Starting phenix.real_space_refine on Thu Jul 31 05:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kex_22842/07_2025/7kex_22842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kex_22842/07_2025/7kex_22842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2025/7kex_22842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2025/7kex_22842.map" model { file = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2025/7kex_22842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2025/7kex_22842.cif" } resolution = 4.25 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= -0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 8181 2.51 5 N 2163 2.21 5 O 2517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12909 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "K" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: O, Q, J, L, C, B, P, R, I, H, D, F Time building chain proxies: 6.45, per 1000 atoms: 0.50 Number of scatterers: 12909 At special positions: 0 Unit cell: (136.85, 146.05, 118.45, 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 48 16.00 O 2517 8.00 N 2163 7.00 C 8181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 228 " " NAG A 402 " - " ASN A 238 " " NAG B 401 " - " ASN B 228 " " NAG B 402 " - " ASN B 238 " " NAG C 401 " - " ASN C 228 " " NAG C 402 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 20.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 101 through 104 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 527 through 532 removed outlier: 4.305A pdb=" N ALA D 530 " --> pdb=" O ILE D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.316A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 4.074A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 51 through 53 No H-bonds generated for 'chain 'K' and resid 51 through 53' Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 101 through 104 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 527 through 532 removed outlier: 4.304A pdb=" N ALA E 530 " --> pdb=" O ILE E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.315A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 4.073A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 101 through 104 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 527 through 532 removed outlier: 4.305A pdb=" N ALA F 530 " --> pdb=" O ILE F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.316A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 4.074A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.658A pdb=" N TYR G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG G 50 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR G 60 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 274 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.927A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 159 through 161 removed outlier: 5.656A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.865A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.644A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.658A pdb=" N TYR H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG H 50 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR H 60 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 274 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.927A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 159 through 161 removed outlier: 5.657A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.866A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.644A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR L 50 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.659A pdb=" N TYR I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG I 50 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR I 60 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 274 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.926A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 159 through 161 removed outlier: 5.657A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AD5, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.866A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.645A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1179 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: 4.01 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2316 1.31 - 1.45: 4144 1.45 - 1.58: 6590 1.58 - 1.72: 90 1.72 - 1.85: 60 Bond restraints: 13200 Sorted by residual: bond pdb=" CB PHE H 108 " pdb=" CG PHE H 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.04e+01 bond pdb=" CB ILE B 185 " pdb=" CG1 ILE B 185 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PHE G 108 " pdb=" CG PHE G 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.02e+01 bond pdb=" CB PHE I 108 " pdb=" CG PHE I 108 " ideal model delta sigma weight residual 1.502 1.357 0.145 2.30e-02 1.89e+03 3.99e+01 bond pdb=" CB ILE C 185 " pdb=" CG1 ILE C 185 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 13195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 14402 2.19 - 4.38: 2896 4.38 - 6.57: 529 6.57 - 8.76: 92 8.76 - 10.95: 15 Bond angle restraints: 17934 Sorted by residual: angle pdb=" C PRO B 93 " pdb=" N PRO B 94 " pdb=" CA PRO B 94 " ideal model delta sigma weight residual 120.31 127.77 -7.46 9.80e-01 1.04e+00 5.80e+01 angle pdb=" C PRO A 93 " pdb=" N PRO A 94 " pdb=" CA PRO A 94 " ideal model delta sigma weight residual 120.31 127.74 -7.43 9.80e-01 1.04e+00 5.75e+01 angle pdb=" C PRO C 93 " pdb=" N PRO C 94 " pdb=" CA PRO C 94 " ideal model delta sigma weight residual 120.31 127.70 -7.39 9.80e-01 1.04e+00 5.69e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.37e+01 angle pdb=" C GLY E 536 " pdb=" N PRO E 537 " pdb=" CA PRO E 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.36e+01 ... (remaining 17929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 7759 21.44 - 42.89: 167 42.89 - 64.33: 51 64.33 - 85.78: 60 85.78 - 107.22: 30 Dihedral angle restraints: 8067 sinusoidal: 3456 harmonic: 4611 Sorted by residual: dihedral pdb=" C3 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.60 107.22 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C3 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.59 107.21 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C3 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.56 107.18 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1347 0.095 - 0.189: 500 0.189 - 0.284: 144 0.284 - 0.379: 43 0.379 - 0.474: 36 Chirality restraints: 2070 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 ... (remaining 2067 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " 0.055 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN C 228 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " -0.055 2.00e-02 2.50e+03 5.65e-02 4.00e+01 pdb=" CG ASN B 228 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.054 2.00e-02 2.50e+03 5.64e-02 3.97e+01 pdb=" CG ASN A 228 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.068 2.00e-02 2.50e+03 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 106 2.59 - 3.17: 11047 3.17 - 3.75: 20636 3.75 - 4.32: 30381 4.32 - 4.90: 46676 Nonbonded interactions: 108846 Sorted by model distance: nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 89 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 89 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " model vdw 2.020 3.760 ... (remaining 108841 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: 0.08 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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 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: 1.390 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.090 Find NCS groups from input model: 0.220 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.022 0.146 13228 Z= 1.133 Angle : 1.891 10.947 18017 Z= 1.227 Chirality : 0.123 0.474 2070 Planarity : 0.009 0.037 2262 Dihedral : 14.860 107.219 5130 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.02 % Favored : 96.42 % Rotamer: Outliers : 0.22 % Allowed : 0.67 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.58 (0.20), residues: 1590 helix: 0.25 (0.32), residues: 186 sheet: 0.24 (0.23), residues: 504 loop : 0.68 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.013 TRP D 531 HIS 0.030 0.005 HIS A 139 PHE 0.048 0.007 PHE B 132 TYR 0.062 0.010 TYR A 109 ARG 0.008 0.001 ARG J 46 Details of bonding type rmsd link_NAG-ASN : bond 0.07692 ( 12) link_NAG-ASN : angle 2.21838 ( 36) link_ALPHA1-6 : bond 0.08348 ( 3) link_ALPHA1-6 : angle 4.55209 ( 9) link_BETA1-4 : bond 0.07144 ( 12) link_BETA1-4 : angle 5.12155 ( 36) hydrogen bonds : bond 0.14579 ( 468) hydrogen bonds : angle 8.17248 ( 1179) SS BOND : bond 0.00734 ( 1) SS BOND : angle 0.94525 ( 2) covalent geometry : bond 0.02164 (13200) covalent geometry : angle 1.87570 (17934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 336 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 71 ASP cc_start: 0.8402 (t0) cc_final: 0.8026 (p0) REVERT: J 76 ILE cc_start: 0.9104 (mt) cc_final: 0.8829 (tt) REVERT: G 43 GLN cc_start: 0.8999 (mt0) cc_final: 0.8764 (pt0) REVERT: G 48 MET cc_start: 0.9245 (mtp) cc_final: 0.8809 (mtp) REVERT: A 100 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8728 (tt0) REVERT: A 184 LEU cc_start: 0.8715 (mt) cc_final: 0.8364 (mt) REVERT: K 71 ASP cc_start: 0.8486 (t0) cc_final: 0.8185 (p0) REVERT: H 48 MET cc_start: 0.9207 (mtp) cc_final: 0.8773 (mtt) REVERT: H 63 GLN cc_start: 0.8888 (pm20) cc_final: 0.8009 (pm20) REVERT: B 184 LEU cc_start: 0.8644 (mt) cc_final: 0.8246 (mt) REVERT: E 592 PHE cc_start: 0.8977 (t80) cc_final: 0.8675 (t80) REVERT: L 71 ASP cc_start: 0.8328 (t0) cc_final: 0.7983 (p0) REVERT: L 76 ILE cc_start: 0.9135 (mt) cc_final: 0.8912 (tt) REVERT: I 48 MET cc_start: 0.9243 (mtp) cc_final: 0.8686 (mtp) REVERT: C 99 TYR cc_start: 0.7387 (m-80) cc_final: 0.6879 (m-10) REVERT: C 100 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8572 (tt0) REVERT: C 127 ASP cc_start: 0.8922 (m-30) cc_final: 0.8721 (t0) REVERT: C 184 LEU cc_start: 0.8689 (mt) cc_final: 0.8354 (mt) REVERT: F 592 PHE cc_start: 0.9135 (t80) cc_final: 0.8820 (t80) outliers start: 3 outliers final: 0 residues processed: 336 average time/residue: 0.2852 time to fit residues: 133.7798 Evaluate side-chains 169 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 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 = 0.3792 r_free = 0.3792 target = 0.056626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.046673 restraints weight = 101161.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.048200 restraints weight = 66205.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.049272 restraints weight = 48373.385| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 13228 Z= 0.264 Angle : 0.864 9.569 18017 Z= 0.443 Chirality : 0.049 0.242 2070 Planarity : 0.006 0.054 2262 Dihedral : 10.353 66.790 2310 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.65 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.00 (0.21), residues: 1590 helix: -0.21 (0.33), residues: 213 sheet: -0.15 (0.21), residues: 633 loop : 0.44 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 531 HIS 0.018 0.003 HIS C 154 PHE 0.031 0.003 PHE A 132 TYR 0.029 0.003 TYR B 99 ARG 0.007 0.001 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 12) link_NAG-ASN : angle 2.24249 ( 36) link_ALPHA1-6 : bond 0.00880 ( 3) link_ALPHA1-6 : angle 2.14981 ( 9) link_BETA1-4 : bond 0.00976 ( 12) link_BETA1-4 : angle 4.15033 ( 36) hydrogen bonds : bond 0.04964 ( 468) hydrogen bonds : angle 7.00652 ( 1179) SS BOND : bond 0.01193 ( 1) SS BOND : angle 4.84752 ( 2) covalent geometry : bond 0.00599 (13200) covalent geometry : angle 0.83665 (17934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 48 LEU cc_start: 0.8345 (mt) cc_final: 0.8142 (mt) REVERT: J 71 ASP cc_start: 0.8637 (t0) cc_final: 0.8088 (p0) REVERT: G 48 MET cc_start: 0.9250 (mtp) cc_final: 0.8649 (mtp) REVERT: A 111 LEU cc_start: 0.9353 (mt) cc_final: 0.9145 (tt) REVERT: A 141 VAL cc_start: 0.9485 (t) cc_final: 0.9269 (p) REVERT: A 162 TYR cc_start: 0.7074 (m-80) cc_final: 0.6615 (m-10) REVERT: D 584 ILE cc_start: 0.9670 (pt) cc_final: 0.9380 (pt) REVERT: D 585 LEU cc_start: 0.9142 (pt) cc_final: 0.8902 (mp) REVERT: D 588 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9246 (mmmt) REVERT: K 71 ASP cc_start: 0.8644 (t0) cc_final: 0.8138 (p0) REVERT: H 48 MET cc_start: 0.9213 (mtp) cc_final: 0.8543 (mtp) REVERT: H 63 GLN cc_start: 0.8845 (pm20) cc_final: 0.8515 (pm20) REVERT: B 141 VAL cc_start: 0.9154 (t) cc_final: 0.8943 (p) REVERT: B 162 TYR cc_start: 0.7177 (m-80) cc_final: 0.6681 (m-10) REVERT: E 585 LEU cc_start: 0.8904 (mt) cc_final: 0.8323 (mt) REVERT: E 588 LYS cc_start: 0.9461 (mmtm) cc_final: 0.9208 (mmmt) REVERT: L 4 MET cc_start: 0.8782 (mmt) cc_final: 0.7743 (tpp) REVERT: L 17 GLU cc_start: 0.8921 (pt0) cc_final: 0.8500 (mp0) REVERT: L 71 ASP cc_start: 0.8559 (t0) cc_final: 0.8003 (p0) REVERT: I 48 MET cc_start: 0.9219 (mtp) cc_final: 0.8682 (mtp) REVERT: C 127 ASP cc_start: 0.8810 (m-30) cc_final: 0.8609 (t0) REVERT: C 141 VAL cc_start: 0.9283 (t) cc_final: 0.9063 (p) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2613 time to fit residues: 85.1648 Evaluate side-chains 145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 12 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN L 6 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.062864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.053864 restraints weight = 125684.