Starting phenix.real_space_refine on Sat Jul 26 08:42:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcz_15971/07_2025/8bcz_15971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcz_15971/07_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_15971/07_2025/8bcz_15971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcz_15971/07_2025/8bcz_15971.map" model { file = "/net/cci-nas-00/data/ceres_data/8bcz_15971/07_2025/8bcz_15971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcz_15971/07_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-5711/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: 6.27, per 1000 atoms: 0.74 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: 2.17 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: 1.44 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: 2.68 Time building geometry restraints manager: 2.58 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: 3.440 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.370 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8715 Z= 0.120 Angle : 0.490 7.243 11842 Z= 0.265 Chirality : 0.042 0.155 1291 Planarity : 0.003 0.029 1514 Dihedral : 9.566 86.704 3088 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.18 % Allowed : 2.69 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.13455 ( 317) hydrogen bonds : angle 7.38592 ( 837) SS BOND : bond 0.00299 ( 12) SS BOND : angle 0.70006 ( 24) covalent geometry : bond 0.00270 ( 8703) covalent geometry : angle 0.48958 (11818) *********************** 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 : 0.970 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: 0.7886 time to fit residues: 180.0945 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 : 1.019 ------------------------------------------------------------------------------- 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: 0.0270 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.149588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114411 restraints weight = 9576.813| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.21 r_work: 0.3289 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8715 Z= 0.119 Angle : 0.493 4.708 11842 Z= 0.264 Chirality : 0.043 0.140 1291 Planarity : 0.004 0.034 1514 Dihedral : 4.428 49.384 1218 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.54 % Allowed : 10.74 % 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: 463 loop : 0.53 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 PHE 0.013 0.001 PHE A 96 TYR 0.024 0.001 TYR R 495 ARG 0.008 0.001 ARG F 24 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 317) hydrogen bonds : angle 5.57963 ( 837) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.10811 ( 24) covalent geometry : bond 0.00275 ( 8703) covalent geometry : angle 0.49126 (11818) *********************** 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 188 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.020 Fit side-chains REVERT: R 378 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8362 (mmtp) REVERT: H 3 GLN cc_start: 0.8244 (tt0) cc_final: 0.7393 (mm110) REVERT: H 21 SER cc_start: 0.7812 (m) cc_final: 0.7358 (p) REVERT: H 25 SER cc_start: 0.7966 (m) cc_final: 0.7737 (t) REVERT: H 116 THR cc_start: 0.8001 (p) cc_final: 0.7651 (t) REVERT: L 7 SER cc_start: 0.8125 (m) cc_final: 0.7597 (p) REVERT: L 77 SER cc_start: 0.7358 (t) cc_final: 0.6978 (m) REVERT: L 103 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7510 (tpp80) REVERT: C 43 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8047 (ttpt) REVERT: C 65 LYS cc_start: 0.7936 (tttt) cc_final: 0.7594 (ttmt) REVERT: C 89 GLU cc_start: 0.8083 (mp0) cc_final: 0.7259 (tm-30) REVERT: C 101 SER cc_start: 0.8080 (t) cc_final: 0.7788 (m) REVERT: D 10 SER cc_start: 0.8780 (t) cc_final: 0.8224 (m) REVERT: D 45 LYS cc_start: 0.8262 (tttt) cc_final: 0.7809 (ttmm) REVERT: D 61 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.7688 (ptt-90) REVERT: D 81 GLU cc_start: 0.7704 (pm20) cc_final: 0.7476 (pm20) REVERT: F 24 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7326 (ttm-80) REVERT: F 45 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7172 (tttt) REVERT: A 78 ASN cc_start: 0.7270 (t0) cc_final: 0.6846 (t0) REVERT: B 45 LYS cc_start: 0.8127 (mttt) cc_final: 0.7497 (tttm) outliers start: 33 outliers final: 18 residues processed: 176 average time/residue: 0.9252 time to fit residues: 177.0416 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 : 0.914 ------------------------------------------------------------------------------- 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: 