Starting phenix.real_space_refine on Fri Mar 6 13:21:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ni2_12349/03_2026/7ni2_12349.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ni2_12349/03_2026/7ni2_12349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ni2_12349/03_2026/7ni2_12349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ni2_12349/03_2026/7ni2_12349.map" model { file = "/net/cci-nas-00/data/ceres_data/7ni2_12349/03_2026/7ni2_12349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ni2_12349/03_2026/7ni2_12349.cif" } resolution = 2.89 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= 0.008 sd= 0.060 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 104 5.16 5 C 20088 2.51 5 N 5264 2.21 5 O 5888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s 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: 31344 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3918 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 487} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 4.43, per 1000 atoms: 0.14 Number of scatterers: 31344 At special positions: 0 Unit cell: (162.876, 162.045, 138.777, 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 104 16.00 O 5888 8.00 N 5264 7.00 C 20088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 32 sheets defined 46.3% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 removed outlier: 3.581A pdb=" N LYS A 101 " --> pdb=" O MET A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 450 Processing helix chain 'A' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.638A pdb=" N MET A 522 " --> pdb=" O HIS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.696A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.039A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 450 Processing helix chain 'B' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET B 522 " --> pdb=" O HIS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 removed outlier: 3.579A pdb=" N LYS C 101 " --> pdb=" O MET C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.970A pdb=" N LEU C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 450 Processing helix chain 'C' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET C 522 " --> pdb=" O HIS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 555 removed outlier: 3.778A pdb=" N THR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 623 through 636 removed outlier: 3.559A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 4.037A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS D 101 " --> pdb=" O MET D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.970A pdb=" N LEU D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 261 removed outlier: 3.525A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 450 Processing helix chain 'D' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET D 522 " --> pdb=" O HIS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY D 575 " --> pdb=" O HIS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 595' Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 623 through 636 removed outlier: 3.559A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS E 101 " --> pdb=" O MET E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 450 Processing helix chain 'E' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET E 522 " --> pdb=" O HIS E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR E 554 " --> pdb=" O THR E 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 575 removed outlier: 3.683A pdb=" N GLY E 575 " --> pdb=" O HIS E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 587 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.694A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 595' Processing helix chain 'E' and resid 615 through 621 Processing helix chain 'E' and resid 623 through 636 removed outlier: 3.559A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 672 through 686 removed outlier: 3.607A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.581A pdb=" N LYS F 101 " --> pdb=" O MET F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 450 Processing helix chain 'F' and resid 457 through 464 removed outlier: 4.036A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET F 522 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR F 554 " --> pdb=" O THR F 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY F 575 " --> pdb=" O HIS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 591 through 595' Processing helix chain 'F' and resid 615 through 621 Processing helix chain 'F' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.608A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 4.038A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS G 101 " --> pdb=" O MET G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.969A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 450 Processing helix chain 'G' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 522 removed outlier: 3.637A pdb=" N MET G 522 " --> pdb=" O HIS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 555 removed outlier: 3.776A pdb=" N THR G 554 " --> pdb=" O THR G 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY G 575 " --> pdb=" O HIS G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 587 Processing helix chain 'G' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE G 595 " --> pdb=" O ALA G 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 595' Processing helix chain 'G' and resid 615 through 621 Processing helix chain 'G' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.608A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 4.037A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.580A pdb=" N LYS H 101 " --> pdb=" O MET H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 removed outlier: 3.968A pdb=" N LEU H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 261 removed outlier: 3.526A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 450 Processing