Starting phenix.real_space_refine on Wed Mar 4 11:08:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kex_22842/03_2026/7kex_22842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kex_22842/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kex_22842/03_2026/7kex_22842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kex_22842/03_2026/7kex_22842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kex_22842/03_2026/7kex_22842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kex_22842/03_2026/7kex_22842.map" } 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-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: K, L, H, I, B, C, E, F, O, Q, P, R Time building chain proxies: 2.34, per 1000 atoms: 0.18 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: 1.21 Conformation dependent library (CDL) restraints added in 524.5 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: 0.62 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: 2.36 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2316 1.31 - 1.45: 4144 1.45 - 1.58: 6590 1.58 - 1.72: 90 1.72 - 1.85: 60 Bond restraints: 13200 Sorted by residual: bond pdb=" CB PHE H 108 " pdb=" CG PHE H 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.04e+01 bond pdb=" CB ILE B 185 " pdb=" CG1 ILE B 185 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PHE G 108 " pdb=" CG PHE G 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.02e+01 bond pdb=" CB PHE I 108 " pdb=" CG PHE I 108 " ideal model delta sigma weight residual 1.502 1.357 0.145 2.30e-02 1.89e+03 3.99e+01 bond pdb=" CB ILE C 185 " pdb=" CG1 ILE C 185 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 13195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 14402 2.19 - 4.38: 2896 4.38 - 6.57: 529 6.57 - 8.76: 92 8.76 - 10.95: 15 Bond angle restraints: 17934 Sorted by residual: angle pdb=" C PRO B 93 " pdb=" N PRO B 94 " pdb=" CA PRO B 94 " ideal model delta sigma weight residual 120.31 127.77 -7.46 9.80e-01 1.04e+00 5.80e+01 angle pdb=" C PRO A 93 " pdb=" N PRO A 94 " pdb=" CA PRO A 94 " ideal model delta sigma weight residual 120.31 127.74 -7.43 9.80e-01 1.04e+00 5.75e+01 angle pdb=" C PRO C 93 " pdb=" N PRO C 94 " pdb=" CA PRO C 94 " ideal model delta sigma weight residual 120.31 127.70 -7.39 9.80e-01 1.04e+00 5.69e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.37e+01 angle pdb=" C GLY E 536 " pdb=" N PRO E 537 " pdb=" CA PRO E 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.36e+01 ... (remaining 17929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 7768 21.44 - 42.89: 185 42.89 - 64.33: 57 64.33 - 85.78: 60 85.78 - 107.22: 30 Dihedral angle restraints: 8100 sinusoidal: 3489 harmonic: 4611 Sorted by residual: dihedral pdb=" C3 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.60 107.22 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C3 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.59 107.21 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C3 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.56 107.18 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8097 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: 0.03 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: 2.350 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.610 Find NCS groups from input model: 0.100 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.146 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 : 14.860 107.219 5130 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 covalent geometry : bond 0.02164 (13200) covalent geometry : angle 1.87570 (17934) SS BOND : bond 0.00973 ( 12) SS BOND : angle 3.22795 ( 24) hydrogen bonds : bond 0.14579 ( 468) hydrogen bonds : angle 8.17248 ( 1179) link_ALPHA1-6 : bond 0.08348 ( 3) link_ALPHA1-6 : angle 4.55209 ( 9) link_BETA1-4 : bond 0.07144 ( 12) link_BETA1-4 : angle 5.12155 ( 36) link_NAG-ASN : bond 0.07692 ( 12) link_NAG-ASN : angle 2.21838 ( 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 : 0.436 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: 0.1204 time to fit residues: 57.0180 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 : 0.324 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN I 43 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3863 r_free = 0.3863 target = 0.059134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.048986 restraints weight = 99032.