Starting phenix.real_space_refine on Fri Jul 3 08:32:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_22842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_22842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_22842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_22842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_22842.map" model { file = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_22842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kex_22842/07_2026/7kex_22842.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12909 Number of models: 1 Model: "" Number of chains: 7 Chain: "J" 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: "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: "D" 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 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 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 chiralities: 2 Restraints were copied for chains: K, L, H, I, B, C, E, F, O, Q, P, R Time building chain proxies: 1.80, per 1000 atoms: 0.14 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=12, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 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: 0.89 Conformation dependent library (CDL) restraints added in 524.8 milliseconds 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: 0.43 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: 2.15 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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 - 17.97: 7276 17.97 - 35.95: 179 35.95 - 53.92: 39 53.92 - 71.89: 33 71.89 - 89.86: 24 Dihedral angle restraints: 7551 sinusoidal: 2940 harmonic: 4611 Sorted by residual: dihedral pdb=" C TYR B 220 " pdb=" N TYR B 220 " pdb=" CA TYR B 220 " pdb=" CB TYR B 220 " ideal model delta harmonic sigma weight residual -122.60 -113.96 -8.64 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C TYR C 220 " pdb=" N TYR C 220 " pdb=" CA TYR C 220 " pdb=" CB TYR C 220 " ideal model delta harmonic sigma weight residual -122.60 -113.97 -8.63 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C TYR A 220 " pdb=" N TYR A 220 " pdb=" CA TYR A 220 " pdb=" CB TYR A 220 " ideal model delta harmonic sigma weight residual -122.60 -114.00 -8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 7548 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: 2.48 - 2.96: 6622 2.96 - 3.45: 12331 3.45 - 3.93: 22911 3.93 - 4.42: 26180 4.42 - 4.90: 40769 Nonbonded interactions: 108813 Sorted by model distance: nonbonded pdb=" N ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.479 3.120 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.479 3.120 nonbonded pdb=" N ASP J 61 " pdb=" OD1 ASP J 61 " model vdw 2.480 3.120 nonbonded pdb=" N ASN C 110 " pdb=" O ASN C 110 " model vdw 2.497 2.496 nonbonded pdb=" N ASN B 110 " pdb=" O ASN B 110 " model vdw 2.497 2.496 ... (remaining 108808 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: 0.04 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } 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: 2.540 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.520 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 13239 Z= 1.132 Angle : 1.893 10.947 18039 Z= 1.228 Chirality : 0.123 0.474 2070 Planarity : 0.009 0.037 2262 Dihedral : 11.251 89.862 4581 Min Nonbonded Distance : 2.479 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG J 46 TYR 0.062 0.010 TYR A 109 PHE 0.048 0.007 PHE B 132 TRP 0.052 0.013 TRP D 531 HIS 0.030 0.005 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.02164 / 1.12 (13200) covalent geometry : angle 1.87570 / 1.23 (17934) SS BOND : bond 0.00973 / 0.54 ( 12) SS BOND : angle 3.22795 / 1.97 ( 24) hydrogen bonds : bond 0.14579 / 9.46 ( 468) hydrogen bonds : angle 8.17248 / 5.70 ( 1179) link_ALPHA1-6 : bond 0.08348 / 4.19 ( 3) link_ALPHA1-6 : angle 4.55209 / 2.72 ( 9) link_BETA1-4 : bond 0.07144 / 4.00 ( 12) link_BETA1-4 : angle 5.12155 / 3.29 ( 36) link_NAG-ASN : bond 0.07692 / 4.35 ( 12) link_NAG-ASN : angle 2.21838 / 1.46 ( 36) *********************** 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 : 0.329 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: 0.9246 (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: 0.8714 (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: 0.8887 (pm20) cc_final: 0.8009 (pm20) REVERT: B 184 LEU cc_start: 0.8645 (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: 0.1097 time to fit residues: 52.2036 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.1980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.058598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.048638 restraints weight = 98215.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.050301 restraints weight = 63149.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.051501 restraints weight = 45424.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.052366 restraints weight = 35244.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.053001 restraints weight = 28891.515| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13239 Z= 0.195 Angle : 0.835 10.024 18039 Z= 0.431 Chirality : 0.050 0.284 2070 Planarity : 0.005 0.047 2262 Dihedral : 6.038 24.391 1761 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1590 helix: -0.30 (0.34), residues: 207 sheet: -0.13 (0.21), residues: 615 loop : 0.39 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 18 TYR 0.028 0.003 TYR A 109 PHE 0.029 0.002 PHE A 132 TRP 0.018 0.002 TRP I 47 HIS 0.016 0.003 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (13200) covalent geometry : angle 0.80621 / 0.42 (17934) SS BOND : bond 0.00450 / 0.25 ( 12) SS BOND : angle 2.58335 / 1.77 ( 24) hydrogen bonds : bond 0.04880 / 3.38 ( 468) hydrogen bonds : angle 7.03081 / 4.88 ( 1179) link_ALPHA1-6 : bond 0.00602 / 0.30 ( 3) link_ALPHA1-6 : angle 1.37785 / 0.89 ( 9) link_BETA1-4 : bond 0.01017 / 0.55 ( 12) link_BETA1-4 : angle 3.74843 / 2.29 ( 36) link_NAG-ASN : bond 0.00381 / 0.22 ( 12) link_NAG-ASN : angle 2.49442 / 1.44 ( 36) *********************** 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 244 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.471 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: 0.8519 (t0) cc_final: 0.8095 (p0) REVERT: G 48 MET cc_start: 0.9189 (mtp) cc_final: 0.8559 (mtp) REVERT: A 141 VAL cc_start: 0.9413 (t) cc_final: 0.9206 (p) REVERT: D 584 ILE cc_start: 0.9669 (pt) cc_final: 0.9413 (pt) REVERT: D 588 LYS cc_start: 0.9524 (mmtm) cc_final: 0.9313 (mmmt) REVERT: K 71 ASP cc_start: 0.8635 (t0) cc_final: 0.8152 (p0) REVERT: H 48 MET cc_start: 0.9144 (mtp) cc_final: 0.8444 (mtp) REVERT: H 63 GLN cc_start: 0.8809 (pm20) cc_final: 0.7963 (pm20) REVERT: B 132 PHE cc_start: 0.5946 (p90) cc_final: 0.5165 (p90) REVERT: B 141 VAL cc_start: 0.9196 (t) cc_final: 0.8981 (p) REVERT: E 588 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9232 (mmmt) REVERT: L 71 ASP cc_start: 0.8435 (t0) cc_final: 0.8043 (p0) REVERT: I 48 MET cc_start: 0.9135 (mtp) cc_final: 0.8527 (mtp) REVERT: C 141 VAL cc_start: 0.9299 (t) cc_final: 0.9064 (p) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.0928 time to fit residues: 33.3589 Evaluate side-chains 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 49 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 118 optimal weight: 10.0000 chunk 101 optimal weight: 0.1980 chunk 126 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 93 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 1 GLN J 6 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN K 6 GLN E 508 GLN L 1 GLN L 6 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN F 508 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.065682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.056707 restraints weight = 125497.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.058260 restraints weight = 76714.