Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 19:18:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/08_2023/8bcz_15971.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/08_2023/8bcz_15971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/08_2023/8bcz_15971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/08_2023/8bcz_15971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/08_2023/8bcz_15971.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcz_15971/08_2023/8bcz_15971.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5376 2.51 5 N 1433 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 4.50, per 1000 atoms: 0.53 Number of scatterers: 8505 At special positions: 0 Unit cell: (91.2875, 102.972, 108.815, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1660 8.00 N 1433 7.00 C 5376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.1 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: 1.11 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: 2.66 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2726 1.34 - 1.46: 2284 1.46 - 1.58: 3645 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 8703 Sorted by residual: bond pdb=" N VAL L 58 " pdb=" CA VAL L 58 " ideal model delta sigma weight residual 1.468 1.459 0.009 1.05e-02 9.07e+03 7.07e-01 bond pdb=" CB PRO R 337 " pdb=" CG PRO R 337 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.90e-01 bond pdb=" C GLN B 38 " pdb=" N LYS B 39 " ideal model delta sigma weight residual 1.331 1.350 -0.019 2.83e-02 1.25e+03 4.43e-01 bond pdb=" C LEU H 111 " pdb=" N GLY H 112 " ideal model delta sigma weight residual 1.322 1.330 -0.008 1.20e-02 6.94e+03 4.14e-01 bond pdb=" CG LEU C 51 " pdb=" CD1 LEU C 51 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.50e-01 ... (remaining 8698 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 227 107.03 - 113.77: 4681 113.77 - 120.51: 3183 120.51 - 127.25: 3633 127.25 - 133.99: 94 Bond angle restraints: 11818 Sorted by residual: angle pdb=" N ASP A 103 " pdb=" CA ASP A 103 " pdb=" C ASP A 103 " ideal model delta sigma weight residual 112.97 109.66 3.31 1.06e+00 8.90e-01 9.73e+00 angle pdb=" CA TYR R 495 " pdb=" CB TYR R 495 " pdb=" CG TYR R 495 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.98e+00 angle pdb=" C GLN B 38 " pdb=" N LYS B 39 " pdb=" CA LYS B 39 " ideal model delta sigma weight residual 120.97 128.21 -7.24 2.84e+00 1.24e-01 6.50e+00 angle pdb=" N ILE A 50 " pdb=" CA ILE A 50 " pdb=" C ILE A 50 " ideal model delta sigma weight residual 110.74 108.62 2.12 9.10e-01 1.21e+00 5.42e+00 angle pdb=" N ALA F 51 " pdb=" CA ALA F 51 " pdb=" CB ALA F 51 " ideal model delta sigma weight residual 113.65 110.64 3.01 1.47e+00 4.63e-01 4.19e+00 ... (remaining 11813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4888 17.34 - 34.68: 189 34.68 - 52.02: 33 52.02 - 69.36: 4 69.36 - 86.70: 4 Dihedral angle restraints: 5118 sinusoidal: 1963 harmonic: 3155 Sorted by residual: dihedral pdb=" CA PHE A 96 " pdb=" C PHE A 96 " pdb=" N CYS A 97 " pdb=" CA CYS A 97 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS C 35 " pdb=" C HIS C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" N GLU L 55 " pdb=" CA GLU L 55 " pdb=" CB GLU L 55 " pdb=" CG GLU L 55 " ideal model delta sinusoidal sigma weight residual -180.00 -127.98 -52.02 3 1.50e+01 4.44e-03 9.07e+00 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 812 0.031 - 0.062: 322 0.062 - 0.093: 70 0.093 - 0.124: 78 0.124 - 0.155: 9 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA ILE A 39 " pdb=" N ILE A 39 " pdb=" C ILE A 39 " pdb=" CB ILE A 39 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE F 75 " pdb=" N ILE F 75 " pdb=" C ILE F 75 " pdb=" CB ILE F 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1288 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 495 " 0.014 2.00e-02 2.50e+03 9.14e-03 1.67e+00 pdb=" CG TYR R 495 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR R 495 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 495 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 495 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 495 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 495 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 86 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO H 87 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO H 87 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO H 87 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO D 80 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.015 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 605 2.74 - 3.28: 7740 3.28 - 3.82: 14232 3.82 - 4.36: 18047 4.36 - 4.90: 31291 Nonbonded interactions: 71915 Sorted by model distance: nonbonded pdb=" OG SER R 359 " pdb=" OD1 ASN R 394 " model vdw 2.204 2.440 nonbonded pdb=" O THR H 28 " pdb=" ND2 ASN H 32 " model vdw 2.265 2.520 nonbonded pdb=" NE2 HIS C 35 " pdb=" O TYR C 105 " model vdw 2.302 2.520 nonbonded pdb=" O SER C 52 " pdb=" NH1 ARG C 72 " model vdw 2.324 2.520 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.333 2.520 ... (remaining 71910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 25 or resid 27 through 30 or resid 32 or resid 3 \ 4 through 50 or resid 52 through 98 or resid 100 or resid 106 through 107 or res \ id 109 or resid 111 through 