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.055356 restraints weight = 77466.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.056414 restraints weight = 53767.376| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13228 Z= 0.170 Angle : 0.714 10.039 18017 Z= 0.369 Chirality : 0.046 0.188 2070 Planarity : 0.005 0.050 2262 Dihedral : 7.436 39.184 2310 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.22 (0.22), residues: 1590 helix: 0.08 (0.34), residues: 213 sheet: -0.34 (0.22), residues: 600 loop : 0.14 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 105 HIS 0.010 0.002 HIS C 154 PHE 0.025 0.002 PHE A 132 TYR 0.035 0.003 TYR B 171 ARG 0.006 0.001 ARG F 580 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 12) link_NAG-ASN : angle 1.20070 ( 36) link_ALPHA1-6 : bond 0.00916 ( 3) link_ALPHA1-6 : angle 1.76998 ( 9) link_BETA1-4 : bond 0.00929 ( 12) link_BETA1-4 : angle 2.79938 ( 36) hydrogen bonds : bond 0.04024 ( 468) hydrogen bonds : angle 6.28492 ( 1179) SS BOND : bond 0.03426 ( 1) SS BOND : angle 3.12723 ( 2) covalent geometry : bond 0.00380 (13200) covalent geometry : angle 0.70063 (17934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8589 (tpp) cc_final: 0.8150 (mmm) REVERT: J 71 ASP cc_start: 0.8572 (t0) cc_final: 0.8042 (p0) REVERT: G 48 MET cc_start: 0.9258 (mtp) cc_final: 0.8459 (mtp) REVERT: A 99 TYR cc_start: 0.6927 (m-80) cc_final: 0.6604 (m-10) REVERT: A 111 LEU cc_start: 0.9317 (mt) cc_final: 0.9048 (tt) REVERT: A 141 VAL cc_start: 0.9526 (t) cc_final: 0.9322 (p) REVERT: A 162 TYR cc_start: 0.7174 (m-80) cc_final: 0.6574 (m-10) REVERT: K 4 MET cc_start: 0.8416 (tpp) cc_final: 0.8094 (mmm) REVERT: K 71 ASP cc_start: 0.8519 (t0) cc_final: 0.8172 (p0) REVERT: H 48 MET cc_start: 0.9143 (mtp) cc_final: 0.8473 (mtp) REVERT: H 63 GLN cc_start: 0.8891 (pm20) cc_final: 0.8546 (pm20) REVERT: B 132 PHE cc_start: 0.5904 (p90) cc_final: 0.5665 (p90) REVERT: B 162 TYR cc_start: 0.6844 (m-80) cc_final: 0.6364 (m-10) REVERT: L 4 MET cc_start: 0.8629 (mmt) cc_final: 0.7743 (tpp) REVERT: L 17 GLU cc_start: 0.9009 (pt0) cc_final: 0.8739 (mp0) REVERT: L 71 ASP cc_start: 0.8506 (t0) cc_final: 0.7899 (p0) REVERT: I 48 MET cc_start: 0.9166 (mtp) cc_final: 0.8528 (mtp) REVERT: C 162 TYR cc_start: 0.6672 (m-80) cc_final: 0.6454 (m-80) REVERT: C 270 THR cc_start: 0.8547 (m) cc_final: 0.8249 (p) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.2300 time to fit residues: 71.4207 Evaluate side-chains 142 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 chunk 125 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 1 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.054036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.044606 restraints weight = 105591.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.046016 restraints weight = 69318.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.047034 restraints weight = 50830.412| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13228 Z= 0.201 Angle : 0.685 7.216 18017 Z= 0.352 Chirality : 0.045 0.213 2070 Planarity : 0.005 0.049 2262 Dihedral : 6.270 40.718 2310 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.44 % Allowed : 2.59 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.40 (0.22), residues: 1590 helix: 0.17 (0.35), residues: 213 sheet: -0.58 (0.21), residues: 600 loop : 0.07 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 531 HIS 0.010 0.002 HIS C 154 PHE 0.027 0.002 PHE B 132 TYR 0.029 0.003 TYR B 109 ARG 0.007 0.001 ARG K 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 1.39863 ( 36) link_ALPHA1-6 : bond 0.00509 ( 3) link_ALPHA1-6 : angle 1.48506 ( 9) link_BETA1-4 : bond 0.00663 ( 12) link_BETA1-4 : angle 2.44501 ( 36) hydrogen bonds : bond 0.03620 ( 468) hydrogen bonds : angle 6.04730 ( 1179) SS BOND : bond 0.00700 ( 1) SS BOND : angle 1.81137 ( 2) covalent geometry : bond 0.00456 (13200) covalent geometry : angle 0.67412 (17934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8599 (tpp) cc_final: 0.8229 (mmm) REVERT: J 71 ASP cc_start: 0.8518 (t0) cc_final: 0.7991 (p0) REVERT: G 48 MET cc_start: 0.9141 (mtp) cc_final: 0.8205 (mpp) REVERT: A 183 PHE cc_start: 0.8094 (m-80) cc_final: 0.7652 (m-80) REVERT: A 270 THR cc_start: 0.8102 (m) cc_final: 0.7782 (p) REVERT: D 584 ILE cc_start: 0.9549 (pt) cc_final: 0.9347 (pt) REVERT: K 4 MET cc_start: 0.8400 (tpp) cc_final: 0.8137 (mmm) REVERT: K 71 ASP cc_start: 0.8610 (t0) cc_final: 0.8224 (p0) REVERT: H 48 MET cc_start: 0.9223 (mtp) cc_final: 0.8692 (mtp) REVERT: H 63 GLN cc_start: 0.8939 (pm20) cc_final: 0.8122 (pm20) REVERT: B 270 THR cc_start: 0.8126 (m) cc_final: 0.7912 (p) REVERT: L 17 GLU cc_start: 0.9253 (pt0) cc_final: 0.8858 (mp0) REVERT: L 71 ASP cc_start: 0.8474 (t0) cc_final: 0.7812 (p0) REVERT: I 48 MET cc_start: 0.9168 (mtp) cc_final: 0.8627 (mtp) REVERT: C 162 TYR cc_start: 0.7039 (m-80) cc_final: 0.6742 (m-80) REVERT: C 270 THR cc_start: 0.8445 (m) cc_final: 0.8136 (p) REVERT: F 588 LYS cc_start: 0.9529 (mmtm) cc_final: 0.9304 (mmmt) outliers start: 6 outliers final: 3 residues processed: 183 average time/residue: 0.2597 time to fit residues: 72.7296 Evaluate side-chains 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 136 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 3.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.052834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.043324 restraints weight = 109538.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.044746 restraints weight = 69617.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.045780 restraints weight = 50248.353| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13228 Z= 0.233 Angle : 0.691 9.557 18017 Z= 0.359 Chirality : 0.044 0.198 2070 Planarity : 0.005 0.046 2262 Dihedral : 6.208 41.349 2310 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.15 % Allowed : 2.15 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.43 (0.22), residues: 1590 helix: 0.15 (0.34), residues: 213 sheet: -0.57 (0.22), residues: 570 loop : -0.02 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 105 HIS 0.008 0.002 HIS C 154 PHE 0.029 0.002 PHE B 132 TYR 0.035 0.003 TYR L 50 ARG 0.005 0.001 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 12) link_NAG-ASN : angle 1.64114 ( 36) link_ALPHA1-6 : bond 0.00414 ( 3) link_ALPHA1-6 : angle 1.44309 ( 9) link_BETA1-4 : bond 0.00688 ( 12) link_BETA1-4 : angle 2.11864 ( 36) hydrogen bonds : bond 0.03446 ( 468) hydrogen bonds : angle 5.80825 ( 1179) SS BOND : bond 0.00416 ( 1) SS BOND : angle 2.45591 ( 2) covalent geometry : bond 0.00526 (13200) covalent geometry : angle 0.68115 (17934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8475 (tpp) cc_final: 0.8107 (mmm) REVERT: J 71 ASP cc_start: 0.8560 (t0) cc_final: 0.7983 (p0) REVERT: G 48 MET cc_start: 0.9213 (mtp) cc_final: 0.8285 (mpp) REVERT: A 109 TYR cc_start: 0.8710 (m-80) cc_final: 0.8315 (m-80) REVERT: A 183 PHE cc_start: 0.8087 (m-80) cc_final: 0.7839 (m-80) REVERT: A 270 THR cc_start: 0.8236 (m) cc_final: 0.7932 (p) REVERT: D 531 TRP cc_start: 0.8591 (p-90) cc_final: 0.8359 (p-90) REVERT: D 578 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8009 (mp0) REVERT: D 592 PHE cc_start: 0.9126 (t80) cc_final: 0.8903 (t80) REVERT: K 4 MET cc_start: 0.8495 (tpp) cc_final: 0.8208 (mmm) REVERT: K 71 ASP cc_start: 0.8470 (t0) cc_final: 0.7954 (p0) REVERT: K 90 GLN cc_start: 0.8692 (tt0) cc_final: 0.8405 (tt0) REVERT: H 48 MET cc_start: 0.9275 (mtp) cc_final: 0.8806 (mtp) REVERT: H 63 GLN cc_start: 0.9037 (pm20) cc_final: 0.8309 (pm20) REVERT: B 270 THR cc_start: 0.8263 (m) cc_final: 0.8056 (p) REVERT: E 588 LYS cc_start: 0.9455 (mmtm) cc_final: 0.9238 (mmmt) REVERT: L 71 ASP cc_start: 0.8508 (t0) cc_final: 0.7793 (p0) REVERT: I 48 MET cc_start: 0.9241 (mtp) cc_final: 0.8810 (mtp) REVERT: C 109 TYR cc_start: 0.8589 (m-80) cc_final: 0.8286 (m-80) REVERT: C 270 THR cc_start: 0.8539 (m) cc_final: 0.8318 (p) outliers start: 2 outliers final: 1 residues processed: 162 average time/residue: 0.2259 time to fit residues: 56.1731 Evaluate side-chains 118 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.054676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.045485 restraints weight = 132923.