helix chain 'H' and resid 457 through 464 removed outlier: 4.035A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 522 removed outlier: 3.638A pdb=" N MET H 522 " --> pdb=" O HIS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 555 removed outlier: 3.777A pdb=" N THR H 554 " --> pdb=" O THR H 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY H 555 " --> pdb=" O ILE H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 575 removed outlier: 3.682A pdb=" N GLY H 575 " --> pdb=" O HIS H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 587 Processing helix chain 'H' and resid 591 through 595 removed outlier: 3.695A pdb=" N ILE H 595 " --> pdb=" O ALA H 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 591 through 595' Processing helix chain 'H' and resid 615 through 621 Processing helix chain 'H' and resid 623 through 636 removed outlier: 3.558A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.608A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP A 136 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 182 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 558 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 607 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 604 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 221 removed outlier: 7.080A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP B 136 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 182 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU B 695 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 471 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY B 697 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 558 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE B 607 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE B 560 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 604 " --> pdb=" O VAL B 599 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU C 60 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP C 136 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 182 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU C 695 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 471 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 697 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 558 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE C 607 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE C 560 " --> pdb=" O ILE C 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 604 " --> pdb=" O VAL C 599 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 221 removed outlier: 7.080A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP D 136 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 182 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL D 558 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE D 607 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 560 " --> pdb=" O ILE D 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE D 604 " --> pdb=" O VAL D 599 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 141 removed outlier: 3.613A pdb=" N ASP E 136 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 182 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU E 695 " --> pdb=" O TYR E 469 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER E 471 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY E 697 " --> pdb=" O SER E 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE E 604 " --> pdb=" O VAL E 599 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP F 136 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 182 " --> pdb=" O LEU F 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE F 604 " --> pdb=" O VAL F 599 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP G 136 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 182 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 7.228A pdb=" N LEU G 695 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER G 471 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY G 697 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY G 533 " --> pdb=" O THR G 643 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE G 604 " --> pdb=" O VAL G 599 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 221 removed outlier: 7.081A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 136 through 141 removed outlier: 3.612A pdb=" N ASP H 136 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 182 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 7.227A pdb=" N LEU H 695 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER H 471 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY H 697 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL H 558 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE H 607 " --> pdb=" O VAL H 558 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE H 560 " --> pdb=" O ILE H 607 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE H 604 " --> pdb=" O VAL H 599 " (cutoff:3.500A) 1564 hydrogen bonds defined for protein. 4572 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: 6.76 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10116 1.34 - 1.45: 3221 1.45 - 1.57: 18279 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 31808 Sorted by residual: bond pdb=" CB ASP H 642 " pdb=" CG ASP H 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.47e+00 bond pdb=" CB ASP G 642 " pdb=" CG ASP G 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.46e+00 bond pdb=" CB ASP B 642 " pdb=" CG ASP B 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.46e+00 bond pdb=" CB ASP D 642 " pdb=" CG ASP D 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.45e+00 bond pdb=" CB ASP A 642 " pdb=" CG ASP A 642 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.45e+00 ... (remaining 31803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 42157 1.87 - 3.73: 789 3.73 - 5.60: 118 5.60 - 7.47: 24 7.47 - 9.34: 16 Bond angle restraints: 43104 Sorted by residual: angle