (t) cc_final: 0.7165 (m) REVERT: L 103 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7583 (tpp80) REVERT: C 43 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8127 (ttpt) REVERT: C 65 LYS cc_start: 0.8014 (tttt) cc_final: 0.7625 (ttmt) REVERT: C 89 GLU cc_start: 0.8140 (mp0) cc_final: 0.7327 (tm-30) REVERT: D 10 SER cc_start: 0.8755 (t) cc_final: 0.8202 (m) REVERT: D 42 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7348 (tttt) REVERT: D 45 LYS cc_start: 0.8252 (tttt) cc_final: 0.7776 (ttmm) REVERT: D 61 ARG cc_start: 0.7905 (ptt-90) cc_final: 0.7697 (ptt-90) REVERT: F 45 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7081 (tttt) REVERT: A 13 LYS cc_start: 0.8554 (mttt) cc_final: 0.8002 (mtpp) REVERT: A 78 ASN cc_start: 0.7428 (t0) cc_final: 0.6746 (t0) REVERT: B 24 ARG cc_start: 0.7185 (mtt90) cc_final: 0.6747 (mtp-110) REVERT: B 45 LYS cc_start: 0.8163 (mttt) cc_final: 0.7481 (tttm) outliers start: 39 outliers final: 27 residues processed: 163 average time/residue: 0.9543 time to fit residues: 169.6121 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.148921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114402 restraints weight = 9615.993| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.17 r_work: 0.3277 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8703 Z= 0.195 Angle : 0.488 6.809 11818 Z= 0.260 Chirality : 0.043 0.143 1291 Planarity : 0.004 0.031 1514 Dihedral : 4.524 52.294 1216 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.76 % Allowed : 13.53 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1082 helix: -2.88 (0.92), residues: 21 sheet: 0.47 (0.23), residues: 473 loop : 0.39 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 49 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE A 96 TYR 0.023 0.001 TYR R 495 ARG 0.005 0.000 ARG L 3 *********************** 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 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.920 Fit side-chains REVERT: R 378 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8362 (mmtp) REVERT: H 3 GLN cc_start: 0.8122 (tt0) cc_final: 0.7327 (mm110) REVERT: H 21 SER cc_start: 0.7721 (m) cc_final: 0.7252 (p) REVERT: H 116 THR cc_start: 0.7992 (p) cc_final: 0.7590 (t) REVERT: L 7 SER cc_start: 0.8130 (m) cc_final: 0.7528 (p) REVERT: L 77 SER cc_start: 0.7503 (t) cc_final: 0.7157 (m) REVERT: L 103 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7522 (tpp80) REVERT: C 43 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8019 (ttpt) REVERT: C 65 LYS cc_start: 0.7937 (tttt) cc_final: 0.7563 (ttmt) REVERT: C 89 GLU cc_start: 0.8089 (mp0) cc_final: 0.7312 (tm-30) REVERT: D 10 SER cc_start: 0.8726 (t) cc_final: 0.8187 (m) REVERT: D 42 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7322 (tttt) REVERT: D 45 LYS cc_start: 0.8214 (tttt) cc_final: 0.7714 (ttmm) REVERT: E 102 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7657 (ptmt) REVERT: F 24 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7127 (ttt90) REVERT: F 45 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7073 (tttt) REVERT: A 13 LYS cc_start: 0.8516 (mttt) cc_final: 0.7954 (mtpp) REVERT: A 78 ASN cc_start: 0.7345 (t0) cc_final: 0.6762 (t0) REVERT: B 45 LYS cc_start: 0.8123 (mttt) cc_final: 0.7394 (tttm) outliers start: 35 outliers final: 24 residues processed: 160 average time/residue: 0.8653 time to fit residues: 150.9730 Evaluate side-chains 153 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.150085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115319 restraints weight = 9621.046| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.18 r_work: 0.3301 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8703 Z= 0.169 Angle : 0.484 7.964 11818 Z= 0.255 Chirality : 0.042 0.138 1291 Planarity : 0.004 0.043 1514 Dihedral : 4.425 52.110 1216 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.97 % Allowed : 13.