Starting phenix.real_space_refine (version: dev) on Fri Feb 17 00:54:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/02_2023/6hud_0274.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/02_2023/6hud_0274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/02_2023/6hud_0274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/02_2023/6hud_0274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/02_2023/6hud_0274.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/02_2023/6hud_0274.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 2905 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "B" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "C" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "E" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.74 Number of scatterers: 2905 At special positions: 0 Unit cell: (85.152, 71.847, 44.35, 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 15 16.00 O 625 8.00 N 470 7.00 C 1795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 91 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 91 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 91 " distance=2.02 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: 1.06 Conformation dependent library (CDL) restraints added in 422.2 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 54.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 6.345A pdb=" N MET A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET B 3 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET D 3 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.098A pdb=" N THR C 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 29 Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.453A pdb=" N HIS A 32 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN B 35 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 34 " --> pdb=" O GLN B 35 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS B 32 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN C 35 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL B 34 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS C 32 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLN D 35 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL C 34 " --> pdb=" O GLN D 35 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS D 32 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN E 35 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL D 34 " --> pdb=" O GLN E 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 73 removed outlier: 5.946A pdb=" N ILE A 67 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N SER B 70 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER A 69 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER A 71 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE B 67 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER C 70 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER B 69 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASN C 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER B 71 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE C 67 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER D 70 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER C 69 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN D 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER C 71 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE D 67 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER E 70 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER D 69 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN E 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER D 71 " --> pdb=" O ASN E 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 94 removed outlier: 8.851A pdb=" N THR A 77 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N GLY B 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER A 79 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS B 82 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 81 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLU B 84 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR A 83 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU B 86 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP A 85 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP B 88 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA A 87 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR B 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR A 89 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN B 92 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS A 91 " --> pdb=" O GLN B 92 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR B 94 " --> pdb=" O CYS A 91 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER A 93 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N THR B 77 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N GLY C 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER B 79 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LYS C 82 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 81 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU C 84 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR B 83 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU C 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 85 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP C 88 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA B 87 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N TYR C 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B 89 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLN C 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 91 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYR C 94 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER B 93 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE D 78 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER C 79 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N THR D 77 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLY E 80 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER D 79 " --> pdb=" O GLY E 80 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LYS E 82 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU D 81 " --> pdb=" O LYS E 82 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU E 84 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR D 83 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLU E 86 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP D 85 " --> pdb=" O GLU E 86 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP E 88 " --> pdb=" O ASP D 85 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA D 87 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR E 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR D 89 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN E 92 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 91 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N TYR E 94 " --> pdb=" O CYS D 91 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N SER D 93 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.526A pdb=" N ASN A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASN C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN D 97 " --> pdb=" O ASN E 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.766A pdb=" N PHE C 102 " --> pdb=" O GLY D 103 " (cutoff:3.500A) 53 hydrogen bonds defined for protein. 159 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: 0.67 Time building geometry restraints manager: 1.16 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: 930 1.34 - 1.46: 798 1.46 - 1.58: 1227 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 2975 Sorted by residual: bond pdb=" CB VAL D 34 " pdb=" CG1 VAL D 34 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 bond pdb=" CB VAL E 34 " pdb=" CG1 VAL E 34 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CB VAL A 34 " pdb=" CG1 VAL A 34 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.93e+00 bond pdb=" CG LEU A 81 " pdb=" CD2 LEU A 81 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.93e+00 bond pdb=" CG LEU D 81 " pdb=" CD2 LEU D 81 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 ... (remaining 2970 not shown) Histogram of bond angle deviations from ideal: 100.95 - 107.55: 136 107.55 - 114.16: 1599 114.16 - 120.76: 1187 120.76 - 127.36: 1083 127.36 - 133.96: 35 Bond angle restraints: 4040 Sorted by residual: angle pdb=" C GLN C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta sigma weight residual 122.36 114.51 7.85 1.60e+00 3.91e-01 2.41e+01 angle pdb=" C GLN D 35 " pdb=" N TRP D 36 " pdb=" CA TRP D 36 " ideal model delta sigma weight residual 122.36 114.52 7.84 1.60e+00 3.91e-01 2.40e+01 angle pdb=" C GLN B 35 " pdb=" N TRP B 36 " pdb=" CA TRP B 36 " ideal model delta sigma weight residual 122.36 114.55 7.81 1.60e+00 3.91e-01 2.38e+01 angle pdb=" C GLN A 35 " pdb=" N TRP A 36 " pdb=" CA TRP A 36 " ideal model delta sigma weight residual 122.36 114.55 7.81 1.60e+00 3.91e-01 2.38e+01 angle pdb=" C GLN E 35 " pdb=" N TRP E 36 " pdb=" CA TRP E 36 " ideal model delta sigma weight residual 122.36 114.59 7.77 1.60e+00 3.91e-01 2.36e+01 ... (remaining 4035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.86: 1316 6.86 - 13.72: 304 13.72 - 20.58: 70 20.58 - 27.44: 10 27.44 - 34.30: 5 Dihedral angle restraints: 1705 sinusoidal: 605 harmonic: 1100 Sorted by residual: dihedral pdb=" CA TYR D 33 " pdb=" C TYR D 33 " pdb=" N VAL D 34 " pdb=" CA VAL D 34 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TYR A 33 " pdb=" C TYR A 33 " pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TYR C 33 " pdb=" C TYR C 33 " pdb=" N VAL C 34 " pdb=" CA VAL C 34 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 1702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 275 0.050 - 0.100: 110 0.100 - 0.150: 35 0.150 - 0.200: 10 0.200 - 0.250: 5 Chirality restraints: 435 Sorted by residual: chirality pdb=" CG LEU B 81 " pdb=" CB LEU B 81 " pdb=" CD1 LEU B 81 " pdb=" CD2 LEU B 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU C 81 " pdb=" CB LEU C 81 " pdb=" CD1 LEU C 81 " pdb=" CD2 LEU C 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU D 81 " pdb=" CB LEU D 81 " pdb=" CD1 LEU D 81 " pdb=" CD2 LEU D 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 432 not shown) Planarity restraints: 515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 6 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO D 7 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 7 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 7 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO C 7 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 6 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO B 7 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " -0.034 5.00e-02 4.00e+02 ... (remaining 512 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 314 2.75 - 3.29: 2579 3.29 - 3.83: 4944 3.83 - 4.36: 5090 4.36 - 4.90: 9062 Nonbonded interactions: 21989 Sorted by model distance: nonbonded pdb=" O SER C 69 " pdb=" OG SER D 70 " model vdw 2.216 2.440 nonbonded pdb=" O SER A 69 " pdb=" OG SER B 70 " model vdw 2.243 2.440 nonbonded pdb=" O SER D 69 " pdb=" OG SER E 70 " model vdw 2.368 2.440 nonbonded pdb=" O SER B 69 " pdb=" OG SER C 70 " model vdw 2.384 2.440 nonbonded pdb=" ND1 HIS B 32 " pdb=" OG SER B 71 " model vdw 2.389 2.520 ... (remaining 21984 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1795 2.51 5 N 470 2.21 5 O 625 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 2.010 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: 0.000 Extract box with map and model: 6.660 Check model and map are aligned: 0.050 Process input model: 13.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.007 0.057 2975 Z= 0.480 Angle : 1.124 8.787 4040 Z= 0.649 Chirality : 0.066 0.250 435 Planarity : 0.008 0.062 515 Dihedral : 8.281 34.301 990 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.06 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.20), residues: 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1175 time to fit residues: 15.1602 Evaluate side-chains 58 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2975 Z= 0.210 Angle : 0.675 7.720 4040 Z= 0.367 Chirality : 0.047 0.151 435 Planarity : 0.004 0.037 515 Dihedral : 6.565 19.990 400 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.98 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.20), residues: 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.1254 time to fit residues: 10.6715 Evaluate side-chains 55 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2975 Z= 0.291 Angle : 0.684 7.620 4040 Z= 0.382 Chirality : 0.047 0.145 435 Planarity : 0.004 0.041 515 Dihedral : 6.566 20.117 400 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.98 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.20), residues: 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 0.1397 time to fit residues: 11.2424 Evaluate side-chains 53 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0270 time to fit residues: 0.5205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 2975 Z= 0.279 Angle : 0.655 6.391 4040 Z= 0.369 Chirality : 0.047 0.143 435 Planarity : 0.004 0.041 515 Dihedral : 6.409 19.420 400 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.97 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.20), residues: 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.1121 time to fit residues: 8.8715 Evaluate side-chains 52 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0412 time to fit residues: 0.5807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 2975 Z= 0.401 Angle : 0.753 6.714 4040 Z= 0.427 Chirality : 0.050 0.152 435 Planarity : 0.005 0.043 515 Dihedral : 6.811 20.957 400 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.06 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.19), residues: 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.1392 time to fit residues: 10.2833 Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0498 time to fit residues: 1.0354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2975 Z= 0.197 Angle : 0.624 6.852 4040 Z= 0.342 Chirality : 0.046 0.145 435 Planarity : 0.004 0.037 515 Dihedral : 6.136 21.455 400 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.00 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.19), residues: 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.369 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.1091 time to fit residues: 7.5693 Evaluate side-chains 48 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0406 time to fit residues: 0.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2975 Z= 0.189 Angle : 0.624 6.892 4040 Z= 0.335 Chirality : 0.046 0.132 435 Planarity : 0.004 0.036 515 Dihedral : 5.997 23.068 400 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.00 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.19), residues: 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.376 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1278 time to fit residues: 8.7456 Evaluate side-chains 45 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 2975 Z= 0.373 Angle : 0.750 6.643 4040 Z= 0.418 Chirality : 0.050 0.153 435 Planarity : 0.005 0.040 515 Dihedral : 6.573 21.665 400 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.10 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.19), residues: 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.345 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 0.1241 time to fit residues: 7.4424 Evaluate side-chains 43 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0328 time to fit residues: 0.5127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2975 Z= 0.187 Angle : 0.644 6.962 4040 Z= 0.343 Chirality : 0.046 0.133 435 Planarity : 0.004 0.036 515 Dihedral : 6.036 19.985 400 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.06 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.19), residues: 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.323 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.1186 time to fit residues: 7.3577 Evaluate side-chains 43 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2975 Z= 0.189 Angle : 0.648 6.875 4040 Z= 0.343 Chirality : 0.045 0.133 435 Planarity : 0.004 0.034 515 Dihedral : 5.924 21.134 400 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.03 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.19), residues: 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0942 time to fit residues: 5.8691 Evaluate side-chains 44 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 13 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.180650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.136938 restraints weight = 7874.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.138739 restraints weight = 5636.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.139521 restraints weight = 4337.930| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 2975 Z= 0.135 Angle : 0.610 6.897 4040 Z= 0.318 Chirality : 0.044 0.129 435 Planarity : 0.004 0.032 515 Dihedral : 5.610 20.298 400 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.02 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.19), residues: 365 =============================================================================== Job complete usr+sys time: 1049.30 seconds wall clock time: 20 minutes 3.36 seconds (1203.36 seconds total)