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.046862 restraints weight = 82596.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.047806 restraints weight = 58782.762| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 13228 Z= 0.349 Angle : 0.832 12.946 18017 Z= 0.426 Chirality : 0.047 0.172 2070 Planarity : 0.006 0.047 2262 Dihedral : 6.857 43.349 2310 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.11 (0.21), residues: 1590 helix: -0.69 (0.32), residues: 219 sheet: -0.90 (0.20), residues: 648 loop : -0.38 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 104 HIS 0.010 0.003 HIS F 516 PHE 0.033 0.003 PHE B 132 TYR 0.034 0.004 TYR D 517 ARG 0.009 0.001 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.01104 ( 12) link_NAG-ASN : angle 2.26561 ( 36) link_ALPHA1-6 : bond 0.00175 ( 3) link_ALPHA1-6 : angle 1.48578 ( 9) link_BETA1-4 : bond 0.00551 ( 12) link_BETA1-4 : angle 2.26722 ( 36) hydrogen bonds : bond 0.04093 ( 468) hydrogen bonds : angle 6.22218 ( 1179) SS BOND : bond 0.00486 ( 1) SS BOND : angle 2.28437 ( 2) covalent geometry : bond 0.00768 (13200) covalent geometry : angle 0.82023 (17934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8346 (tpp) cc_final: 0.7990 (mmm) REVERT: G 48 MET cc_start: 0.9296 (mtp) cc_final: 0.8770 (mtp) REVERT: A 270 THR cc_start: 0.8260 (m) cc_final: 0.7988 (p) REVERT: D 531 TRP cc_start: 0.8827 (p-90) cc_final: 0.8543 (p-90) REVERT: K 4 MET cc_start: 0.8582 (tpp) cc_final: 0.8242 (mmm) REVERT: H 48 MET cc_start: 0.9297 (mtp) cc_final: 0.8905 (mtp) REVERT: B 270 THR cc_start: 0.8256 (m) cc_final: 0.8004 (p) REVERT: E 588 LYS cc_start: 0.9400 (mmtm) cc_final: 0.9175 (mmmt) REVERT: L 4 MET cc_start: 0.8217 (mmm) cc_final: 0.7229 (tpt) REVERT: L 50 TYR cc_start: 0.8272 (t80) cc_final: 0.7891 (t80) REVERT: I 48 MET cc_start: 0.9267 (mtp) cc_final: 0.8856 (mtm) REVERT: F 531 TRP cc_start: 0.8805 (p-90) cc_final: 0.8550 (p-90) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2978 time to fit residues: 66.3547 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 12 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.051900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.042797 restraints weight = 107280.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.044103 restraints weight = 69737.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.045075 restraints weight = 51151.525| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13228 Z= 0.167 Angle : 0.681 12.283 18017 Z= 0.343 Chirality : 0.045 0.176 2070 Planarity : 0.005 0.044 2262 Dihedral : 6.395 39.117 2310 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.85 (0.21), residues: 1590 helix: -0.06 (0.34), residues: 210 sheet: -0.86 (0.21), residues: 606 loop : -0.26 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 104 HIS 0.006 0.002 HIS C 139 PHE 0.033 0.002 PHE E 535 TYR 0.029 0.002 TYR C 109 ARG 0.007 0.001 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 12) link_NAG-ASN : angle 1.97493 ( 36) link_ALPHA1-6 : bond 0.00413 ( 3) link_ALPHA1-6 : angle 1.37681 ( 9) link_BETA1-4 : bond 0.00717 ( 12) link_BETA1-4 : angle 1.98830 ( 36) hydrogen bonds : bond 0.03384 ( 468) hydrogen bonds : angle 5.85865 ( 1179) SS BOND : bond 0.00504 ( 1) SS BOND : angle 1.69262 ( 2) covalent geometry : bond 0.00382 (13200) covalent geometry : angle 0.66978 (17934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 48 MET cc_start: 0.9221 (mtp) cc_final: 0.8380 (mpp) REVERT: G 66 ASP cc_start: 0.8522 (m-30) cc_final: 0.8285 (m-30) REVERT: G 93 MET cc_start: 0.8672 (tpt) cc_final: 0.8377 (tpp) REVERT: D 531 TRP cc_start: 0.8820 (p-90) cc_final: 0.8370 (p-90) REVERT: K 4 MET cc_start: 0.8522 (tpp) cc_final: 0.8156 (mmm) REVERT: H 48 MET cc_start: 0.9252 (mtp) cc_final: 0.8855 (mtp) REVERT: H 66 ASP cc_start: 0.8685 (m-30) cc_final: 0.8415 (m-30) REVERT: H 93 MET cc_start: 0.8494 (tpp) cc_final: 0.8031 (tpp) REVERT: E 588 LYS cc_start: 0.9313 (mmtm) cc_final: 0.9099 (mmmt) REVERT: L 4 MET cc_start: 0.8003 (mmm) cc_final: 0.7165 (tpt) REVERT: L 21 LEU cc_start: 0.9001 (mp) cc_final: 0.8768 (mm) REVERT: L 50 TYR cc_start: 0.8198 (t80) cc_final: 0.7838 (t80) REVERT: I 48 MET cc_start: 0.9155 (mtp) cc_final: 0.8854 (mtp) REVERT: F 588 LYS cc_start: 0.9494 (mmtm) cc_final: 0.9276 (mmmt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2902 time to fit residues: 63.8181 Evaluate side-chains 103 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.052978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.043734 restraints weight = 107296.