Starting phenix.real_space_refine on Fri Nov 15 15:39:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0n_35104/11_2024/8i0n_35104.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0n_35104/11_2024/8i0n_35104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0n_35104/11_2024/8i0n_35104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0n_35104/11_2024/8i0n_35104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0n_35104/11_2024/8i0n_35104.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0n_35104/11_2024/8i0n_35104.cif" } resolution = 3.26 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= 0.000 sd= 0.040 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 32 5.16 5 C 5798 2.51 5 N 1546 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9141 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2775 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 333} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2767 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 28, 'TRANS': 333} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "I" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 799 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 6.08, per 1000 atoms: 0.67 Number of scatterers: 9141 At special positions: 0 Unit cell: (113.436, 168.104, 84.7354, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 10 15.00 O 1755 8.00 N 1546 7.00 C 5798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 22 sheets defined 5.6% alpha, 47.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.686A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 278 through 282 removed outlier: 4.114A pdb=" N ARG A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.912A pdb=" N LYS B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.700A pdb=" N ARG B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.108A pdb=" N ARG B 282 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.176A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 68 removed outlier: 3.640A pdb=" N LYS I 68 " --> pdb=" O ASP I 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 65 through 68' Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'I' and resid 90 through 94 removed outlier: 4.142A pdb=" N THR I 94 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.260A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.742A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.742A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 189 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.215A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 249 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 117 Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.750A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.750A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 183 through 189 Processing sheet with id=AB1, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.518A pdb=" N PHE B 349 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 249 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.892A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.892A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 6 through 10 Processing sheet with id=AB6, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.885A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER I 55 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N SER I 35 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.885A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER I 55 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N SER I 35 " --> pdb=" O SER I 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.505A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.874A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AC3, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.484A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.838A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1035 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: 2.92 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1767 1.33 - 1.45: 2226 1.45 - 1.57: 5284 1.57 - 1.69: 28 1.69 - 1.81: 42 Bond restraints: 9347 Sorted by residual: bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.616 0.101 2.00e-02 2.50e+03 2.56e+01 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 12561 2.52 - 5.04: 138 5.04 - 7.55: 20 7.55 - 10.07: 8 10.07 - 12.59: 6 Bond angle restraints: 12733 Sorted by residual: angle pdb=" N PRO B 360 " pdb=" CA PRO B 360 " pdb=" C PRO B 360 " ideal model delta sigma weight residual 110.70 103.37 7.33 1.22e+00 6.72e-01 3.61e+01 angle pdb=" CB TPO V 339 " pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 119.31 106.72 12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB TPO U 339 " pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 119.31 107.13 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB TPO V 336 " pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 119.31 107.38 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " pdb=" O1P TPO U 342 " ideal model delta sigma weight residual 100.43 112.33 -11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 12728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5117 17.97 - 35.94: 389 35.94 - 53.90: 77 53.90 - 71.87: 20 71.87 - 89.84: 16 Dihedral angle restraints: 5619 sinusoidal: 2151 harmonic: 3468 Sorted by residual: dihedral pdb=" CA GLU A 364 " pdb=" C GLU A 364 " pdb=" N VAL A 365 " pdb=" CA VAL A 365 " ideal model delta harmonic sigma weight residual 180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU B 206 " pdb=" CG GLU B 206 " pdb=" CD GLU B 206 " pdb=" OE1 GLU B 