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.059374 restraints weight = 52561.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.060127 restraints weight = 38886.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.060677 restraints weight = 30600.063| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13239 Z= 0.140 Angle : 0.694 9.591 18039 Z= 0.359 Chirality : 0.046 0.202 2070 Planarity : 0.005 0.056 2262 Dihedral : 5.508 23.114 1761 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1590 helix: -0.18 (0.35), residues: 213 sheet: -0.30 (0.22), residues: 588 loop : 0.11 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 18 TYR 0.034 0.002 TYR A 109 PHE 0.022 0.002 PHE A 132 TRP 0.019 0.002 TRP I 105 HIS 0.010 0.002 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (13200) covalent geometry : angle 0.68296 / 0.36 (17934) SS BOND : bond 0.00486 / 0.26 ( 12) SS BOND : angle 1.71690 / 1.22 ( 24) hydrogen bonds : bond 0.03864 / 2.65 ( 468) hydrogen bonds : angle 6.34837 / 4.46 ( 1179) link_ALPHA1-6 : bond 0.00637 / 0.32 ( 3) link_ALPHA1-6 : angle 1.37840 / 0.83 ( 9) link_BETA1-4 : bond 0.00913 / 0.50 ( 12) link_BETA1-4 : angle 2.32677 / 1.45 ( 36) link_NAG-ASN : bond 0.00422 / 0.23 ( 12) link_NAG-ASN : angle 1.05354 / 0.62 ( 36) *********************** 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 214 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.500 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: 0.8275 (tpp) cc_final: 0.7483 (tpp) REVERT: J 71 ASP cc_start: 0.8499 (t0) cc_final: 0.8025 (p0) REVERT: G 48 MET cc_start: 0.9136 (mtp) cc_final: 0.8341 (mtp) REVERT: A 183 PHE cc_start: 0.7833 (m-80) cc_final: 0.7430 (m-80) REVERT: A 234 PHE cc_start: 0.9139 (t80) cc_final: 0.8743 (t80) REVERT: D 584 ILE cc_start: 0.9601 (pt) cc_final: 0.9381 (pt) REVERT: D 586 ASN cc_start: 0.9403 (m110) cc_final: 0.9185 (m110) REVERT: K 4 MET cc_start: 0.8104 (tpp) cc_final: 0.7479 (tpp) REVERT: K 71 ASP cc_start: 0.8505 (t0) cc_final: 0.8206 (p0) REVERT: H 48 MET cc_start: 0.9054 (mtp) cc_final: 0.8397 (mtp) REVERT: H 63 GLN cc_start: 0.8813 (pm20) cc_final: 0.8486 (pm20) REVERT: B 132 PHE cc_start: 0.5848 (p90) cc_final: 0.5552 (p90) REVERT: B 162 TYR cc_start: 0.6185 (m-80) cc_final: 0.5908 (m-10) REVERT: B 184 LEU cc_start: 0.8941 (mt) cc_final: 0.8711 (mt) REVERT: L 4 MET cc_start: 0.8182 (tpp) cc_final: 0.6809 (tpp) REVERT: L 17 GLU cc_start: 0.8961 (pt0) cc_final: 0.8761 (pm20) REVERT: L 71 ASP cc_start: 0.8477 (t0) cc_final: 0.8058 (p0) REVERT: I 48 MET cc_start: 0.9079 (mtp) cc_final: 0.8379 (mtp) REVERT: C 162 TYR cc_start: 0.6156 (m-80) cc_final: 0.5781 (m-80) REVERT: C 270 THR cc_start: 0.8328 (m) cc_final: 0.8041 (p) REVERT: F 586 ASN cc_start: 0.9223 (m110) cc_final: 0.8998 (m110) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.0911 time to fit residues: 29.1178 Evaluate side-chains 147 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 109 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 126 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 58 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN ** K 27 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** L 91 GLN 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 = 0.3691 r_free = 0.3691 target = 0.052768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.043333 restraints weight = 109337.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.044726 restraints weight = 71977.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.045738 restraints weight = 52816.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.046465 restraints weight = 41749.