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1082 helix: -2.93 (0.86), residues: 21 sheet: 0.60 (0.23), residues: 465 loop : 0.40 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.011 0.001 PHE A 96 TYR 0.021 0.001 TYR R 495 ARG 0.008 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: R 378 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8264 (mmtp) REVERT: H 3 GLN cc_start: 0.8149 (tt0) cc_final: 0.7411 (mm110) REVERT: L 7 SER cc_start: 0.8181 (m) cc_final: 0.7573 (p) REVERT: L 103 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7684 (tpp80) REVERT: C 43 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8064 (ttpt) REVERT: C 65 LYS cc_start: 0.7995 (tttt) cc_final: 0.7645 (ttmt) REVERT: C 89 GLU cc_start: 0.8015 (mp0) cc_final: 0.7322 (tm-30) REVERT: D 10 SER cc_start: 0.8727 (t) cc_final: 0.8204 (m) REVERT: D 42 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7411 (tttt) REVERT: D 45 LYS cc_start: 0.8234 (tttt) cc_final: 0.7753 (ttmm) REVERT: E 102 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7727 (ptmt) REVERT: F 45 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7136 (tttt) REVERT: A 13 LYS cc_start: 0.8526 (mttt) cc_final: 0.7901 (ttpp) REVERT: A 78 ASN cc_start: 0.7381 (t0) cc_final: 0.6874 (t0) REVERT: B 45 LYS cc_start: 0.8158 (mttt) cc_final: 0.7489 (tttm) outliers start: 37 outliers final: 25 residues processed: 150 average time/residue: 0.8883 time to fit residues: 145.4735 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 : 0.840 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.0370 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113166 restraints weight = 9717.067| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.19 r_work: 0.3270 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8703 Z= 0.240 Angle : 0.519 7.342 11818 Z= 0.271 Chirality : 0.044 0.144 1291 Planarity : 0.004 0.042 1514 Dihedral : 4.590 53.198 1216 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.19 % Allowed : 13.86 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1082 helix: -3.09 (0.83), residues: 21 sheet: 0.61 (0.23), residues: 462 loop : 0.34 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 49 HIS 0.005 0.001 HIS C 35 PHE 0.014 0.002 PHE A 96 TYR 0.025 0.002 TYR R 495 ARG 0.008 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.968 Fit side-chains REVERT: R 406 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7789 (mp0) REVERT: R 467 ASP cc_start: 0.8392 (t70) cc_final: 0.8040 (t70) REVERT: H 3 GLN cc_start: 0.8182 (tt0) cc_final: 0.7451 (mm110) REVERT: L 4 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.6917 (mtp) REVERT: L 7 SER cc_start: 0.8257 (m) cc_final: 0.7652 (p) REVERT: L 103 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7731 (tpp80) REVERT: C 43 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8136 (ttpt) REVERT: C 65 LYS cc_start: 0.8052 (tttt) cc_final: 0.7712 (ttmt) REVERT: C 84 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: C 89 GLU cc_start: 0.8044 (mp0) cc_final: 0.7308 (tm-30) REVERT: D 10 SER cc_start: 0.8762 (t) cc_final: 0.8238 (m) REVERT: D 42 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7366 (pttt) REVERT: D 45 LYS cc_start: 0.8284 (tttt) cc_final: 0.7827 (ttmm) REVERT: E 102 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7745 (ptmt) REVERT: F 24 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.6691 (ttp80) REVERT: F 45 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7121 (tttt) REVERT: F 70 ASP cc_start: 0.6593 (m-30) cc_final: 0.6366 (m-30) REVERT: A 13 LYS cc_start: 0.8545 (mttt) cc_final: 0.7921 (ttpp) REVERT: A 78 ASN cc_start: 0.7443 (t0) cc_final: 0.6824 (t0) REVERT: B 45 LYS cc_start: 0.8206 (mttt) cc_final: 0.7533 (tttm) outliers start: 39 outliers final: 27 residues processed: 148 average time/residue: 0.8538 time to fit residues: 138.3444 Evaluate side-chains 151 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.151129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116459 restraints weight = 9775.761| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.20 r_work: 0.3313 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8703 Z= 0.146 Angle : 0.475 