112 or resid 114 through 115 or resid 117 through 12 \ 1)) selection = (chain 'E' and (resid 2 through 25 or resid 27 through 30 or resid 32 or resid 3 \ 4 through 50 or resid 52 through 98 or resid 100 or resid 106 through 107 or res \ id 109 or resid 111 through 112 or resid 114 through 115 or resid 117 through 12 \ 1)) } ncs_group { reference = (chain 'D' and (resid 2 or resid 5 through 18 or resid 20 through 23 or resid 25 \ through 27 or resid 29 or resid 32 through 49 or resid 51 through 52 or resid 5 \ 4 or resid 57 through 64 or resid 66 through 72 or resid 74 through 75 or resid \ 77 through 82 or resid 84 through 90 or resid 97 through 99 or resid 101 through \ 102 or resid 106 through 107)) selection = (chain 'F' and (resid 2 or resid 5 through 18 or resid 20 through 23 or resid 25 \ through 27 or resid 29 or resid 32 through 49 or resid 51 through 52 or resid 5 \ 4 or resid 57 through 64 or resid 66 through 72 or resid 74 through 75 or resid \ 77 through 82 or resid 84 through 90 or resid 98 through 100 or resid 102 throug \ h 103 or resid 107 through 108)) selection = (chain 'L' and (resid 2 or resid 5 through 18 or resid 20 through 23 or resid 25 \ through 27 or resid 29 or resid 32 through 49 or resid 51 through 52 or resid 5 \ 4 or resid 57 through 64 or resid 66 through 72 or resid 74 through 75 or resid \ 77 through 82 or resid 84 through 90 or resid 97 through 99 or resid 101 through \ 102 or resid 106 through 107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 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: 13.890 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 24.630 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8703 Z= 0.176 Angle : 0.490 7.243 11818 Z= 0.265 Chirality : 0.042 0.155 1291 Planarity : 0.003 0.029 1514 Dihedral : 9.566 86.704 3088 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.18 % 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 0.976 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 208 average time/residue: 0.7779 time to fit residues: 177.7031 Evaluate side-chains 142 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 0.0010 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN D 3 GLN D 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8703 Z= 0.214 Angle : 0.502 5.489 11818 Z= 0.268 Chirality : 0.044 0.143 1291 Planarity : 0.004 0.035 1514 Dihedral : 4.022 17.688 1209 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 3.54 % 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: 0.40 (0.23), residues: 460 loop : 0.55 (0.27), residues: 595 *********************** 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 174 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 163 average time/residue: 0.8326 time to fit residues: 148.4590 Evaluate side-chains 150 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.0829 time to fit residues: 2.3608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 0.0060 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN A 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8703 Z= 0.239 Angle : 0.513 6.029 11818 Z= 0.273 Chirality : 0.044 0.144 1291 Planarity : 0.004 0.038 1514 Dihedral : 4.134 17.897 1209 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 4.94 % 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: -3.10 (0.86), residues: 27 sheet: 0.43 (0.23), residues: 465 loop : 0.47 (0.27), residues: 590 *********************** 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 174 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 0.960 Fit side-chains outliers start: 46 outliers final: 31 residues processed: 162 average time/residue: 0.8441 time to fit residues: 149.4251 Evaluate side-chains 153 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 25 residues processed: 6 average time/residue: 0.0889 time to fit residues: 2.3085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.0070 chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 8703 Z= 0.179 Angle : 0.480 5.993 11818 Z= 0.255 Chirality : 0.043 0.142 1291 Planarity : 0.003 0.028 1514 Dihedral : 3.976 16.655 1209 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 4.19 % 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: 0.53 (0.26), residues: 1082 helix: -3.11 (0.81), residues: 27 sheet: 0.53 (0.23), residues: 466 loop : 0.53 (0.27), residues: 589 *********************** 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 157 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.051 Fit side-chains outliers start: 39 outliers final: 29 residues processed: 150 average time/residue: 0.8063 time to fit residues: 133.0517 Evaluate side-chains 144 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.0788 time to fit residues: 1.7662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8703 Z= 0.247 Angle : 0.518 7.097 11818 Z= 0.274 Chirality : 0.044 0.150 1291 Planarity : 0.004 0.040 1514 Dihedral : 4.147 19.203 1209 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 4.62 % 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: -3.29 (0.71), residues: 27 sheet: 0.58 (0.23), residues: 458 loop : 0.45 (0.27), residues: 597 *********************** 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 165 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 0.995 Fit side-chains outliers start: 43 outliers