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.047022 restraints weight = 34789.569| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 13239 Z= 0.302 Angle : 0.803 8.668 18039 Z= 0.415 Chirality : 0.046 0.260 2070 Planarity : 0.006 0.056 2262 Dihedral : 5.922 20.925 1761 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.15 % Allowed : 2.52 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1590 helix: -0.30 (0.34), residues: 210 sheet: -0.60 (0.21), residues: 636 loop : -0.01 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 219 TYR 0.024 0.003 TYR C 109 PHE 0.030 0.003 PHE A 132 TRP 0.041 0.004 TRP I 105 HIS 0.017 0.004 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.30 (13200) covalent geometry : angle 0.79103 / 0.41 (17934) SS BOND : bond 0.00849 / 0.50 ( 12) SS BOND : angle 1.76003 / 1.35 ( 24) hydrogen bonds : bond 0.03945 / 2.65 ( 468) hydrogen bonds : angle 6.06029 / 4.22 ( 1179) link_ALPHA1-6 : bond 0.00353 / 0.18 ( 3) link_ALPHA1-6 : angle 1.46605 / 0.90 ( 9) link_BETA1-4 : bond 0.00675 / 0.37 ( 12) link_BETA1-4 : angle 2.26954 / 1.33 ( 36) link_NAG-ASN : bond 0.00727 / 0.41 ( 12) link_NAG-ASN : angle 1.82844 / 1.12 ( 36) *********************** 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 173 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.467 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: 0.8239 (tpp) cc_final: 0.7629 (tpp) REVERT: J 71 ASP cc_start: 0.8590 (t0) cc_final: 0.8031 (p0) REVERT: G 48 MET cc_start: 0.9161 (mtp) cc_final: 0.8564 (mtp) REVERT: A 111 LEU cc_start: 0.9511 (mt) cc_final: 0.9276 (mt) REVERT: A 270 THR cc_start: 0.8183 (m) cc_final: 0.7921 (p) REVERT: K 4 MET cc_start: 0.8284 (tpp) cc_final: 0.7840 (mmm) REVERT: K 71 ASP cc_start: 0.8650 (t0) cc_final: 0.8272 (p0) REVERT: H 48 MET cc_start: 0.9197 (mtp) cc_final: 0.8666 (mtp) REVERT: H 63 GLN cc_start: 0.8940 (pm20) cc_final: 0.8054 (pm20) REVERT: B 132 PHE cc_start: 0.6405 (p90) cc_final: 0.6158 (p90) REVERT: L 4 MET cc_start: 0.8107 (tpp) cc_final: 0.7733 (tpp) REVERT: L 17 GLU cc_start: 0.9138 (pt0) cc_final: 0.8651 (mp0) REVERT: L 48 LEU cc_start: 0.8697 (mt) cc_final: 0.8443 (mt) REVERT: L 71 ASP cc_start: 0.8674 (t0) cc_final: 0.8063 (p0) REVERT: I 48 MET cc_start: 0.9272 (mtp) cc_final: 0.8763 (mtp) REVERT: C 270 THR cc_start: 0.8441 (m) cc_final: 0.8153 (p) outliers start: 2 outliers final: 2 residues processed: 173 average time/residue: 0.0897 time to fit residues: 23.8002 Evaluate side-chains 127 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.052914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.043164 restraints weight = 109760.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.044670 restraints weight = 69452.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.045752 restraints weight = 49908.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.046495 restraints weight = 38921.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.047066 restraints weight = 32295.773| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13239 Z= 0.193 Angle : 0.671 8.701 18039 Z= 0.347 Chirality : 0.045 0.213 2070 Planarity : 0.005 0.052 2262 Dihedral : 5.619 26.905 1761 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.15 % Allowed : 2.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1590 helix: -0.04 (0.34), residues: 213 sheet: -0.56 (0.22), residues: 591 loop : -0.07 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 18 TYR 0.029 0.002 TYR A 171 PHE 0.030 0.002 PHE B 132 TRP 0.035 0.003 TRP H 105 HIS 0.007 0.002 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (13200) covalent geometry : angle 0.66278 / 0.35 (17934) SS BOND : bond 0.00350 / 0.20 ( 12) SS BOND : angle 1.55046 / 1.14 ( 24) hydrogen bonds : bond 0.03264 / 2.19 ( 468) hydrogen bonds : angle 5.58436 / 3.90 ( 1179) link_ALPHA1-6 : bond 0.00420 / 0.21 ( 3) link_ALPHA1-6 : angle 1.35812 / 0.83 ( 9) link_BETA1-4 : bond 0.00573 / 0.31 ( 12) link_BETA1-4 : angle 1.67562 / 1.05 ( 36) link_NAG-ASN : bond 0.00259 / 0.14 ( 12) link_NAG-ASN : angle 1.42720 / 0.87 ( 36) *********************** 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 171 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.445 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: J 4 MET cc_start: 0.8031 (tpp) cc_final: 