0.0470 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 7 optimal weight: 0.1980 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 360 ASN C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119123 restraints weight = 9646.344| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.18 r_work: 0.3347 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8715 Z= 0.079 Angle : 0.449 5.316 11842 Z= 0.241 Chirality : 0.042 0.137 1291 Planarity : 0.003 0.028 1514 Dihedral : 4.207 48.853 1218 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.11 % Allowed : 11.71 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1082 helix: -3.02 (0.84), residues: 27 sheet: 0.59 (0.23), residues: 479 loop : 0.61 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 PHE 0.012 0.001 PHE R 392 TYR 0.016 0.001 TYR R 495 ARG 0.004 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02369 ( 317) hydrogen bonds : angle 4.99135 ( 837) SS BOND : bond 0.00300 ( 12) SS BOND : angle 1.16367 ( 24) covalent geometry : bond 0.00178 ( 8703) covalent geometry : angle 0.44595 (11818) *********************** 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 164 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.016 Fit side-chains REVERT: R 378 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8316 (mmtp) REVERT: H 3 GLN cc_start: 0.8230 (tt0) cc_final: 0.7454 (mm110) REVERT: H 116 THR cc_start: 0.8040 (p) cc_final: 0.7667 (t) REVERT: L 7 SER cc_start: 0.8158 (m) cc_final: 0.7557 (p) REVERT: L 103 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7529 (tpp80) REVERT: C 43 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8067 (ttpt) REVERT: C 65 LYS cc_start: 0.7942 (tttt) cc_final: 0.7605 (ttmt) REVERT: C 84 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7561 (m-40) REVERT: C 89 GLU cc_start: 0.7940 (mp0) cc_final: 0.7204 (tm-30) REVERT: D 10 SER cc_start: 0.8774 (t) cc_final: 0.8232 (m) REVERT: D 45 LYS cc_start: 0.8274 (tttt) cc_final: 0.7826 (ttmm) REVERT: D 81 GLU cc_start: 0.7662 (pm20) cc_final: 0.7439 (pm20) REVERT: F 45 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7312 (tttt) REVERT: A 78 ASN cc_start: 0.7200 (t0) cc_final: 0.6845 (t0) REVERT: B 45 LYS cc_start: 0.8124 (mttt) cc_final: 0.7537 (tttm) outliers start: 29 outliers final: 12 residues processed: 155 average time/residue: 0.9789 time to fit residues: 164.1012 Evaluate side-chains 140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 SER Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain D residue 60 SER 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 82 LEU 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: 5.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 506 GLN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112332 restraints weight = 9696.511| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.15 r_work: 0.3246 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8715 Z= 0.209 Angle : 0.563 7.725 11842 Z= 0.296 Chirality : 0.045 0.173 1291 Planarity : 0.004 0.046 1514 Dihedral : 4.641 52.076 1215 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.19 % Allowed : 12.24 % Favored : 83.57 % 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: -3.21 (0.79), residues: 27 sheet: 0.49 (0.23), residues: 470 loop : 0.41 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 111 HIS 0.005 0.002 HIS E 35 PHE 0.018 0.002 PHE A 96 TYR 0.029 0.002 TYR R 495 ARG 0.004 0.001 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 317) hydrogen bonds : angle 5.55305 ( 837) SS BOND : bond 0.00557 ( 12) SS BOND : angle 1.71599 ( 24) covalent geometry : bond 0.00504 ( 8703) covalent geometry : angle 0.55811 (11818) *********************** 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 : 0.921 Fit side-chains REVERT: R 378 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8420 (mmtp) REVERT: R 467 ASP cc_start: 0.8377 (t70) cc_final: 0.7999 (t70) REVERT: H 3 GLN cc_start: 0.8273 (tt0) cc_final: 0.7465 (mm110) REVERT: H 21 SER cc_start: 0.7861 (m) cc_final: 0.7384 (p) REVERT: L 7 SER cc_start: 0.8189 (m) cc_final: 0.7594 (p) REVERT: L 77 SER cc_start: 0.7476 (t) cc_final: 0.7166 (m) REVERT: L 103 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7588 (tpp80) REVERT: C 43 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8184 (ttpt) REVERT: C 65 LYS cc_start: 0.8032 (tttt) cc_final: 0.7675 (ttmt) REVERT: C 89 GLU cc_start: 0.8111 (mp0) cc_final: 0.7301 (tm-30) REVERT: D 10 SER cc_start: 0.8779 (t) cc_final: 0.8228 (m) REVERT: D 42 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7381 (tttt) REVERT: D 45 LYS