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.045101 restraints weight = 68140.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.046107 restraints weight = 49549.765| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13228 Z= 0.120 Angle : 0.622 9.923 18017 Z= 0.311 Chirality : 0.044 0.173 2070 Planarity : 0.004 0.039 2262 Dihedral : 5.750 33.791 2310 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.59 (0.21), residues: 1590 helix: 0.14 (0.35), residues: 210 sheet: -0.62 (0.21), residues: 606 loop : -0.16 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 104 HIS 0.004 0.001 HIS F 516 PHE 0.022 0.002 PHE B 132 TYR 0.024 0.002 TYR B 99 ARG 0.004 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 12) link_NAG-ASN : angle 1.32020 ( 36) link_ALPHA1-6 : bond 0.00411 ( 3) link_ALPHA1-6 : angle 1.41157 ( 9) link_BETA1-4 : bond 0.00772 ( 12) link_BETA1-4 : angle 1.70601 ( 36) hydrogen bonds : bond 0.03072 ( 468) hydrogen bonds : angle 5.54928 ( 1179) SS BOND : bond 0.00553 ( 1) SS BOND : angle 2.96372 ( 2) covalent geometry : bond 0.00274 (13200) covalent geometry : angle 0.61395 (17934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 48 MET cc_start: 0.9187 (mtp) cc_final: 0.8337 (mpp) REVERT: A 162 TYR cc_start: 0.6649 (m-80) cc_final: 0.6355 (m-80) REVERT: D 531 TRP cc_start: 0.8780 (p-90) cc_final: 0.8403 (p-90) REVERT: D 592 PHE cc_start: 0.9234 (t80) cc_final: 0.8927 (t80) REVERT: K 4 MET cc_start: 0.8532 (tpp) cc_final: 0.8121 (mmm) REVERT: H 48 MET cc_start: 0.9216 (mtp) cc_final: 0.8826 (mtp) REVERT: L 21 LEU cc_start: 0.8929 (mp) cc_final: 0.8705 (mm) REVERT: L 50 TYR cc_start: 0.8140 (t80) cc_final: 0.7777 (t80) REVERT: I 48 MET cc_start: 0.9064 (mtp) cc_final: 0.8735 (mtp) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2343 time to fit residues: 51.9068 Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 141 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 85 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN G 43 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.052392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.043327 restraints weight = 108077.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.044649 restraints weight = 69877.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045636 restraints weight = 51258.650| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13228 Z= 0.140 Angle : 0.623 8.405 18017 Z= 0.316 Chirality : 0.043 0.160 2070 Planarity : 0.005 0.063 2262 Dihedral : 5.692 33.322 2310 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.59 (0.21), residues: 1590 helix: 0.20 (0.36), residues: 210 sheet: -0.62 (0.21), residues: 612 loop : -0.19 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.004 0.001 HIS E 516 PHE 0.026 0.002 PHE B 132 TYR 0.018 0.002 TYR A 99 ARG 0.016 0.001 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 12) link_NAG-ASN : angle 1.33092 ( 36) link_ALPHA1-6 : bond 0.00342 ( 3) link_ALPHA1-6 : angle 1.45883 ( 9) link_BETA1-4 : bond 0.00671 ( 12) link_BETA1-4 : angle 1.69702 ( 36) hydrogen bonds : bond 0.03085 ( 468) hydrogen bonds : angle 5.57892 ( 1179) SS BOND : bond 0.00405 ( 1) SS BOND : angle 2.42844 ( 2) covalent geometry : bond 0.00326 (13200) covalent geometry : angle 0.61555 (17934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8677 (tpt) cc_final: 0.8306 (tpt) REVERT: G 48 MET cc_start: 0.9247 (mtp) cc_final: 0.8426 (mpp) REVERT: G 93 MET cc_start: 0.8486 (tpp) cc_final: 0.8046 (tpp) REVERT: A 161 LEU cc_start: 0.8605 (mp) cc_final: 0.8353 (mp) REVERT: A 162 TYR cc_start: 0.6978 (m-80) cc_final: 0.6532 (m-80) REVERT: D 531 TRP cc_start: 0.8790 (p-90) cc_final: 0.8403 (p-90) REVERT: D 592 PHE cc_start: 0.9253 (t80) cc_final: 0.8957 (t80) REVERT: K 4 MET cc_start: 0.8531 (tpp) cc_final: 0.8143 (mmm) REVERT: H 48 MET cc_start: 0.9227 (mtp) cc_final: 0.8843 (mtp) REVERT: H 93 MET cc_start: 0.8301 (tpp) cc_final: 0.7867 (tpp) REVERT: L 21 LEU cc_start: 0.8987 (mp) cc_final: 0.8784 (mm) REVERT: L 50 TYR cc_start: 0.8225 (t80) cc_final: 0.7862 (t80) REVERT: I 48 MET cc_start: 0.9150 (mtp) cc_final: 0.8854 (mtp) REVERT: I 93 MET cc_start: 0.8700 (tpp) cc_final: 0.8125 (tpp) REVERT: F 531 TRP cc_start: 0.8705 (p-90) cc_final: 0.8380 (p-90) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2334 time to fit residues: 48.6203 Evaluate side-chains 110 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN G 43 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.051993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.043032 restraints weight = 108081.