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.050695 restraints weight = 62992.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.051900 restraints weight = 45087.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.052773 restraints weight = 34841.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.053421 restraints weight = 28506.297| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13239 Z= 0.194 Angle : 0.840 11.172 18039 Z= 0.429 Chirality : 0.051 0.253 2070 Planarity : 0.005 0.050 2262 Dihedral : 10.403 67.851 2310 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.33 % 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: -0.10 (0.22), residues: 1590 helix: -0.37 (0.34), residues: 207 sheet: -0.23 (0.21), residues: 621 loop : 0.39 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 18 TYR 0.028 0.003 TYR B 99 PHE 0.027 0.002 PHE A 132 TRP 0.017 0.002 TRP I 47 HIS 0.015 0.003 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00436 (13200) covalent geometry : angle 0.81117 (17934) SS BOND : bond 0.00399 ( 12) SS BOND : angle 2.35006 ( 24) hydrogen bonds : bond 0.04851 ( 468) hydrogen bonds : angle 7.04314 ( 1179) link_ALPHA1-6 : bond 0.00978 ( 3) link_ALPHA1-6 : angle 2.11480 ( 9) link_BETA1-4 : bond 0.00961 ( 12) link_BETA1-4 : angle 4.02341 ( 36) link_NAG-ASN : bond 0.00358 ( 12) link_NAG-ASN : angle 2.19974 ( 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 : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 17 GLU cc_start: 0.8969 (pt0) cc_final: 0.8715 (mp0) REVERT: J 71 ASP cc_start: 0.8528 (t0) cc_final: 0.8076 (p0) REVERT: G 48 MET cc_start: 0.9220 (mtp) cc_final: 0.8574 (mtp) REVERT: A 141 VAL cc_start: 0.9444 (t) cc_final: 0.9215 (p) REVERT: D 584 ILE cc_start: 0.9676 (pt) cc_final: 0.9441 (pt) REVERT: D 588 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9269 (mmmt) REVERT: K 71 ASP cc_start: 0.8669 (t0) cc_final: 0.8151 (p0) REVERT: H 48 MET cc_start: 0.9174 (mtp) cc_final: 0.8471 (mtp) REVERT: H 63 GLN cc_start: 0.8802 (pm20) cc_final: 0.7993 (pm20) REVERT: B 132 PHE cc_start: 0.5895 (p90) cc_final: 0.5080 (p90) REVERT: B 141 VAL cc_start: 0.9216 (t) cc_final: 0.9000 (p) REVERT: E 588 LYS cc_start: 0.9447 (mmtm) cc_final: 0.9220 (mmmt) REVERT: L 4 MET cc_start: 0.8705 (mmt) cc_final: 0.8473 (tpp) REVERT: L 17 GLU cc_start: 0.8908 (pt0) cc_final: 0.8525 (mp0) REVERT: L 71 ASP cc_start: 0.8473 (t0) cc_final: 0.8066 (p0) REVERT: I 48 MET cc_start: 0.9166 (mtp) cc_final: 0.8548 (mtp) REVERT: C 141 VAL cc_start: 0.9318 (t) cc_final: 0.9079 (p) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.1114 time to fit residues: 39.7635 Evaluate side-chains 149 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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: 0.9980 chunk 85 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 101 optimal weight: 0.0030 chunk 126 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 1 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN I 43 GLN ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.061912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.052661 restraints weight = 128975.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.054198 restraints weight = 78968.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.055289 restraints weight = 54730.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.056034 restraints weight = 41128.