cc_start: 0.8261 (tttt) cc_final: 0.7793 (ttmm) REVERT: F 45 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7068 (tttt) REVERT: A 13 LYS cc_start: 0.8557 (mttt) cc_final: 0.7974 (ttpp) REVERT: A 78 ASN cc_start: 0.7458 (t0) cc_final: 0.6754 (t0) REVERT: B 45 LYS cc_start: 0.8153 (mttt) cc_final: 0.7512 (tttm) outliers start: 39 outliers final: 27 residues processed: 162 average time/residue: 0.8867 time to fit residues: 156.6898 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 523 THR 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 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.0020 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.148728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114332 restraints weight = 9649.501| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.13 r_work: 0.3290 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8715 Z= 0.119 Angle : 0.487 6.566 11842 Z= 0.259 Chirality : 0.043 0.139 1291 Planarity : 0.003 0.028 1514 Dihedral : 4.426 52.110 1215 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.65 % Allowed : 13.86 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1082 helix: -2.89 (0.89), residues: 21 sheet: 0.53 (0.23), residues: 473 loop : 0.49 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.005 0.001 HIS C 35 PHE 0.011 0.001 PHE A 96 TYR 0.022 0.001 TYR R 495 ARG 0.004 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02469 ( 317) hydrogen bonds : angle 5.17876 ( 837) SS BOND : bond 0.00483 ( 12) SS BOND : angle 1.33575 ( 24) covalent geometry : bond 0.00282 ( 8703) covalent geometry : angle 0.48336 (11818) *********************** 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 164 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.887 Fit side-chains REVERT: R 378 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8356 (mmtp) REVERT: R 406 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8178 (mp0) REVERT: R 467 ASP cc_start: 0.8340 (t70) cc_final: 0.7978 (t70) REVERT: H 3 GLN cc_start: 0.8179 (tt0) cc_final: 0.7404 (mm110) REVERT: L 7 SER cc_start: 0.8146 (m) cc_final: 0.7545 (p) REVERT: L 77 SER cc_start: 0.7502 (t) cc_final: 0.7154 (m) REVERT: L 103 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7694 (tpp80) REVERT: C 43 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8024 (ttpt) REVERT: C 65 LYS cc_start: 0.7976 (tttt) cc_final: 0.7628 (ttmt) REVERT: C 89 GLU cc_start: 0.8014 (mp0) cc_final: 0.7255 (tm-30) REVERT: D 10 SER cc_start: 0.8747 (t) cc_final: 0.8188 (m) REVERT: D 42 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7366 (tttt) REVERT: D 45 LYS cc_start: 0.8220 (tttt) cc_final: 0.7728 (ttmm) REVERT: E 102 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7703 (ptmt) REVERT: F 24 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7535 (ttm110) REVERT: F 45 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7045 (tttt) REVERT: A 13 LYS cc_start: 0.8573 (mttt) cc_final: 0.7994 (ttpp) REVERT: A 78 ASN cc_start: 0.7352 (t0) cc_final: 0.6791 (t0) REVERT: B 45 LYS cc_start: 0.8122 (mttt) cc_final: 0.7448 (tttm) outliers start: 34 outliers final: 25 residues processed: 153 average time/residue: 0.8502 time to fit residues: 142.1025 Evaluate side-chains 150 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 31 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 101 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 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: 1.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.148380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113280 restraints weight = 9632.748| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.18 r_work: 0.3260 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8715 Z= 0.152 Angle : 0.514 6.272 11842 Z= 0.272 Chirality : 0.043 0.145 1291 Planarity : 0.004 0.038 1514 Dihedral : 4.543 53.675 1215 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 0.50 (0.26), residues: 1082 helix: -2.88 (0.90), residues: 21 sheet: 0.55 (0.23), residues: 465 loop : 0.42 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 49 HIS 0.004 0.001 HIS C 35 PHE 0.015 0.002 PHE A 96 TYR 0.025 0.001 TYR R 495 ARG 0.005 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02617 ( 317) hydrogen bonds : angle 5.26705 ( 837) SS BOND : bond 0.00398 ( 12) SS BOND : angle 1.29096 ( 24) covalent geometry : bond 0.00367 ( 8703) covalent geometry : angle 0.51104 (11818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.000 Fit side-chains REVERT: R 378 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8412 (mmtp) REVERT: R 467 ASP cc_start: 0.8359 (t70) cc_final: 