final: 32 residues processed: 156 average time/residue: 0.8452 time to fit residues: 144.5288 Evaluate side-chains 151 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 0.0893 time to fit residues: 2.3040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.0050 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8703 Z= 0.173 Angle : 0.494 7.873 11818 Z= 0.259 Chirality : 0.043 0.136 1291 Planarity : 0.004 0.030 1514 Dihedral : 4.002 18.992 1209 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1082 helix: -3.00 (0.85), residues: 21 sheet: 0.74 (0.24), residues: 450 loop : 0.49 (0.27), residues: 611 *********************** 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 159 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.038 Fit side-chains outliers start: 42 outliers final: 28 residues processed: 151 average time/residue: 0.7883 time to fit residues: 130.8871 Evaluate side-chains 147 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.0822 time to fit residues: 1.7459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 0.0070 chunk 61 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 3 GLN A 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8703 Z= 0.135 Angle : 0.469 7.249 11818 Z= 0.247 Chirality : 0.042 0.134 1291 Planarity : 0.003 0.034 1514 Dihedral : 3.809 14.283 1209 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 3.97 % 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: 0.78 (0.26), residues: 1082 helix: -3.07 (0.83), residues: 21 sheet: 0.77 (0.24), residues: 457 loop : 0.61 (0.27), residues: 604 *********************** 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 161 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 0.948 Fit side-chains outliers start: 37 outliers final: 29 residues processed: 156 average time/residue: 0.7911 time to fit residues: 135.9511 Evaluate side-chains 146 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.0832 time to fit residues: 1.9391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 79 optimal weight: 0.0170 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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** A 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 8703 Z= 0.149 Angle : 0.479 7.007 11818 Z= 0.252 Chirality : 0.042 0.156 1291 Planarity : 0.004 0.047 1514 Dihedral : 3.851 17.301 1209 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 3.22 % 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: 0.83 (0.26), residues: 1082 helix: -3.08 (0.84), residues: 21 sheet: 0.79 (0.24), residues: 460 loop : 0.64 (0.28), residues: 601 *********************** 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 145 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.051 Fit side-chains outliers start: 30 outliers final: 29 residues processed: 142 average time/residue: 0.7920 time to fit residues: 124.1229 Evaluate side-chains 140 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 0.0767 time to fit residues: 1.5263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 8703 Z= 0.321 Angle : 0.571 7.106 11818 Z= 0.297 Chirality : 0.045 0.152 1291 Planarity : 0.004 0.056 1514 Dihedral : 4.312 18.284 1209 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 3.54 % 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: -3.30 (0.80), residues: 21 sheet: 0.76 (0.24), residues: 447 loop : 0.43 (0.27), residues: 614 *********************** 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 152 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 0.985 Fit side-chains outliers start: 33 outliers final: 26 residues processed: 149 average time/residue: 0.7457 time to fit residues: 123.6427 Evaluate side-chains 142 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 0.1052 time to fit residues: 1.8994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8703 Z= 0.193 Angle : 0.511 6.832 11818 Z= 0.269 Chirality : 0.043 0.148 1291 Planarity : 0.004 0.037 1514 Dihedral : 4.139 20.892 1209 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 3.22 % 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: 0.65 (0.26), residues: 1082 helix: -3.26 (0.79), residues: 21 sheet: 0.67 (0.24), residues: 456 loop : 0.52 (0.27), residues: 605 ********************** 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 143 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 0.965 Fit side-chains outliers start: 30 outliers final: 25 residues processed: 140 average time/residue: 0.7895 time to fit residues: 122.3321 Evaluate side-chains 136 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.0744 time to fit residues: 1.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114332 restraints weight = 9692.211| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.16 r_work: 0.3287 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8703 Z= 0.209 Angle : 0.517 6.732 11818 Z= 0.271 Chirality : 0.043 0.147 1291 Planarity : 0.004 0.039 1514 Dihedral : 4.124 18.705 1209 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 2.90 % 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: 0.65 (0.26), residues: 1082 helix: -3.27 (0.80), residues: 21 sheet: 0.68 (0.24), residues: 454 loop : 0.52 (0.27), residues: 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.09 seconds wall clock time: 61 minutes 22.27 seconds (3682.27 seconds total)