0.7453 (tpp) REVERT: J 71 ASP cc_start: 0.8623 (t0) cc_final: 0.8005 (p0) REVERT: G 48 MET cc_start: 0.9193 (mtp) cc_final: 0.8302 (mpp) REVERT: A 270 THR cc_start: 0.8124 (m) cc_final: 0.7865 (p) REVERT: D 592 PHE cc_start: 0.9128 (t80) cc_final: 0.8883 (t80) REVERT: K 4 MET cc_start: 0.8057 (tpp) cc_final: 0.7737 (mmm) REVERT: K 71 ASP cc_start: 0.8639 (t0) cc_final: 0.8221 (p0) REVERT: H 48 MET cc_start: 0.9228 (mtp) cc_final: 0.8760 (mtp) REVERT: H 63 GLN cc_start: 0.9027 (pm20) cc_final: 0.8322 (pm20) REVERT: B 132 PHE cc_start: 0.6088 (p90) cc_final: 0.5856 (p90) REVERT: L 4 MET cc_start: 0.8075 (tpp) cc_final: 0.7738 (tpp) REVERT: L 17 GLU cc_start: 0.9165 (pt0) cc_final: 0.8821 (mp0) REVERT: L 48 LEU cc_start: 0.8639 (mt) cc_final: 0.8407 (mt) REVERT: L 71 ASP cc_start: 0.8694 (t0) cc_final: 0.8064 (p0) REVERT: I 48 MET cc_start: 0.9217 (mtp) cc_final: 0.8326 (mpp) REVERT: C 270 THR cc_start: 0.8464 (m) cc_final: 0.8223 (p) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.0891 time to fit residues: 23.4555 Evaluate side-chains 119 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 82 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.055936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.046682 restraints weight = 129646.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.048063 restraints weight = 80886.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.049050 restraints weight = 57421.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.049730 restraints weight = 44356.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.050228 restraints weight = 36421.653| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13239 Z= 0.286 Angle : 0.773 8.495 18039 Z= 0.400 Chirality : 0.045 0.176 2070 Planarity : 0.006 0.040 2262 Dihedral : 6.018 24.558 1761 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1590 helix: -0.16 (0.34), residues: 195 sheet: -0.73 (0.21), residues: 630 loop : -0.10 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 18 TYR 0.029 0.003 TYR D 517 PHE 0.031 0.003 PHE B 132 TRP 0.042 0.004 TRP D 531 HIS 0.008 0.003 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 (13200) covalent geometry : angle 0.76003 / 0.40 (17934) SS BOND : bond 0.00331 / 0.18 ( 12) SS BOND : angle 1.55092 / 1.13 ( 24) hydrogen bonds : bond 0.03820 / 2.59 ( 468) hydrogen bonds : angle 5.95637 / 4.16 ( 1179) link_ALPHA1-6 : bond 0.00322 / 0.16 ( 3) link_ALPHA1-6 : angle 1.41685 / 0.87 ( 9) link_BETA1-4 : bond 0.00578 / 0.31 ( 12) link_BETA1-4 : angle 2.08569 / 1.21 ( 36) link_NAG-ASN : bond 0.00800 / 0.45 ( 12) link_NAG-ASN : angle 2.26227 / 1.32 ( 36) *********************** 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 137 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.520 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: 0.8175 (tpp) cc_final: 0.7585 (tpp) REVERT: G 48 MET cc_start: 0.9266 (mtp) cc_final: 0.8443 (mpp) REVERT: A 109 TYR cc_start: 0.8772 (m-80) cc_final: 0.8527 (m-80) REVERT: A 270 THR cc_start: 0.8226 (m) cc_final: 0.7988 (p) REVERT: K 4 MET cc_start: 0.8272 (tpp) cc_final: 0.7865 (mmm) REVERT: H 48 MET cc_start: 0.9230 (mtp) cc_final: 0.8855 (mtp) REVERT: B 132 PHE cc_start: 0.6411 (p90) cc_final: 0.6188 (p90) REVERT: L 4 MET cc_start: 0.8045 (tpp) cc_final: 0.7697 (tpp) REVERT: L 17 GLU cc_start: 0.9194 (pt0) cc_final: 0.8765 (mp0) REVERT: L 48 LEU cc_start: 0.8489 (mt) cc_final: 0.8278 (mt) REVERT: I 48 MET cc_start: 0.9269 (mtp) cc_final: 0.8478 (mpp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0896 time to fit residues: 18.9373 Evaluate side-chains 99 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 110 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** L 27 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 = 0.3665 r_free = 0.3665 target = 0.052719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.043309 restraints weight = 109348.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.044713 restraints weight = 70019.