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.056598 restraints weight = 32908.665| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13239 Z= 0.228 Angle : 0.750 9.168 18039 Z= 0.389 Chirality : 0.047 0.203 2070 Planarity : 0.006 0.059 2262 Dihedral : 7.310 40.979 2310 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.15 % Allowed : 2.81 % Favored : 97.04 % 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: -0.35 (0.22), residues: 576 loop : 0.15 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 18 TYR 0.029 0.002 TYR K 50 PHE 0.028 0.002 PHE A 132 TRP 0.020 0.003 TRP H 105 HIS 0.013 0.003 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00507 (13200) covalent geometry : angle 0.73363 (17934) SS BOND : bond 0.01194 ( 12) SS BOND : angle 1.97433 ( 24) hydrogen bonds : bond 0.04018 ( 468) hydrogen bonds : angle 6.28573 ( 1179) link_ALPHA1-6 : bond 0.00807 ( 3) link_ALPHA1-6 : angle 1.90090 ( 9) link_BETA1-4 : bond 0.00887 ( 12) link_BETA1-4 : angle 2.75506 ( 36) link_NAG-ASN : bond 0.00327 ( 12) link_NAG-ASN : angle 1.51715 ( 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 193 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.387 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: J 4 MET cc_start: 0.8352 (tpp) cc_final: 0.7784 (mmm) REVERT: J 71 ASP cc_start: 0.8474 (t0) cc_final: 0.8002 (p0) REVERT: G 48 MET cc_start: 0.9110 (mtp) cc_final: 0.8474 (mtp) REVERT: A 117 ASP cc_start: 0.9261 (p0) cc_final: 0.9036 (p0) REVERT: A 162 TYR cc_start: 0.6982 (m-80) cc_final: 0.6323 (m-10) REVERT: K 4 MET cc_start: 0.8300 (tpp) cc_final: 0.7726 (mmm) REVERT: K 17 GLU cc_start: 0.9152 (pt0) cc_final: 0.8882 (mp0) REVERT: K 71 ASP cc_start: 0.8414 (t0) cc_final: 0.8089 (p0) REVERT: H 48 MET cc_start: 0.9025 (mtp) cc_final: 0.8469 (mtp) REVERT: H 63 GLN cc_start: 0.8880 (pm20) cc_final: 0.8533 (pm20) REVERT: L 17 GLU cc_start: 0.8925 (pt0) cc_final: 0.8680 (pt0) REVERT: L 71 ASP cc_start: 0.8586 (t0) cc_final: 0.8027 (p0) REVERT: I 48 MET cc_start: 0.9168 (mtp) cc_final: 0.8761 (mtp) REVERT: C 117 ASP cc_start: 0.9334 (p0) cc_final: 0.9124 (p0) REVERT: C 162 TYR cc_start: 0.7071 (m-80) cc_final: 0.6703 (m-80) REVERT: C 270 THR cc_start: 0.8435 (m) cc_final: 0.8160 (p) outliers start: 2 outliers final: 2 residues processed: 193 average time/residue: 0.1023 time to fit residues: 29.8657 Evaluate side-chains 134 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 9.9990 chunk 51 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 148 optimal weight: 0.0470 chunk 112 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN K 6 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.055784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.046218 restraints weight = 105486.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.047757 restraints weight = 67381.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.048878 restraints weight = 48605.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.049681 restraints weight = 38108.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.050278 restraints weight = 31465.977| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13239 Z= 0.162 Angle : 0.660 9.118 18039 Z= 0.342 Chirality : 0.045 0.222 2070 Planarity : 0.005 0.050 2262 Dihedral : 6.287 39.013 2310 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -0.40 (0.22), residues: 1590 helix: -0.22 (0.34), residues: 213 sheet: -0.41 (0.22), residues: 570 loop : 0.02 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 85 TYR 0.025 0.002 TYR C 109 PHE 0.024 0.002 PHE B 132 TRP 0.032 0.002 TRP I 105 HIS 0.008 0.002 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00371 (13200) covalent geometry : angle 0.64762 (17934) SS BOND : bond 0.00383 ( 12) SS BOND : angle 1.27680 ( 24) hydrogen bonds : bond 0.03551 ( 468) hydrogen bonds : angle 5.93887 ( 1179) link_ALPHA1-6 : bond 0.00595 ( 3) link_ALPHA1-6 : angle 1.49404 ( 9) link_BETA1-4 : bond 0.00712 ( 12) link_BETA1-4 : angle 2.45573 ( 36) link_NAG-ASN : bond 0.00115 ( 