7.016 11818 Z= 0.251 Chirality : 0.042 0.135 1291 Planarity : 0.004 0.036 1514 Dihedral : 4.400 52.481 1216 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.90 % Allowed : 15.47 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1082 helix: -3.04 (0.83), residues: 21 sheet: 0.61 (0.23), residues: 476 loop : 0.49 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.011 0.001 PHE A 80 TYR 0.019 0.001 TYR R 495 ARG 0.007 0.000 ARG B 24 *********************** 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 147 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.947 Fit side-chains REVERT: R 406 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7925 (mp0) REVERT: H 3 GLN cc_start: 0.8127 (tt0) cc_final: 0.7374 (mm110) REVERT: L 7 SER cc_start: 0.8137 (m) cc_final: 0.7503 (p) REVERT: L 103 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7649 (tpp80) REVERT: C 65 LYS cc_start: 0.7938 (tttt) cc_final: 0.7576 (ttmt) REVERT: C 83 MET cc_start: 0.7986 (mtm) cc_final: 0.7700 (mtp) REVERT: C 84 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7779 (m-40) REVERT: C 89 GLU cc_start: 0.7992 (mp0) cc_final: 0.7242 (tm-30) REVERT: D 10 SER cc_start: 0.8697 (t) cc_final: 0.8162 (m) REVERT: D 42 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7390 (tttt) REVERT: D 45 LYS cc_start: 0.8203 (tttt) cc_final: 0.7706 (ttmm) REVERT: E 102 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7741 (ptmt) REVERT: F 24 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6514 (ttp80) REVERT: F 45 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7050 (tttt) REVERT: F 70 ASP cc_start: 0.6331 (m-30) cc_final: 0.6081 (m-30) REVERT: A 13 LYS cc_start: 0.8490 (mttt) cc_final: 0.7828 (ttpp) REVERT: A 78 ASN cc_start: 0.7337 (t0) cc_final: 0.6833 (t0) REVERT: B 28 ASP cc_start: 0.8476 (t70) cc_final: 0.8228 (t70) REVERT: B 45 LYS cc_start: 0.8143 (mttt) cc_final: 0.7427 (tttm) outliers start: 27 outliers final: 22 residues processed: 139 average time/residue: 0.8557 time to fit residues: 129.7811 Evaluate side-chains 140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 84 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112726 restraints weight = 9861.640| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.16 r_work: 0.3238 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8703 Z= 0.335 Angle : 0.576 7.523 11818 Z= 0.299 Chirality : 0.045 0.150 1291 Planarity : 0.004 0.049 1514 Dihedral : 4.809 54.045 1216 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.87 % Allowed : 14.61 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1082 helix: -3.20 (0.82), residues: 21 sheet: 0.56 (0.23), residues: 460 loop : 0.31 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 49 HIS 0.005 0.002 HIS E 35 PHE 0.017 0.002 PHE A 96 TYR 0.028 0.002 TYR R 495 ARG 0.007 0.001 ARG L 3 *********************** 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 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.876 Fit side-chains REVERT: R 406 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8159 (mp0) REVERT: R 467 ASP cc_start: 0.8393 (t70) cc_final: 0.8019 (t70) REVERT: H 3 GLN cc_start: 0.8174 (tt0) cc_final: 0.7392 (mm110) REVERT: H 21 SER cc_start: 0.7799 (m) cc_final: 0.7308 (p) REVERT: L 4 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.6959 (mtp) REVERT: L 7 SER cc_start: 0.8250 (m) cc_final: 0.7632 (p) REVERT: L 103 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7663 (tpp80) REVERT: C 43 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8130 (ttpt) REVERT: C 65 LYS cc_start: 0.7973 (tttt) cc_final: 0.7593 (ttmt) REVERT: C 89 GLU cc_start: 0.8102 (mp0) cc_final: 0.7342 (tm-30) REVERT: D 10 SER cc_start: 0.8754 (t) cc_final: 0.8203 (m) REVERT: D 42 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7299 (pttt) REVERT: D 45 LYS cc_start: 0.8271 (tttt) cc_final: 0.7780 (ttmm) REVERT: E 102 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7688 (ptmt) REVERT: F 24 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.6673 (ttp80) REVERT: F 45 