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.045754 restraints weight = 51070.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.046510 restraints weight = 40252.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.047054 restraints weight = 33534.067| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13239 Z= 0.153 Angle : 0.660 10.711 18039 Z= 0.336 Chirality : 0.044 0.195 2070 Planarity : 0.005 0.038 2262 Dihedral : 5.663 24.727 1761 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1590 helix: -0.27 (0.34), residues: 213 sheet: -0.74 (0.21), residues: 606 loop : -0.17 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 64 TYR 0.025 0.002 TYR B 109 PHE 0.027 0.002 PHE B 132 TRP 0.019 0.002 TRP G 105 HIS 0.018 0.002 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13200) covalent geometry : angle 0.64868 / 0.33 (17934) SS BOND : bond 0.00233 / 0.12 ( 12) SS BOND : angle 1.54271 / 1.17 ( 24) hydrogen bonds : bond 0.03241 / 2.19 ( 468) hydrogen bonds : angle 5.60116 / 3.92 ( 1179) link_ALPHA1-6 : bond 0.00429 / 0.22 ( 3) link_ALPHA1-6 : angle 1.34314 / 0.82 ( 9) link_BETA1-4 : bond 0.00506 / 0.27 ( 12) link_BETA1-4 : angle 1.64181 / 1.00 ( 36) link_NAG-ASN : bond 0.00548 / 0.39 ( 12) link_NAG-ASN : angle 1.93544 / 1.14 ( 36) *********************** 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 144 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.488 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: J 4 MET cc_start: 0.8078 (tpp) cc_final: 0.7542 (tpp) REVERT: J 48 LEU cc_start: 0.8555 (mt) cc_final: 0.8350 (mt) REVERT: G 48 MET cc_start: 0.9221 (mtp) cc_final: 0.8307 (mpp) REVERT: A 109 TYR cc_start: 0.8777 (m-80) cc_final: 0.8522 (m-80) REVERT: A 161 LEU cc_start: 0.8813 (mp) cc_final: 0.8590 (mp) REVERT: A 270 THR cc_start: 0.8224 (m) cc_final: 0.7948 (p) REVERT: K 4 MET cc_start: 0.8180 (tpp) cc_final: 0.7841 (mmm) REVERT: H 48 MET cc_start: 0.9227 (mtp) cc_final: 0.8805 (mtp) REVERT: B 132 PHE cc_start: 0.6090 (p90) cc_final: 0.5806 (p90) REVERT: E 588 LYS cc_start: 0.9429 (mmtm) cc_final: 0.9226 (mmmt) REVERT: L 4 MET cc_start: 0.7927 (tpp) cc_final: 0.7640 (tpp) REVERT: L 48 LEU cc_start: 0.8468 (mt) cc_final: 0.8242 (mt) REVERT: I 48 MET cc_start: 0.9215 (mtp) cc_final: 0.8381 (mpp) REVERT: F 555 ILE cc_start: 0.9634 (mm) cc_final: 0.9434 (mt) REVERT: F 588 LYS cc_start: 0.9552 (mmtm) cc_final: 0.9326 (mmmt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0801 time to fit residues: 18.1331 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 : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.055550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.046348 restraints weight = 129702.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.047711 restraints weight = 79866.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.048685 restraints weight = 57005.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.049374 restraints weight = 43887.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.049873 restraints weight = 35930.830| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13239 Z= 0.243 Angle : 0.718 12.653 18039 Z= 0.366 Chirality : 0.044 0.169 2070 Planarity : 0.005 0.049 2262 Dihedral : 5.809 23.655 1761 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.21), residues: 1590 helix: -0.58 (0.33), residues: 219 sheet: -0.65 (0.22), residues: 597 loop : -0.47 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 84 TYR 0.025 0.002 TYR D 517 PHE 0.027 0.002 PHE B 132 TRP 0.020 0.003 TRP C 104 HIS 0.016 0.003 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (13200) covalent geometry : angle 0.70780 / 0.36 (17934) SS BOND : bond 0.00584 / 0.30 ( 12) SS BOND : angle 1.60491 / 1.14 ( 24) hydrogen bonds : bond 0.03447 / 2.33 ( 468) hydrogen bonds : angle 5.71551 / 4.00 ( 1179) link_ALPHA1-6 : bond 0.00370 / 0.19 ( 3) link_ALPHA1-6 : angle 1.42027 / 0.87 ( 9) link_BETA1-4 : bond 0.00560 / 