pdb=" CB MET F 540 " pdb=" CG MET F 540 " pdb=" SD MET F 540 " ideal model delta sigma weight residual 112.70 104.27 8.43 3.00e+00 1.11e-01 7.90e+00 angle pdb=" CB MET B 540 " pdb=" CG MET B 540 " pdb=" SD MET B 540 " ideal model delta sigma weight residual 112.70 104.28 8.42 3.00e+00 1.11e-01 7.88e+00 angle pdb=" CB MET G 540 " pdb=" CG MET G 540 " pdb=" SD MET G 540 " ideal model delta sigma weight residual 112.70 104.28 8.42 3.00e+00 1.11e-01 7.87e+00 angle pdb=" CB MET A 540 " pdb=" CG MET A 540 " pdb=" SD MET A 540 " ideal model delta sigma weight residual 112.70 104.29 8.41 3.00e+00 1.11e-01 7.87e+00 angle pdb=" CB MET C 540 " pdb=" CG MET C 540 " pdb=" SD MET C 540 " ideal model delta sigma weight residual 112.70 104.29 8.41 3.00e+00 1.11e-01 7.87e+00 ... (remaining 43099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 18207 17.68 - 35.36: 1041 35.36 - 53.05: 104 53.05 - 70.73: 40 70.73 - 88.41: 16 Dihedral angle restraints: 19408 sinusoidal: 7712 harmonic: 11696 Sorted by residual: dihedral pdb=" CA HIS D 576 " pdb=" C HIS D 576 " pdb=" N LYS D 577 " pdb=" CA LYS D 577 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA HIS E 576 " pdb=" C HIS E 576 " pdb=" N LYS E 577 " pdb=" CA LYS E 577 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA HIS H 576 " pdb=" C HIS H 576 " pdb=" N LYS H 577 " pdb=" CA LYS H 577 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 19405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3301 0.041 - 0.082: 1424 0.082 - 0.123: 405 0.123 - 0.164: 67 0.164 - 0.206: 11 Chirality restraints: 5208 Sorted by residual: chirality pdb=" CB THR E 233 " pdb=" CA THR E 233 " pdb=" OG1 THR E 233 " pdb=" CG2 THR E 233 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR A 233 " pdb=" CA THR A 233 " pdb=" OG1 THR A 233 " pdb=" CG2 THR A 233 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB THR H 233 " pdb=" CA THR H 233 " pdb=" OG1 THR H 233 " pdb=" CG2 THR H 233 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 5205 not shown) Planarity restraints: 5480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 197 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO E 198 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 198 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 198 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 197 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO D 198 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 197 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO H 198 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO H 198 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 198 " 0.041 5.00e-02 4.00e+02 ... (remaining 5477 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3302 2.74 - 3.28: 33021 3.28 - 3.82: 51443 3.82 - 4.36: 62769 4.36 - 4.90: 106249 Nonbonded interactions: 256784 Sorted by model distance: nonbonded pdb=" OG SER G 86 " pdb=" OD2 ASP G 224 " model vdw 2.198 3.040 nonbonded pdb=" OG SER E 86 " pdb=" OD2 ASP E 224 " model vdw 2.199 3.040 nonbonded pdb=" OG SER F 86 " pdb=" OD2 ASP F 224 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 86 " pdb=" OD2 ASP A 224 " model vdw 2.199 3.040 nonbonded pdb=" OG SER D 86 " pdb=" OD2 ASP D 224 " model vdw 2.199 3.040 ... (remaining 256779 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.340 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 31808 Z= 0.283 Angle : 0.696 9.336 43104 Z= 0.370 Chirality : 0.049 0.206 5208 Planarity : 0.005 0.076 5480 Dihedral : 11.383 88.410 11872 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.51 (0.12), residues: 4016 helix: -0.47 (0.12), residues: 1760 sheet: 0.09 (0.23), residues: 512 loop : -1.86 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 609 TYR 0.020 0.002 TYR A 165 PHE 0.031 0.003 PHE C 220 TRP 0.012 0.003 TRP E 631 HIS 0.003 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00659 (31808) covalent geometry : angle 0.69626 (43104) hydrogen bonds : bond 0.15747 ( 1564) hydrogen bonds : angle 6.80163 ( 4572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 127 LEU cc_start: 0.9218 (mt) cc_final: 0.8980 (mt) outliers start: 0 outliers final: 3 residues processed: 454 average time/residue: 0.6197 time to fit residues: 336.4469 Evaluate side-chains 348 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 345 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain H residue 192 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.4980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 183 ASN A 192 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 183 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 183 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 183 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 183 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN F 164 ASN F 183 ASN ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN G 183 ASN ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN H 183 ASN ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.158598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105664 restraints weight = 47335.106| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.44 r_work: 0.3205 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31808 Z= 0.134 Angle : 0.626 9.670 43104 Z= 0.303 Chirality : 0.046 0.169 5208 Planarity : 0.004 0.042 5480 Dihedral : 4.523 29.883 4334 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.50 % Allowed : 8.98 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.13), residues: 4016 helix: 0.38 (0.12), residues: 1800 sheet: -0.07 (0.20), residues: 680 loop : -1.65 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.014 0.001 TYR C 569 PHE 0.017 0.001 PHE F 220 TRP 0.004 0.001 TRP E 631 HIS 0.006 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00299 (31808) covalent geometry : angle 0.62598 (43104) hydrogen bonds : bond 0.03844 ( 1564) hydrogen bonds : angle 4.69353 ( 4572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 