0.7993 (t70) REVERT: H 3 GLN cc_start: 0.8188 (tt0) cc_final: 0.7425 (mm110) REVERT: L 4 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.6839 (mtp) REVERT: L 7 SER cc_start: 0.8187 (m) cc_final: 0.7587 (p) REVERT: L 103 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7699 (tpp80) REVERT: C 43 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8099 (ttpt) REVERT: C 65 LYS cc_start: 0.8003 (tttt) cc_final: 0.7651 (ttmt) REVERT: C 89 GLU cc_start: 0.8096 (mp0) cc_final: 0.7299 (tm-30) REVERT: D 10 SER cc_start: 0.8747 (t) cc_final: 0.8212 (m) REVERT: D 42 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7396 (tttt) REVERT: D 45 LYS cc_start: 0.8251 (tttt) cc_final: 0.7769 (ttmm) REVERT: E 102 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7699 (ptmt) REVERT: F 45 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7095 (tttt) REVERT: A 13 LYS cc_start: 0.8547 (mttt) cc_final: 0.7904 (ttpp) REVERT: A 78 ASN cc_start: 0.7404 (t0) cc_final: 0.6760 (t0) REVERT: B 45 LYS cc_start: 0.8170 (mttt) cc_final: 0.7481 (tttm) outliers start: 37 outliers final: 26 residues processed: 151 average time/residue: 1.2396 time to fit residues: 206.1784 Evaluate side-chains 154 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 523 THR 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 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 101 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 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: 0.7980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.149796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115036 restraints weight = 9667.023| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.17 r_work: 0.3294 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8715 Z= 0.117 Angle : 0.492 8.387 11842 Z= 0.258 Chirality : 0.043 0.138 1291 Planarity : 0.003 0.028 1514 Dihedral : 4.424 52.863 1215 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.76 % Allowed : 14.18 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1082 helix: -2.99 (0.85), residues: 21 sheet: 0.64 (0.24), residues: 465 loop : 0.48 (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 0.012 0.001 PHE A 96 TYR 0.022 0.001 TYR R 495 ARG 0.005 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02457 ( 317) hydrogen bonds : angle 5.07160 ( 837) SS BOND : bond 0.00349 ( 12) SS BOND : angle 1.08270 ( 24) covalent geometry : bond 0.00279 ( 8703) covalent geometry : angle 0.49009 (11818) *********************** 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 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.000 Fit side-chains REVERT: R 378 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8269 (mmtp) REVERT: R 467 ASP cc_start: 0.8343 (t70) cc_final: 0.8060 (t70) REVERT: H 3 GLN cc_start: 0.8182 (tt0) cc_final: 0.7406 (mm110) REVERT: L 4 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.6886 (mtp) REVERT: L 7 SER cc_start: 0.8172 (m) cc_final: 0.7559 (p) REVERT: L 103 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7673 (tpp80) REVERT: C 43 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8052 (ttpt) REVERT: C 65 LYS cc_start: 0.8018 (tttt) cc_final: 0.7621 (ttmt) REVERT: C 89 GLU cc_start: 0.8020 (mp0) cc_final: 0.7298 (tm-30) REVERT: D 10 SER cc_start: 0.8726 (t) cc_final: 0.8193 (m) REVERT: D 42 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7422 (tttt) REVERT: D 45 LYS cc_start: 0.8235 (tttt) cc_final: 0.7743 (ttmm) REVERT: E 102 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7759 (ptmt) REVERT: F 24 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7579 (ttm110) REVERT: F 45 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7072 (tttt) REVERT: A 13 LYS cc_start: 0.8510 (mttt) cc_final: 0.7869 (ttpp) REVERT: A 78 ASN cc_start: 0.7392 (t0) cc_final: 0.6833 (t0) REVERT: B 45 LYS cc_start: 0.8156 (mttt) cc_final: 0.7469 (tttm) outliers start: 35 outliers final: 24 residues processed: 146 average time/residue: 0.9621 time to fit residues: 152.8617 Evaluate side-chains 146 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 523 THR 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 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 101 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 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: 0.9980 chunk 78 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115080 restraints weight = 9776.992| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.19 r_work: 0.3288 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8715 Z= 0.118 Angle : 0.493 7.686 11842 Z= 0.260 Chirality : 0.043 0.139 