0.31 ( 12) link_BETA1-4 : angle 1.51750 / 0.93 ( 36) link_NAG-ASN : bond 0.00731 / 0.41 ( 12) link_NAG-ASN : angle 2.05312 / 1.26 ( 36) *********************** 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 125 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.444 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: 0.7944 (tpp) cc_final: 0.7402 (tpp) REVERT: G 48 MET cc_start: 0.9350 (mtp) cc_final: 0.8504 (mpp) REVERT: G 93 MET cc_start: 0.8773 (tpt) cc_final: 0.8533 (tpp) REVERT: K 4 MET cc_start: 0.8221 (tpp) cc_final: 0.7872 (mmm) REVERT: H 48 MET cc_start: 0.9357 (mtp) cc_final: 0.8982 (mtp) REVERT: B 33 ILE cc_start: 0.9085 (tt) cc_final: 0.8745 (mt) REVERT: E 588 LYS cc_start: 0.9394 (mmtm) cc_final: 0.9153 (mmmt) REVERT: L 4 MET cc_start: 0.7951 (tpp) cc_final: 0.7418 (tpp) REVERT: L 48 LEU cc_start: 0.8460 (mt) cc_final: 0.8232 (mt) REVERT: I 48 MET cc_start: 0.9379 (mtp) cc_final: 0.8538 (mpp) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0741 time to fit residues: 14.6185 Evaluate side-chains 100 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 16 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN I 43 GLN F 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.052121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.042676 restraints weight = 109586.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.044122 restraints weight = 68648.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.045171 restraints weight = 49354.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.045898 restraints weight = 38532.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.046443 restraints weight = 31947.647| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13239 Z= 0.120 Angle : 0.639 9.219 18039 Z= 0.324 Chirality : 0.044 0.186 2070 Planarity : 0.004 0.036 2262 Dihedral : 5.366 24.028 1761 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1590 helix: -0.27 (0.35), residues: 219 sheet: -0.55 (0.22), residues: 570 loop : -0.31 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.020 0.002 TYR C 109 PHE 0.021 0.002 PHE B 132 TRP 0.020 0.002 TRP C 104 HIS 0.007 0.001 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13200) covalent geometry : angle 0.62991 / 0.32 (17934) SS BOND : bond 0.00237 / 0.12 ( 12) SS BOND : angle 1.69634 / 1.22 ( 24) hydrogen bonds : bond 0.03062 / 2.07 ( 468) hydrogen bonds : angle 5.48001 / 3.86 ( 1179) link_ALPHA1-6 : bond 0.00490 / 0.25 ( 3) link_ALPHA1-6 : angle 1.35446 / 0.83 ( 9) link_BETA1-4 : bond 0.00555 / 0.31 ( 12) link_BETA1-4 : angle 1.44794 / 0.93 ( 36) link_NAG-ASN : bond 0.00120 / 0.07 ( 12) link_NAG-ASN : angle 1.47022 / 0.89 ( 36) *********************** 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 139 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.378 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 48 LEU cc_start: 0.8488 (mt) cc_final: 0.8272 (mt) REVERT: G 48 MET cc_start: 0.9265 (mtp) cc_final: 0.8359 (mpp) REVERT: G 93 MET cc_start: 0.8726 (tpt) cc_final: 0.8431 (tpp) REVERT: H 48 MET cc_start: 0.9257 (mtp) cc_final: 0.8829 (mtp) REVERT: H 93 MET cc_start: 0.8284 (tpp) cc_final: 0.7824 (tpp) REVERT: B 33 ILE cc_start: 0.8968 (tt) cc_final: 0.8609 (mt) REVERT: B 132 PHE cc_start: 0.6034 (p90) cc_final: 0.5764 (p90) REVERT: E 588 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9176 (mmmt) REVERT: L 4 MET cc_start: 0.7736 (tpp) cc_final: 0.7494 (tpp) REVERT: L 48 LEU cc_start: 0.8462 (mt) cc_final: 0.8227 (mt) REVERT: I 48 MET cc_start: 0.9278 (mtp) cc_final: 0.8421 (mpp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0845 time to fit residues: 18.1815 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 : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN I 43 GLN F 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.052532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.043498 restraints weight = 108689.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.044855 restraints weight = 70198.