12) link_NAG-ASN : angle 1.23735 ( 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 177 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8349 (tpp) cc_final: 0.7622 (tpp) REVERT: J 17 GLU cc_start: 0.8882 (pt0) cc_final: 0.8653 (mp0) REVERT: J 71 ASP cc_start: 0.8540 (t0) cc_final: 0.8042 (p0) REVERT: G 48 MET cc_start: 0.9080 (mtp) cc_final: 0.8177 (mpp) REVERT: A 162 TYR cc_start: 0.6867 (m-80) cc_final: 0.6277 (m-10) REVERT: A 234 PHE cc_start: 0.8908 (t80) cc_final: 0.8590 (t80) REVERT: A 270 THR cc_start: 0.8027 (m) cc_final: 0.7719 (p) REVERT: K 4 MET cc_start: 0.8323 (tpp) cc_final: 0.7648 (tpp) REVERT: K 17 GLU cc_start: 0.9154 (pt0) cc_final: 0.8635 (mp0) REVERT: K 50 TYR cc_start: 0.6122 (t80) cc_final: 0.2818 (t80) REVERT: K 71 ASP cc_start: 0.8573 (t0) cc_final: 0.8225 (p0) REVERT: H 48 MET cc_start: 0.8994 (mtp) cc_final: 0.8508 (mtp) REVERT: H 63 GLN cc_start: 0.8910 (pm20) cc_final: 0.8074 (pm20) REVERT: L 4 MET cc_start: 0.7970 (tpp) cc_final: 0.7580 (tpp) REVERT: L 17 GLU cc_start: 0.9050 (pt0) cc_final: 0.8687 (mp0) REVERT: L 71 ASP cc_start: 0.8639 (t0) cc_final: 0.8047 (p0) REVERT: I 48 MET cc_start: 0.9016 (mtp) cc_final: 0.8494 (mtp) REVERT: C 162 TYR cc_start: 0.6897 (m-80) cc_final: 0.6562 (m-80) REVERT: C 270 THR cc_start: 0.8452 (m) cc_final: 0.8172 (p) REVERT: F 588 LYS cc_start: 0.9508 (mmtm) cc_final: 0.9285 (mmmt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0970 time to fit residues: 25.6658 Evaluate side-chains 130 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN D 560 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.054871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.045139 restraints weight = 107814.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.046637 restraints weight = 69470.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.047710 restraints weight = 50381.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.048503 restraints weight = 39479.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.049090 restraints weight = 32643.421| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13239 Z= 0.157 Angle : 0.650 9.044 18039 Z= 0.336 Chirality : 0.045 0.239 2070 Planarity : 0.005 0.050 2262 Dihedral : 5.910 37.893 2310 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 0.15 % Allowed : 1.33 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.44 (0.22), residues: 1590 helix: -0.11 (0.34), residues: 213 sheet: -0.52 (0.22), residues: 579 loop : 0.02 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 85 TYR 0.040 0.002 TYR K 50 PHE 0.028 0.002 PHE B 132 TRP 0.055 0.002 TRP H 105 HIS 0.009 0.002 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00357 (13200) covalent geometry : angle 0.63967 (17934) SS BOND : bond 0.00321 ( 12) SS BOND : angle 1.36062 ( 24) hydrogen bonds : bond 0.03334 ( 468) hydrogen bonds : angle 5.80730 ( 1179) link_ALPHA1-6 : bond 0.00470 ( 3) link_ALPHA1-6 : angle 1.41281 ( 9) link_BETA1-4 : bond 0.00753 ( 12) link_BETA1-4 : angle 2.20627 ( 36) link_NAG-ASN : bond 0.00158 ( 12) link_NAG-ASN : angle 1.16332 ( 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 180 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.441 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: 0.8019 (tpp) cc_final: 0.7374 (tpp) REVERT: J 71 ASP cc_start: 0.8644 (t0) cc_final: 0.8123 (p0) REVERT: G 48 MET cc_start: 0.9140 (mtp) cc_final: 0.8186 (mpp) REVERT: A 109 TYR cc_start: 0.8454 (m-80) cc_final: 0.8214 (m-80) REVERT: A 162 TYR cc_start: 0.6762 (m-80) cc_final: 0.6236 (m-80) REVERT: A 183 PHE cc_start: 0.7778 (m-80) cc_final: 0.7511 (m-80) REVERT: A 270 THR cc_start: 0.8132 (m) cc_final: 0.7916 (p) REVERT: K 4 MET cc_start: 0.8222 (tpp) cc_final: 0.7836 (mmm) REVERT: K 17 GLU cc_start: 0.9264 (pt0) cc_final: 0.8873 (mp0) REVERT: K 71 ASP cc_start: 0.8664 (t0) cc_final: 0.8263 (p0) REVERT: H 48 MET cc_start: 0.9165 (mtp) cc_final: 0.8632 (mtp) REVERT: H 63 GLN