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7011 (tttt) REVERT: F 70 ASP cc_start: 0.6538 (m-30) cc_final: 0.6287 (m-30) REVERT: A 13 LYS cc_start: 0.8518 (mttt) cc_final: 0.7945 (mtpp) REVERT: A 78 ASN cc_start: 0.7424 (t0) cc_final: 0.6679 (t0) REVERT: B 45 LYS cc_start: 0.8156 (mttt) cc_final: 0.7428 (tttm) outliers start: 36 outliers final: 27 residues processed: 150 average time/residue: 0.9333 time to fit residues: 152.4077 Evaluate side-chains 154 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 4 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 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 31 optimal weight: 0.0030 chunk 85 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.0270 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN D 3 GLN A 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117700 restraints weight = 9619.075| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.19 r_work: 0.3342 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8703 Z= 0.132 Angle : 0.471 6.795 11818 Z= 0.249 Chirality : 0.042 0.132 1291 Planarity : 0.004 0.036 1514 Dihedral : 4.392 52.306 1216 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.36 % Allowed : 16.86 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1082 helix: -3.06 (0.83), residues: 21 sheet: 0.67 (0.24), residues: 459 loop : 0.43 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.010 0.001 PHE A 80 TYR 0.017 0.001 TYR R 495 ARG 0.008 0.001 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.006 Fit side-chains REVERT: R 406 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7905 (mp0) REVERT: H 3 GLN cc_start: 0.8104 (tt0) cc_final: 0.7415 (mm110) REVERT: L 7 SER cc_start: 0.8165 (m) cc_final: 0.7546 (p) REVERT: L 103 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7691 (tpp80) REVERT: C 43 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8077 (ttpt) REVERT: C 65 LYS cc_start: 0.7928 (tttt) cc_final: 0.7585 (ttmt) REVERT: C 83 MET cc_start: 0.8021 (mtm) cc_final: 0.7706 (mtp) REVERT: C 84 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7754 (m-40) REVERT: C 89 GLU cc_start: 0.7897 (mp0) cc_final: 0.7217 (tm-30) REVERT: C 101 SER cc_start: 0.8126 (t) cc_final: 0.7742 (m) REVERT: D 3 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7831 (mp10) REVERT: D 10 SER cc_start: 0.8723 (t) cc_final: 0.8195 (m) REVERT: D 42 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7463 (tttt) REVERT: D 45 LYS cc_start: 0.8232 (tttt) cc_final: 0.7761 (ttmm) REVERT: D 70 ASP cc_start: 0.8139 (m-30) cc_final: 0.7901 (m-30) REVERT: E 102 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7831 (ptmt) REVERT: F 45 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7107 (tttt) REVERT: F 72 THR cc_start: 0.8558 (m) cc_final: 0.8351 (t) REVERT: A 13 LYS cc_start: 0.8511 (mttt) cc_final: 0.7867 (ttpp) REVERT: A 78 ASN cc_start: 0.7287 (t0) cc_final: 0.6860 (t0) REVERT: B 45 LYS cc_start: 0.8159 (mttt) cc_final: 0.7467 (tttm) outliers start: 22 outliers final: 17 residues processed: 139 average time/residue: 0.9402 time to fit residues: 142.3509 Evaluate side-chains 141 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 ASN 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 70 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116039 restraints weight = 9789.820| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.20 r_work: 0.3311 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8703 Z= 0.181 Angle : 0.491 6.685 11818 Z= 0.258 Chirality : 0.043 0.138 1291 Planarity : 0.004 0.037 1514 Dihedral : 4.378 52.329 1215 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.47 % Allowed : 16.76 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1082 helix: -3.02 (0.85), residues: 21 sheet: 0.74 (0.24), residues: 456 loop : 0.43 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE A 96 TYR 0.021 0.001 TYR R 495 ARG 0.008 0.000 ARG L 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7125.24 seconds wall clock time: 125 minutes 15.80 seconds (7515.80 seconds total)