206 " ideal model delta sinusoidal sigma weight residual 0.00 87.52 -87.52 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA GLU B 364 " pdb=" C GLU B 364 " pdb=" N VAL B 365 " pdb=" CA VAL B 365 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1040 0.040 - 0.080: 260 0.080 - 0.121: 131 0.121 - 0.161: 18 0.161 - 0.201: 1 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CA PRO B 360 " pdb=" N PRO B 360 " pdb=" C PRO B 360 " pdb=" CB PRO B 360 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL A 84 " pdb=" N VAL A 84 " pdb=" C VAL A 84 " pdb=" CB VAL A 84 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1447 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 359 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C GLU A 359 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 359 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO A 360 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 337 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C ASP A 337 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 337 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU A 338 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 359 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C GLU B 359 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU B 359 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO B 360 " 0.010 2.00e-02 2.50e+03 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2245 2.80 - 3.32: 7626 3.32 - 3.85: 14136 3.85 - 4.37: 15956 4.37 - 4.90: 30113 Nonbonded interactions: 70076 Sorted by model distance: nonbonded pdb=" NH1 ARG B 76 " pdb=" OD1 ASP B 78 " model vdw 2.273 3.120 nonbonded pdb=" N GLU L 82 " pdb=" OE1 GLU L 82 " model vdw 2.284 3.120 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.317 3.040 nonbonded pdb=" O ALA B 301 " pdb=" OH TYR B 321 " model vdw 2.325 3.040 nonbonded pdb=" NZ LYS A 292 " pdb=" OG1 THR A 298 " model vdw 2.347 3.120 ... (remaining 70071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 175 or \ (resid 176 through 177 and (name N or name CA or name C or name O or name CB )) \ or resid 178 through 368)) selection = (chain 'B' and (resid 7 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 214 or (resid 215 and (name N or \ name CA or name C or name O or name CB )) or resid 216 through 336 or (resid 33 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 338 through \ 368)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 50 or (resid 51 through 52 and (name N \ or name CA or name C or name O or name CB )) or resid 53 through 107)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } 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: 0.010 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.006 0.110 9347 Z= 0.376 Angle : 0.714 12.591 12733 Z= 0.331 Chirality : 0.044 0.201 1450 Planarity : 0.004 0.040 1622 Dihedral : 14.608 89.840 3379 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.62 % Allowed : 12.13 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.08 (0.25), residues: 1160 helix: 0.07 (1.25), residues: 20 sheet: 0.53 (0.23), residues: 534 loop : -0.33 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 39 HIS 0.005 0.001 HIS A 353 PHE 0.013 0.002 PHE A 349 TYR 0.012 0.001 TYR M 92 ARG 0.008 0.001 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.141 Fit side-chains REVERT: B 204 ASP cc_start: 0.7870 (m-30) cc_final: 0.7634 (m-30) REVERT: L 43 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8207 (mmtp) REVERT: M 43 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8151 (mmtp) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.2603 time to fit residues: 34.2154 Evaluate side-chains 87 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9347 Z= 0.176 Angle : 0.546 4.867 12733 Z= 0.287 Chirality : 0.044 0.144 1450 Planarity : 0.004 0.030 1622 Dihedral : 5.876 66.853 1320 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.26 % Allowed : 10.79 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.36 (0.25), residues: 1160 helix: -0.01 (1.15), residues: 20 sheet: 0.74 (0.23), residues: 534 loop : -0.14 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 50 HIS 0.004 0.001 HIS A 353 PHE 0.012 0.002 PHE M 84 TYR 0.014 0.001 TYR A 21 ARG 0.004 0.000 ARG M 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.115 Fit side-chains REVERT: B 204 ASP cc_start: 0.7919 (m-30) cc_final: 0.7674 (m-30) REVERT: H 120 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8046 (p) REVERT: I 120 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8034 (p) REVERT: L 43 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8233 (mmtp) REVERT: L 82 GLU cc_start: 0.7098 (pm20) cc_final: 0.6851 (pm20) REVERT: M 43 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8156 (mmtp) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.2294 time to fit residues: 34.3082 Evaluate side-chains 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain U residue 335 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.0270 chunk 83 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN L 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9347 Z= 0.165 Angle : 0.512 7.797 12733 Z= 0.265 Chirality : 0.043 0.167 1450 Planarity : 0.003 0.027 1622 Dihedral : 5.357 62.864 1314 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.36 % Allowed : 12.23 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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 (0.25), residues: 1160 helix: 0.52 (1.08), residues: 24 sheet: 0.85 (0.23), residues: 534 loop : -0.09 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 PHE 0.009 0.001 PHE A 