cc_start: 0.8918 (pm20) cc_final: 0.8116 (pm20) REVERT: E 531 TRP cc_start: 0.8217 (p-90) cc_final: 0.7971 (p-90) REVERT: L 4 MET cc_start: 0.7986 (tpp) cc_final: 0.7576 (tpp) REVERT: L 17 GLU cc_start: 0.9257 (pt0) cc_final: 0.9002 (mp0) REVERT: L 71 ASP cc_start: 0.8740 (t0) cc_final: 0.8184 (p0) REVERT: I 48 MET cc_start: 0.9211 (mtp) cc_final: 0.8201 (mpp) REVERT: C 162 TYR cc_start: 0.6773 (m-80) cc_final: 0.6413 (m-80) REVERT: C 270 THR cc_start: 0.8517 (m) cc_final: 0.8264 (p) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.0974 time to fit residues: 26.6496 Evaluate side-chains 122 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** 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 = 0.3700 r_free = 0.3700 target = 0.056403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.047255 restraints weight = 130035.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.048659 restraints weight = 80588.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.049632 restraints weight = 57136.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.050344 restraints weight = 44060.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.050825 restraints weight = 35929.843| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 13239 Z= 0.313 Angle : 0.803 11.349 18039 Z= 0.419 Chirality : 0.046 0.231 2070 Planarity : 0.006 0.046 2262 Dihedral : 6.550 41.892 2310 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.04 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.02 (0.34), residues: 195 sheet: -0.71 (0.21), residues: 630 loop : -0.16 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 38 TYR 0.045 0.003 TYR J 50 PHE 0.029 0.003 PHE B 132 TRP 0.065 0.004 TRP G 105 HIS 0.009 0.003 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00690 (13200) covalent geometry : angle 0.79109 (17934) SS BOND : bond 0.00377 ( 12) SS BOND : angle 1.57103 ( 24) hydrogen bonds : bond 0.04004 ( 468) hydrogen bonds : angle 6.01948 ( 1179) link_ALPHA1-6 : bond 0.00250 ( 3) link_ALPHA1-6 : angle 1.52860 ( 9) link_BETA1-4 : bond 0.00755 ( 12) link_BETA1-4 : angle 2.25112 ( 36) link_NAG-ASN : bond 0.00809 ( 12) link_NAG-ASN : angle 1.99173 ( 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 140 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 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: J 4 MET cc_start: 0.8037 (tpp) cc_final: 0.7523 (mmm) REVERT: J 71 ASP cc_start: 0.8602 (t0) cc_final: 0.7986 (p0) REVERT: G 48 MET cc_start: 0.9219 (mtp) cc_final: 0.8410 (mpp) REVERT: A 109 TYR cc_start: 0.8760 (m-80) cc_final: 0.8484 (m-10) REVERT: K 4 MET cc_start: 0.8288 (tpp) cc_final: 0.7605 (tpp) REVERT: K 71 ASP cc_start: 0.8416 (t0) cc_final: 0.7901 (p0) REVERT: H 48 MET cc_start: 0.9224 (mtp) cc_final: 0.8824 (mtp) REVERT: L 4 MET cc_start: 0.8100 (tpp) cc_final: 0.7734 (tpp) REVERT: L 71 ASP cc_start: 0.8640 (t0) cc_final: 0.7931 (p0) REVERT: I 48 MET cc_start: 0.9270 (mtp) cc_final: 0.8430 (mpp) REVERT: F 531 TRP cc_start: 0.8528 (p-90) cc_final: 0.8261 (p-90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0967 time to fit residues: 20.9733 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 : 0.376 ------------------------------------------------------------------------------- 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: 10.0000 chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 560 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** ** 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 = 0.3664 r_free = 0.3664 target = 0.052573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.043151 restraints weight = 108852.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.044551 restraints weight = 69688.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.045595 restraints weight = 50756.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.046344 restraints weight = 39969.