1291 Planarity : 0.003 0.033 1514 Dihedral : 4.398 52.823 1215 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.87 % Allowed : 13.96 % 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: 0.64 (0.26), residues: 1082 helix: -3.08 (0.83), residues: 21 sheet: 0.67 (0.24), residues: 465 loop : 0.49 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE A 96 TYR 0.022 0.001 TYR R 495 ARG 0.006 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02516 ( 317) hydrogen bonds : angle 5.05227 ( 837) SS BOND : bond 0.00427 ( 12) SS BOND : angle 1.19622 ( 24) covalent geometry : bond 0.00281 ( 8703) covalent geometry : angle 0.49104 (11818) *********************** 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 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.979 Fit side-chains REVERT: R 378 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8284 (mmtp) REVERT: R 406 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7764 (mp0) REVERT: H 3 GLN cc_start: 0.8173 (tt0) cc_final: 0.7420 (mm110) REVERT: L 7 SER cc_start: 0.8170 (m) cc_final: 0.7539 (p) REVERT: L 103 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7680 (tpp80) REVERT: C 43 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8068 (ttpt) REVERT: C 65 LYS cc_start: 0.8028 (tttt) cc_final: 0.7691 (ttmt) REVERT: C 83 MET cc_start: 0.8056 (mtm) cc_final: 0.7761 (mtp) REVERT: C 89 GLU cc_start: 0.8006 (mp0) cc_final: 0.7259 (tm-30) REVERT: D 10 SER cc_start: 0.8738 (t) cc_final: 0.8221 (m) REVERT: D 42 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7447 (tttt) REVERT: D 45 LYS cc_start: 0.8265 (tttt) cc_final: 0.7779 (ttmm) REVERT: E 102 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7776 (ptmt) REVERT: F 24 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7527 (ttm110) REVERT: F 45 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7104 (tttt) REVERT: A 13 LYS cc_start: 0.8506 (mttt) cc_final: 0.7875 (ttpp) REVERT: A 78 ASN cc_start: 0.7401 (t0) cc_final: 0.6845 (t0) REVERT: B 45 LYS cc_start: 0.8167 (mttt) cc_final: 0.7487 (tttm) outliers start: 36 outliers final: 28 residues processed: 146 average time/residue: 0.9078 time to fit residues: 144.9906 Evaluate side-chains 149 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 523 THR 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 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 101 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 24 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114650 restraints weight = 9778.870| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.19 r_work: 0.3281 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8715 Z= 0.128 Angle : 0.503 7.509 11842 Z= 0.263 Chirality : 0.043 0.140 1291 Planarity : 0.004 0.036 1514 Dihedral : 4.450 53.104 1215 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.76 % Allowed : 14.07 % 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: 0.62 (0.26), residues: 1082 helix: -3.11 (0.82), residues: 21 sheet: 0.68 (0.24), residues: 463 loop : 0.46 (0.27), residues: 598 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 0.007 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02504 ( 317) hydrogen bonds : angle 5.08659 ( 837) SS BOND : bond 0.00380 ( 12) SS BOND : angle 1.19168 ( 24) covalent geometry : bond 0.00306 ( 8703) covalent geometry : angle 0.50055 (11818) *********************** 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 156 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.910 Fit side-chains REVERT: R 378 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8377 (mttp) REVERT: R 406 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7776 (mp0) REVERT: R 467 ASP cc_start: 0.8368 (t70) cc_final: 0.8053 (t70) REVERT: H 3 GLN cc_start: 0.8181 (tt0) cc_final: 0.7444 (mm110) REVERT: L 7 SER cc_start: 0.8163 (m) cc_final: 0.7527 (p) REVERT: L 103 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7705 (tpp80) REVERT: C 43 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8074 (ttpt) REVERT: C 65 LYS cc_start: 0.8031 (tttt) cc_final: 0.7701 (ttmt) REVERT: C 83 MET cc_start: 0.8073 (mtm) cc_final: 0.7791 (mtp) REVERT: C 89 GLU cc_start: 0.8035 (mp0) cc_final: 0.7299 (tm-30) REVERT: D 10 SER cc_start: 0.8744 (t) cc_final: 0.8216 (m) REVERT: D 42 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7455 (tttt) REVERT: D 45 LYS cc_start: 0.8257 (tttt) cc_final: 0.7783 (ttmm) REVERT: E 102 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7768 (ptmt) REVERT: F 24 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7541 (ttm110) REVERT: F 45 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7105 (tttt) REVERT: A 13 LYS cc_start: 0.8523 (mttt) cc_final: 0.7958 (mtpp) REVERT: A 78 ASN cc_start: 0.7400 (t0) cc_final: 0.6821 (t0) REVERT: B 45 LYS cc_start: 0.8165 (mttt) cc_final: 0.7480 (tttm) outliers start: 35 outliers final: 27 residues processed: 145 average time/residue: 0.8502 time to fit residues: 134.4828 Evaluate side-chains 148 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 101 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: 0.0970 chunk 85 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 44 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.152713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118451 restraints weight = 9628.182| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.18 r_work: 0.3342 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 8715 Z= 0.085 Angle : 0.466 7.448 11842 Z= 0.246 Chirality : 0.042 0.133 1291 Planarity : 0.003 0.037 1514 Dihedral : 4.241 51.616 1215 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.90 % Allowed : 14.82 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1082 helix: -3.04 (0.83), residues: 21 sheet: 0.73 (0.24), residues: 469 loop : 0.56 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.011 0.001 PHE A 80 TYR 0.018 0.001 TYR R 495 ARG 0.008 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02288 ( 317) hydrogen bonds : angle 4.78909 ( 837) SS BOND : bond 0.00345 ( 12) SS BOND : angle 1.02339 ( 24) covalent geometry : bond 0.00197 ( 8703) covalent geometry : angle 0.46409 (11818) ********************** 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 152 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.885 Fit side-chains REVERT: R 378 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8254 (mmtp) REVERT: R 406 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7869 (mp0) REVERT: R 467 ASP cc_start: 0.8354 (t70) cc_final: 0.7959 (t70) REVERT: H 3 GLN cc_start: 0.8136 (tt0) cc_final: 0.7433 (mm110) REVERT: L 7 SER cc_start: 0.8162 (m) cc_final: 0.7537 (p) REVERT: L 103 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7713 (tpp80) REVERT: C 65 LYS cc_start: 0.7998 (tttt) cc_final: 0.7634 (ttmt) REVERT: C 89 GLU cc_start: 0.7867 (mp0) cc_final: 0.7248 (tm-30) REVERT: D 3 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7852 (mp10) REVERT: D 10 SER cc_start: 0.8743 (t) cc_final: 0.8234 (m) REVERT: D 42 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7471 (tttt) REVERT: D 45 LYS cc_start: 0.8250 (tttt) cc_final: 0.7781 (ttmm) REVERT: E 102 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7847 (ptmt) REVERT: F 24 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7477 (ttm110) REVERT: F 45 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7141 (tttt) REVERT: A 13 LYS cc_start: 0.8538 (mttt) cc_final: 0.7921 (ttpp) REVERT: A 78 ASN cc_start: 0.7299 (t0) cc_final: 0.6880 (t0) REVERT: B 45 LYS cc_start: 0.8158 (mttt) cc_final: 0.7506 (tttm) outliers start: 27 outliers final: 22 residues processed: 142 average time/residue: 0.9069 time to fit residues: 140.1265 Evaluate side-chains 141 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 14 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 101 SER 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 D residue 63 SER Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 0.0020 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 506 GLN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3798 r_free = 0.3798 target = 0.152706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117952 restraints weight = 9769.206| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.21 r_work: 0.3340 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8715 Z= 0.094 Angle : 0.474 7.275 11842 Z= 0.250 Chirality : 0.042 0.135 1291 Planarity : 0.003 0.036 1514 Dihedral : 4.257 51.182 1215 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.58 % Allowed : 16.00 % Favored : 81.42 % 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: 0.77 (0.27), residues: 1082 helix: -3.02 (0.84), residues: 21 sheet: 0.75 (0.24), residues: 469 loop : 0.59 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.004 0.001 HIS C 35 PHE 0.011 0.001 PHE A 80 TYR 0.019 0.001 TYR R 495 ARG 0.008 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.02352 ( 317) hydrogen bonds : angle 4.78523 ( 837) SS BOND : bond 0.00320 ( 12) SS BOND : angle 1.01138 ( 24) covalent geometry : bond 0.00223 ( 8703) covalent geometry : angle 0.47220 (11818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7079.67 seconds wall clock time: 123 minutes 57.54 seconds (7437.54 seconds total)