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.045841 restraints weight = 51522.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.046560 restraints weight = 40957.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.047082 restraints weight = 34275.932| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13239 Z= 0.136 Angle : 0.643 10.100 18039 Z= 0.326 Chirality : 0.044 0.182 2070 Planarity : 0.004 0.035 2262 Dihedral : 5.302 23.293 1761 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1590 helix: -0.26 (0.36), residues: 219 sheet: -0.53 (0.22), residues: 570 loop : -0.32 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.015 0.002 TYR C 99 PHE 0.021 0.002 PHE H 108 TRP 0.017 0.002 TRP C 104 HIS 0.008 0.001 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13200) covalent geometry : angle 0.63456 / 0.32 (17934) SS BOND : bond 0.00276 / 0.17 ( 12) SS BOND : angle 1.76650 / 1.26 ( 24) hydrogen bonds : bond 0.03040 / 2.05 ( 468) hydrogen bonds : angle 5.54926 / 3.90 ( 1179) link_ALPHA1-6 : bond 0.00400 / 0.20 ( 3) link_ALPHA1-6 : angle 1.36626 / 0.84 ( 9) link_BETA1-4 : bond 0.00540 / 0.30 ( 12) link_BETA1-4 : angle 1.42833 / 0.90 ( 36) link_NAG-ASN : bond 0.00209 / 0.12 ( 12) link_NAG-ASN : angle 1.40684 / 0.85 ( 36) ********************** 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 : 0.490 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: J 48 LEU cc_start: 0.8527 (mt) cc_final: 0.8283 (mt) REVERT: G 48 MET cc_start: 0.9224 (mtp) cc_final: 0.8380 (mpp) REVERT: H 48 MET cc_start: 0.9197 (mtp) cc_final: 0.8807 (mtp) REVERT: H 93 MET cc_start: 0.8330 (tpp) cc_final: 0.7880 (tpp) REVERT: B 33 ILE cc_start: 0.8995 (tt) cc_final: 0.8593 (mt) REVERT: B 132 PHE cc_start: 0.6083 (p90) cc_final: 0.5777 (p90) REVERT: E 588 LYS cc_start: 0.9423 (mmtm) cc_final: 0.9147 (mmmt) REVERT: L 17 GLU cc_start: 0.9288 (pt0) cc_final: 0.8991 (mp0) REVERT: L 48 LEU cc_start: 0.8246 (mt) cc_final: 0.8020 (mt) REVERT: I 48 MET cc_start: 0.9226 (mtp) cc_final: 0.8944 (mtp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0811 time to fit residues: 17.0077 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 0.0770 chunk 60 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN I 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.050787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.041717 restraints weight = 111540.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.043039 restraints weight = 71181.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.044013 restraints weight = 51881.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.044715 restraints weight = 41213.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.045228 restraints weight = 34516.921| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13239 Z= 0.219 Angle : 0.700 9.818 18039 Z= 0.356 Chirality : 0.044 0.182 2070 Planarity : 0.005 0.038 2262 Dihedral : 5.606 22.064 1761 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.23 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1590 helix: -0.53 (0.34), residues: 219 sheet: -0.41 (0.23), residues: 540 loop : -0.54 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 84 TYR 0.021 0.002 TYR D 517 PHE 0.020 0.002 PHE H 108 TRP 0.023 0.003 TRP L 36 HIS 0.012 0.002 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (13200) covalent geometry : angle 0.69069 / 0.35 (17934) SS BOND : bond 0.00264 / 0.15 ( 12) SS BOND : angle 1.59696 / 1.13 ( 24) hydrogen bonds : bond 0.03291 / 2.25 ( 468) hydrogen bonds : angle 5.71401 / 4.01 ( 1179) link_ALPHA1-6 : bond 0.00348 / 0.17 ( 3) link_ALPHA1-6 : angle 1.39893 / 0.86 ( 9) link_BETA1-4 : bond 0.00513 / 0.28 ( 12) link_BETA1-4 : angle 1.49529 / 0.91 ( 36) link_NAG-ASN : bond 0.00605 / 0.34 ( 12) link_NAG-ASN : angle 1.93525 / 1.17 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.30 seconds wall clock time: 30 minutes 24.04 seconds (1824.04 seconds total)