349 TYR 0.013 0.001 TYR B 249 ARG 0.006 0.000 ARG V 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.924 Fit side-chains REVERT: A 48 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5882 (tp) REVERT: B 29 ASP cc_start: 0.7962 (t0) cc_final: 0.7742 (t0) REVERT: B 204 ASP cc_start: 0.8007 (m-30) cc_final: 0.7770 (m-30) REVERT: H 120 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8079 (p) REVERT: I 120 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.7953 (p) REVERT: L 43 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8241 (mmtp) outliers start: 23 outliers final: 13 residues processed: 111 average time/residue: 0.2311 time to fit residues: 35.5375 Evaluate side-chains 102 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9347 Z= 0.138 Angle : 0.489 7.746 12733 Z= 0.249 Chirality : 0.042 0.136 1450 Planarity : 0.003 0.026 1622 Dihedral : 4.957 57.811 1312 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.47 % Allowed : 13.26 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.56 (0.25), residues: 1160 helix: 0.77 (1.07), residues: 24 sheet: 0.95 (0.24), residues: 532 loop : -0.11 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 50 HIS 0.004 0.001 HIS I 38 PHE 0.009 0.001 PHE A 349 TYR 0.015 0.001 TYR A 249 ARG 0.002 0.000 ARG M 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.134 Fit side-chains REVERT: A 48 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5887 (tp) REVERT: B 248 GLN cc_start: 0.8492 (tp40) cc_final: 0.8277 (tp40) REVERT: I 120 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7930 (p) REVERT: L 43 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8240 (mmtp) REVERT: M 43 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8198 (mmtp) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.2535 time to fit residues: 38.6110 Evaluate side-chains 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS L 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9347 Z= 0.255 Angle : 0.541 6.172 12733 Z= 0.278 Chirality : 0.044 0.145 1450 Planarity : 0.004 0.027 1622 Dihedral : 5.051 59.255 1312 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.60 % Allowed : 13.57 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.55 (0.26), residues: 1160 helix: 0.62 (1.05), residues: 24 sheet: 0.92 (0.24), residues: 530 loop : -0.08 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 50 HIS 0.006 0.001 HIS A 353 PHE 0.012 0.002 PHE M 99 TYR 0.017 0.002 TYR L 92 ARG 0.004 0.001 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 1.125 Fit side-chains REVERT: A 48 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5685 (tp) REVERT: B 248 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8259 (tp40) REVERT: H 120 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8100 (p) REVERT: I 120 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8035 (p) REVERT: L 43 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8302 (mmtp) REVERT: M 43 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8259 (mmtp) outliers start: 35 outliers final: 24 residues processed: 110 average time/residue: 0.2419 time to fit residues: 36.4805 Evaluate side-chains 111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9347 Z= 0.272 Angle : 0.549 7.293 12733 Z= 0.281 Chirality : 0.044 0.146 1450 Planarity : 0.004 0.028 1622 Dihedral : 5.047 58.480 1312 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.60 % Allowed : 13.87 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.51 (0.25), residues: 1160 helix: 0.63 (1.06), residues: 24 sheet: 0.88 (0.23), residues: 532 loop : -0.10 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.005 0.001 HIS A 353 PHE 0.011 0.002 PHE M 99 TYR 0.016 0.002 TYR L 92 ARG 0.006 0.001 ARG M 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 1.101 Fit side-chains REVERT: A 48 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5751 (tp) REVERT: B 75 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6456 (p90) REVERT: B 248 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8298 (tp40) REVERT: I 120 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8151 (p) REVERT: L 43 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8398 (mmtp) REVERT: M 43 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8234 (mmtp) outliers start: 35 outliers final: 25 residues processed: 105 average time/residue: 0.2421 time to fit residues: 35.3004 Evaluate side-chains 107 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9347 Z= 0.203 Angle : 0.515 5.780 12733 Z= 0.264 Chirality : 0.043 0.142 1450 Planarity : 0.004 0.027 1622 Dihedral : 4.864 55.538 1312 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.67 % Allowed : 15.72 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.55 (0.25), residues: 1160 helix: 0.64 (1.03), residues: 24 sheet: 0.90 (0.23), residues: 534 loop : -0.07 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 50 HIS 0.004 0.001 HIS A 353 PHE 0.009 0.001 PHE M 99 TYR 0.013 0.001 TYR L 92 ARG 0.006 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.072 Fit side-chains REVERT: A 48 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5763 (tp) REVERT: B 75 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6391 (p90) REVERT: B 248 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8311 (tp40) REVERT: H 90 ARG cc_start: 0.7470 (ttm110) cc_final: 0.7265 (ttm110) REVERT: H 92 GLU cc_start: 0.7941 (mm-30) cc_final: 0.6797 (pm20) REVERT: I 90 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7186 (ttm110) REVERT: I 92 GLU cc_start: 0.7966 (mm-30) cc_final: 0.6733 (pm20) REVERT: I 120 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (p) REVERT: L 43 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8379 (mmtp) REVERT: M 43 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8129 (mmtp) outliers start: 26 outliers final: 19 residues processed: 104 average time/residue: 0.2796 time to fit residues: 40.4006 Evaluate side-chains 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 9347 Z= 0.434 Angle : 0.627 6.236 12733 Z= 0.326 Chirality : 0.047 0.150 1450 Planarity : 0.005 0.041 1622 Dihedral : 5.229 56.150 1312 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.39 % Allowed : 15.52 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.20 (0.25), residues: 1160 helix: 0.35 (0.99), residues: 24 sheet: 0.71 (0.24), residues: 504 loop : -0.31 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 50 HIS 0.007 0.002 HIS A 353 PHE 0.015 0.002 PHE L 99 TYR 0.019 0.002 TYR L 92 ARG 0.007 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 1.173 Fit side-chains REVERT: A 48 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5827 (tp) REVERT: B 75 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6453 (p90) REVERT: B 189 GLN cc_start: 0.7674 (tp-100) cc_final: 0.7387 (tp40) REVERT: B 248 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8381 (tp40) REVERT: H 92 GLU cc_start: 0.8052 (mm-30) cc_final: 0.6849 (pm20) REVERT: I 92 GLU cc_start: 0.8089 (mm-30) cc_final: 0.6774 (pm20) REVERT: I 120 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8192 (p) REVERT: L 43 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8504 (mmtp) REVERT: M 18 ASP cc_start: 0.8889 (t0) cc_final: 0.8632 (t0) REVERT: M 43 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8239 (mmtp) outliers start: 33 outliers final: 26 residues processed: 104 average time/residue: 0.2517 time to fit residues: 36.1040 Evaluate side-chains 110 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 66 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9347 Z= 0.165 Angle : 0.511 6.395 12733 Z= 0.262 Chirality : 0.043 0.143 1450 Planarity : 0.004 0.033 1622 Dihedral : 4.799 50.954 1312 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.06 % Allowed : 16.65 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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 (0.25), residues: 1160 helix: 0.74 (1.04), residues: 24 sheet: 0.79 (0.23), residues: 534 loop : -0.17 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 50 HIS 0.004 0.001 HIS A 353 PHE 0.010 0.001 PHE L 84 TYR 0.015 0.001 TYR B 249 ARG 0.008 0.000 ARG M 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.177 Fit side-chains REVERT: A 48 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5761 (tp) REVERT: B 75 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6379 (p90) REVERT: H 92 GLU cc_start: 0.7956 (mm-30) cc_final: 0.6909 (pm20) REVERT: I 90 ARG cc_start: 0.7351 (ttm110) cc_final: 0.7112 (ttm110) REVERT: I 92 GLU cc_start: 0.8005 (mm-30) cc_final: 0.6857 (pm20) REVERT: L 18 ASP cc_start: 0.8851 (t0) cc_final: 0.8601 (t0) REVERT: L 25 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7564 (ttm110) REVERT: L 43 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8367 (mmtp) REVERT: M 43 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8166 (mmtp) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.2568 time to fit residues: 35.1432 Evaluate side-chains 99 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 104 optimal weight: 0.0370 chunk 90 optimal weight: 0.1980 chunk 9 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9347 Z= 0.135 Angle : 0.492 5.396 12733 Z= 0.250 Chirality : 0.042 0.142 1450 Planarity : 0.004 0.042 1622 Dihedral : 4.460 45.934 1312 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.64 % Allowed : 16.86 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1160 helix: 0.79 (1.04), residues: 24 sheet: 0.94 (0.24), residues: 528 loop : -0.13 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 50 HIS 0.003 0.001 HIS I 38 PHE 0.010 0.001 PHE M 84 TYR 0.015 0.001 TYR A 249 ARG 0.007 0.000 ARG H 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.291 Fit side-chains REVERT: B 75 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6458 (p90) REVERT: H 92 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7075 (pm20) REVERT: I 90 ARG cc_start: 0.7302 (ttm110) cc_final: 0.7071 (ttm110) REVERT: I 92 GLU cc_start: 0.7959 (mm-30) cc_final: 0.6892 (pm20) REVERT: L 25 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7551 (ttm110) REVERT: L 43 LYS cc_start: 0.8594 (mmmm) cc_final: 0.8360 (mmtp) REVERT: M 43 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8214 (mmtp) outliers start: 16 outliers final: 13 residues processed: 104 average time/residue: 0.2529 time to fit residues: 36.2494 Evaluate side-chains 102 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108718 restraints weight = 12899.953| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.76 r_work: 0.3162 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9347 Z= 0.319 Angle : 0.566 5.672 12733 Z= 0.290 Chirality : 0.044 0.148 1450 Planarity : 0.004 0.038 1622 Dihedral : 4.741 47.290 1312 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.85 % Allowed : 16.75 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.39 (0.25), residues: 1160 helix: 0.52 (1.00), residues: 24 sheet: 0.79 (0.24), residues: 530 loop : -0.17 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 50 HIS 0.005 0.001 HIS A 353 PHE 0.013 0.002 PHE L 99 TYR 0.013 0.002 TYR M 92 ARG 0.008 0.001 ARG H 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.11 seconds wall clock time: 39 minutes 37.57 seconds (2377.57 seconds total)