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.046899 restraints weight = 33331.955| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13239 Z= 0.182 Angle : 0.685 7.929 18039 Z= 0.351 Chirality : 0.045 0.187 2070 Planarity : 0.005 0.046 2262 Dihedral : 6.299 38.899 2310 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % 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: -0.72 (0.21), residues: 1590 helix: -0.13 (0.34), residues: 195 sheet: -0.63 (0.22), residues: 576 loop : -0.29 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 64 TYR 0.027 0.002 TYR C 109 PHE 0.025 0.002 PHE B 132 TRP 0.022 0.002 TRP A 104 HIS 0.006 0.002 HIS E 516 Details of bonding type rmsd covalent geometry : bond 0.00408 (13200) covalent geometry : angle 0.67141 (17934) SS BOND : bond 0.00354 ( 12) SS BOND : angle 1.35019 ( 24) hydrogen bonds : bond 0.03425 ( 468) hydrogen bonds : angle 5.72844 ( 1179) link_ALPHA1-6 : bond 0.00455 ( 3) link_ALPHA1-6 : angle 1.38010 ( 9) link_BETA1-4 : bond 0.00611 ( 12) link_BETA1-4 : angle 2.23605 ( 36) link_NAG-ASN : bond 0.00675 ( 12) link_NAG-ASN : angle 2.03111 ( 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 154 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.572 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: 0.7928 (tpp) cc_final: 0.7338 (tpp) REVERT: J 71 ASP cc_start: 0.8615 (t0) cc_final: 0.7974 (p0) REVERT: G 48 MET cc_start: 0.9226 (mtp) cc_final: 0.8324 (mpp) REVERT: G 66 ASP cc_start: 0.8360 (m-30) cc_final: 0.8039 (m-30) REVERT: A 109 TYR cc_start: 0.8866 (m-80) cc_final: 0.8617 (m-10) REVERT: A 161 LEU cc_start: 0.8709 (mt) cc_final: 0.8505 (mp) REVERT: D 592 PHE cc_start: 0.9172 (t80) cc_final: 0.8936 (t80) REVERT: K 4 MET cc_start: 0.8141 (tpp) cc_final: 0.7768 (mmm) REVERT: K 71 ASP cc_start: 0.8613 (t0) cc_final: 0.8099 (p0) REVERT: H 48 MET cc_start: 0.9225 (mtp) cc_final: 0.9007 (mtp) REVERT: L 4 MET cc_start: 0.7952 (tpp) cc_final: 0.7613 (tpp) REVERT: L 21 LEU cc_start: 0.8940 (mp) cc_final: 0.8675 (mm) REVERT: L 71 ASP cc_start: 0.8705 (t0) cc_final: 0.8005 (p0) REVERT: I 48 MET cc_start: 0.9243 (mtp) cc_final: 0.8403 (mpp) REVERT: F 531 TRP cc_start: 0.8536 (p-90) cc_final: 0.8207 (p-90) REVERT: F 588 LYS cc_start: 0.9538 (mmtm) cc_final: 0.9335 (mmmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0901 time to fit residues: 21.3936 Evaluate side-chains 106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 20.0000 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** L 27 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 = 0.3635 r_free = 0.3635 target = 0.051850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.042631 restraints weight = 109110.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.044038 restraints weight = 69356.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.045059 restraints weight = 50072.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.045807 restraints weight = 39367.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.046307 restraints weight = 32609.738| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13239 Z= 0.207 Angle : 0.693 11.791 18039 Z= 0.356 Chirality : 0.044 0.199 2070 Planarity : 0.005 0.065 2262 Dihedral : 6.263 40.612 2310 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: -0.82 (0.21), residues: 1590 helix: -0.05 (0.35), residues: 195 sheet: -0.78 (0.20), residues: 681 loop : -0.21 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 219 TYR 0.023 0.002 TYR F 517 PHE 0.026 0.002 PHE B 132 TRP 0.035 0.003 TRP H 105 HIS 0.005 0.002 HIS E 516 Details of bonding type rmsd covalent geometry : bond 0.00465 (13200) covalent geometry : angle 0.68284 (17934) SS BOND : bond 0.00271 ( 12) SS BOND : angle 1.49053 ( 24) hydrogen bonds : bond 0.03440 ( 468) hydrogen bonds : angle 5.77053 ( 1179) link_ALPHA1-6 : bond 0.00286 ( 3) link_ALPHA1-6 : angle 1.47067 ( 9) link_BETA1-4 : bond 0.00647 ( 12) link_BETA1-4 : angle 1.80402 ( 36) link_NAG-ASN : bond 0.00572 ( 12) link_NAG-ASN : angle 1.80292 ( 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 134 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.7889 (tpp) cc_final: 0.7386 (tpp) REVERT: G 48 MET cc_start: 0.9205 (mtp) cc_final: 0.8383 (mpp) REVERT: A 161 LEU cc_start: 0.8745 (mt) cc_final: 0.8527 (mp) REVERT: D 592 PHE cc_start: 0.9200 (t80) cc_final: 0.8953 (t80) REVERT: K 4 MET cc_start: 0.8213 (tpp) cc_final: 0.7865 (mmm) REVERT: K 50 TYR cc_start: 0.6520 (t80) cc_final: 0.5110 (t80) REVERT: H 48 MET cc_start: 0.9246 (mtp) cc_final: 0.8853 (mtp) REVERT: E 588 LYS cc_start: 0.9433 (mmtm) cc_final: 0.9227 (mmmt) REVERT: L 4 MET cc_start: 0.8027 (tpp) cc_final: 0.7677 (tpp) REVERT: L 21 LEU cc_start: 0.8869 (mp) cc_final: 0.8650 (mm) REVERT: I 48 MET cc_start: 0.9257 (mtp) cc_final: 0.8472 (mpp) REVERT: F 531 TRP cc_start: 0.8614 (p-90) cc_final: 0.8259 (p-90) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0855 time to fit residues: 17.9215 Evaluate side-chains 98 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN D 570 GLN H 43 GLN ** E 560 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.050198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.041118 restraints weight = 112161.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.042471 restraints weight = 70683.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.043444 restraints weight = 50943.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.044163 restraints weight = 40155.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.044662 restraints weight = 33318.619| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.6926 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= 0.263 Angle : 0.755 7.919 18039 Z= 0.391 Chirality : 0.046 0.170 2070 Planarity : 0.006 0.066 2262 Dihedral : 6.676 43.165 2310 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -0.91 (0.21), residues: 1590 helix: -0.54 (0.33), residues: 201 sheet: -0.53 (0.22), residues: 549 loop : -0.55 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 219 TYR 0.030 0.003 TYR F 517 PHE 0.032 0.003 PHE H 110 TRP 0.028 0.003 TRP A 104 HIS 0.011 0.003 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00583 (13200) covalent geometry : angle 0.74321 (17934) SS BOND : bond 0.00328 ( 12) SS BOND : angle 1.47126 ( 24) hydrogen bonds : bond 0.03661 ( 468) hydrogen bonds : angle 6.03274 ( 1179) link_ALPHA1-6 : bond 0.00183 ( 3) link_ALPHA1-6 : angle 1.50208 ( 9) link_BETA1-4 : bond 0.00621 ( 12) link_BETA1-4 : angle 1.72020 ( 36) link_NAG-ASN : bond 0.00717 ( 12) link_NAG-ASN : angle 2.30851 ( 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 128 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.506 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: J 4 MET cc_start: 0.7822 (tpp) cc_final: 0.7244 (tpp) REVERT: G 48 MET cc_start: 0.9305 (mtp) cc_final: 0.8890 (mtm) REVERT: G 93 MET cc_start: 0.8529 (tpp) cc_final: 0.8149 (tpp) REVERT: A 161 LEU cc_start: 0.8849 (mt) cc_final: 0.8632 (mp) REVERT: D 531 TRP cc_start: 0.8865 (p-90) cc_final: 0.8526 (p-90) REVERT: K 74 LEU cc_start: 0.8832 (tp) cc_final: 0.8611 (tp) REVERT: H 48 MET cc_start: 0.9303 (mtp) cc_final: 0.8922 (mtm) REVERT: B 33 ILE cc_start: 0.9023 (tt) cc_final: 0.8674 (mt) REVERT: E 588 LYS cc_start: 0.9423 (mmtm) cc_final: 0.9198 (mmmt) REVERT: L 4 MET cc_start: 0.8003 (tpp) cc_final: 0.7713 (tpp) REVERT: I 48 MET cc_start: 0.9319 (mtp) cc_final: 0.8957 (mtm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0943 time to fit residues: 18.6844 Evaluate side-chains 96 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 6.9990 chunk 146 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 0.0020 chunk 135 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.051442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.042246 restraints weight = 110858.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.043634 restraints weight = 70053.