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.044340 restraints weight = 69775.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.045307 restraints weight = 51248.054| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13228 Z= 0.156 Angle : 0.637 11.125 18017 Z= 0.324 Chirality : 0.044 0.163 2070 Planarity : 0.005 0.062 2262 Dihedral : 5.661 36.982 2310 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.16 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.65 (0.21), residues: 1590 helix: 0.20 (0.36), residues: 210 sheet: -0.67 (0.21), residues: 606 loop : -0.24 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.005 0.001 HIS E 516 PHE 0.023 0.002 PHE B 132 TYR 0.022 0.002 TYR B 99 ARG 0.012 0.001 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 12) link_NAG-ASN : angle 1.46895 ( 36) link_ALPHA1-6 : bond 0.00298 ( 3) link_ALPHA1-6 : angle 1.47639 ( 9) link_BETA1-4 : bond 0.00703 ( 12) link_BETA1-4 : angle 1.67513 ( 36) hydrogen bonds : bond 0.03151 ( 468) hydrogen bonds : angle 5.58378 ( 1179) SS BOND : bond 0.00453 ( 1) SS BOND : angle 2.46251 ( 2) covalent geometry : bond 0.00355 (13200) covalent geometry : angle 0.62917 (17934) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8414 (tpt) cc_final: 0.8066 (tpt) REVERT: J 48 LEU cc_start: 0.8524 (mt) cc_final: 0.8312 (mt) REVERT: G 48 MET cc_start: 0.9234 (mtp) cc_final: 0.8452 (mpp) REVERT: G 93 MET cc_start: 0.8509 (tpp) cc_final: 0.8083 (tpp) REVERT: D 531 TRP cc_start: 0.8793 (p-90) cc_final: 0.8364 (p-90) REVERT: K 4 MET cc_start: 0.8543 (tpp) cc_final: 0.8148 (mmm) REVERT: H 48 MET cc_start: 0.9219 (mtp) cc_final: 0.8758 (mtm) REVERT: H 93 MET cc_start: 0.8321 (tpp) cc_final: 0.7883 (tpp) REVERT: B 33 ILE cc_start: 0.8946 (tt) cc_final: 0.8599 (mt) REVERT: E 573 LEU cc_start: 0.9163 (mt) cc_final: 0.8914 (mt) REVERT: E 588 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9134 (mmmt) REVERT: L 4 MET cc_start: 0.8218 (tpt) cc_final: 0.7831 (tpt) REVERT: I 48 MET cc_start: 0.9162 (mtp) cc_final: 0.8874 (mtp) REVERT: I 93 MET cc_start: 0.8637 (tpp) cc_final: 0.8034 (tpp) REVERT: C 109 TYR cc_start: 0.8722 (m-10) cc_final: 0.8337 (m-10) REVERT: F 531 TRP cc_start: 0.8703 (p-90) cc_final: 0.8422 (p-90) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2215 time to fit residues: 44.8592 Evaluate side-chains 105 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN E 570 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.052051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.042922 restraints weight = 108929.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.044235 restraints weight = 69139.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.045228 restraints weight = 50945.288| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13228 Z= 0.148 Angle : 0.630 13.379 18017 Z= 0.319 Chirality : 0.043 0.165 2070 Planarity : 0.004 0.051 2262 Dihedral : 5.620 35.962 2310 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.97 % Favored : 94.84 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.66 (0.21), residues: 1590 helix: 0.18 (0.36), residues: 210 sheet: -0.50 (0.22), residues: 579 loop : -0.43 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.005 0.001 HIS E 516 PHE 0.023 0.002 PHE B 132 TYR 0.017 0.002 TYR A 99 ARG 0.011 0.001 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 12) link_NAG-ASN : angle 1.42349 ( 36) link_ALPHA1-6 : bond 0.00307 ( 3) link_ALPHA1-6 : angle 1.46944 ( 9) link_BETA1-4 : bond 0.00603 ( 12) link_BETA1-4 : angle 1.62037 ( 36) hydrogen bonds : bond 0.03070 ( 468) hydrogen bonds : angle 5.54698 ( 1179) SS BOND : bond 0.00403 ( 1) SS BOND : angle 2.33165 ( 2) covalent geometry : bond 0.00340 (13200) covalent geometry : angle 0.62282 (17934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3901.96 seconds wall clock time: 71 minutes 26.42 seconds (4286.42 seconds total)