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.044647 restraints weight = 50795.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.045368 restraints weight = 39910.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.045893 restraints weight = 33190.525| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.7021 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= 0.169 Angle : 0.685 9.693 18039 Z= 0.351 Chirality : 0.045 0.212 2070 Planarity : 0.005 0.047 2262 Dihedral : 6.344 38.788 2310 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.79 (0.21), residues: 1590 helix: 0.08 (0.36), residues: 192 sheet: -0.48 (0.23), residues: 546 loop : -0.59 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.027 0.002 TYR A 109 PHE 0.029 0.002 PHE B 132 TRP 0.027 0.003 TRP K 36 HIS 0.007 0.002 HIS E 516 Details of bonding type rmsd covalent geometry : bond 0.00390 (13200) covalent geometry : angle 0.67511 (17934) SS BOND : bond 0.00272 ( 12) SS BOND : angle 1.51466 ( 24) hydrogen bonds : bond 0.03331 ( 468) hydrogen bonds : angle 5.82626 ( 1179) link_ALPHA1-6 : bond 0.00302 ( 3) link_ALPHA1-6 : angle 1.45011 ( 9) link_BETA1-4 : bond 0.00614 ( 12) link_BETA1-4 : angle 1.60833 ( 36) link_NAG-ASN : bond 0.00353 ( 12) link_NAG-ASN : angle 1.81385 ( 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 130 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.525 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: J 4 MET cc_start: 0.7760 (tpp) cc_final: 0.7204 (tpp) REVERT: G 48 MET cc_start: 0.9336 (mtp) cc_final: 0.8521 (mpp) REVERT: G 93 MET cc_start: 0.8671 (tpp) cc_final: 0.8258 (tpp) REVERT: K 48 LEU cc_start: 0.9153 (pp) cc_final: 0.8649 (mm) REVERT: H 48 MET cc_start: 0.9353 (mtp) cc_final: 0.8925 (mtm) REVERT: B 33 ILE cc_start: 0.9044 (tt) cc_final: 0.8677 (mt) REVERT: E 588 LYS cc_start: 0.9426 (mmtm) cc_final: 0.9184 (mmmt) REVERT: E 595 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8778 (tm-30) REVERT: L 4 MET cc_start: 0.7897 (tpp) cc_final: 0.7644 (tpp) REVERT: I 48 MET cc_start: 0.9316 (mtp) cc_final: 0.8487 (mpp) REVERT: F 531 TRP cc_start: 0.8670 (p-90) cc_final: 0.8387 (p-90) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0959 time to fit residues: 18.8404 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 38 GLN J 91 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.054034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.045006 restraints weight = 131691.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.046371 restraints weight = 80349.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.047331 restraints weight = 56436.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.048008 restraints weight = 43290.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.048461 restraints weight = 35343.094| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13239 Z= 0.277 Angle : 0.764 9.626 18039 Z= 0.395 Chirality : 0.045 0.170 2070 Planarity : 0.005 0.051 2262 Dihedral : 6.598 40.354 2310 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.60 % Favored : 93.21 % 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: -1.00 (0.21), residues: 1590 helix: -0.29 (0.35), residues: 192 sheet: -0.63 (0.22), residues: 552 loop : -0.67 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.030 0.003 TYR F 517 PHE 0.032 0.002 PHE B 132 TRP 0.027 0.003 TRP A 104 HIS 0.009 0.002 HIS E 516 Details of bonding type rmsd covalent geometry : bond 0.00616 (13200) covalent geometry : angle 0.75279 (17934) SS BOND : bond 0.00283 ( 12) SS BOND : angle 1.41775 ( 24) hydrogen bonds : bond 0.03577 ( 468) hydrogen bonds : angle 5.95434 ( 1179) link_ALPHA1-6 : bond 0.00123 ( 3) link_ALPHA1-6 : angle 1.56622 ( 9) link_BETA1-4 : bond 0.00665 ( 12) link_BETA1-4 : angle 1.70837 ( 36) link_NAG-ASN : bond 0.00814 ( 12) link_NAG-ASN : angle 2.34414 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.42 seconds wall clock time: 33 minutes 14.66 seconds (1994.66 seconds total)