408 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 90 THR cc_start: 0.8543 (m) cc_final: 0.8220 (t) REVERT: A 164 ASN cc_start: 0.8903 (t0) cc_final: 0.8542 (p0) REVERT: A 410 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7663 (ttp80) REVERT: A 707 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7820 (tmm160) REVERT: B 164 ASN cc_start: 0.8741 (t0) cc_final: 0.8509 (p0) REVERT: B 410 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7750 (ttp80) REVERT: B 474 ILE cc_start: 0.9167 (tt) cc_final: 0.8917 (tp) REVERT: C 90 THR cc_start: 0.8513 (m) cc_final: 0.8256 (t) REVERT: C 164 ASN cc_start: 0.8810 (t0) cc_final: 0.8531 (p0) REVERT: C 410 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7590 (ttp80) REVERT: C 707 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7807 (tmm160) REVERT: D 164 ASN cc_start: 0.8827 (t0) cc_final: 0.8573 (p0) REVERT: D 474 ILE cc_start: 0.9174 (tt) cc_final: 0.8922 (tp) REVERT: E 164 ASN cc_start: 0.8634 (t0) cc_final: 0.8348 (p0) REVERT: E 410 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7670 (ttp80) REVERT: G 90 THR cc_start: 0.8550 (m) cc_final: 0.8288 (t) REVERT: G 127 LEU cc_start: 0.9251 (mt) cc_final: 0.9004 (mt) REVERT: G 164 ASN cc_start: 0.8712 (t0) cc_final: 0.8375 (p0) REVERT: G 410 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7689 (ttp80) REVERT: H 164 ASN cc_start: 0.8752 (t0) cc_final: 0.8532 (p0) REVERT: H 474 ILE cc_start: 0.9209 (tt) cc_final: 0.8972 (tp) outliers start: 52 outliers final: 13 residues processed: 432 average time/residue: 0.5112 time to fit residues: 273.1157 Evaluate side-chains 371 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 356 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 chunk 217 optimal weight: 20.0000 chunk 307 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 354 optimal weight: 1.9990 chunk 305 optimal weight: 0.0570 chunk 319 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN ** H 671 ASN ** 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 = 0.4075 r_free = 0.4075 target = 0.156647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105348 restraints weight = 47203.380| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.41 r_work: 0.3159 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31808 Z= 0.194 Angle : 0.633 9.494 43104 Z= 0.310 Chirality : 0.046 0.203 5208 Planarity : 0.004 0.034 5480 Dihedral : 4.505 28.121 4328 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.14 % Allowed : 11.55 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.50 (0.13), residues: 4016 helix: 0.44 (0.12), residues: 1800 sheet: 0.21 (0.19), residues: 720 loop : -1.50 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 514 TYR 0.012 0.002 TYR G 569 PHE 0.019 0.002 PHE H 220 TRP 0.005 0.001 TRP F 631 HIS 0.004 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00454 (31808) covalent geometry : angle 0.63338 (43104) hydrogen bonds : bond 0.03919 ( 1564) hydrogen bonds : angle 4.55769 ( 4572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 381 time to evaluate : 1.194 Fit side-chains REVERT: A 90 THR cc_start: 0.8604 (m) cc_final: 0.8357 (t) REVERT: A 164 ASN cc_start: 0.8888 (t0) cc_final: 0.8493 (p0) REVERT: A 221 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8602 (m) REVERT: A 410 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7748 (ttp80) REVERT: A 707 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7958 (tmm160) REVERT: B 164 ASN cc_start: 0.8787 (t0) cc_final: 0.8537 (p0) REVERT: B 410 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7754 (ttp80) REVERT: C 90 THR cc_start: 0.8602 (m) cc_final: 0.8362 (t) REVERT: C 164 ASN cc_start: 0.8798 (t0) cc_final: 0.8448 (p0) REVERT: C 221 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8606 (m) REVERT: C 410 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7740 (ttp80) REVERT: C 707 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7932 (tmm160) REVERT: D 103 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8620 (mp) REVERT: D 164 ASN cc_start: 0.8857 (t0) cc_final: 0.8597 (p0) REVERT: D 192 ASN cc_start: 0.8686 (m-40) cc_final: 0.8229 (p0) REVERT: E 103 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8610 (mt) REVERT: E 164 ASN cc_start: 0.8705 (t0) cc_final: 0.8369 (p0) REVERT: E 410 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7657 (ttp80) REVERT: G 90 THR cc_start: 0.8638 (m) cc_final: 0.8429 (t) REVERT: G 127 LEU cc_start: 0.9239 (mt) cc_final: 0.8986 (mt) REVERT: G 164 ASN cc_start: 0.8770 (t0) cc_final: 0.8403 (p0) REVERT: G 221 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8601 (m) REVERT: G 410 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7711 (ttp80) REVERT: H 164 ASN cc_start: 0.8840 (t0) cc_final: 0.8578 (p0) outliers start: 74 outliers final: 33 residues processed: 412 average time/residue: 0.5007 time to fit residues: 253.8267 Evaluate side-chains 383 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 343 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 333 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 210 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 393 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 101 optimal weight: 0.0010 chunk 353 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** 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 = 0.4117 r_free = 0.4117 target = 0.160258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108298 restraints weight = 46750.196| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.48 r_work: 0.3232 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31808 Z= 0.101 Angle : 0.579 9.450 43104 Z= 0.277 Chirality : 0.045 0.295 5208 Planarity : 0.004 0.051 5480 Dihedral : 4.004 26.309 4328 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.44 % Allowed : 15.30 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.19 (0.13), residues: 4016 helix: 0.86 (0.12), residues: 1784 sheet: -0.22 (0.19), residues: 808 loop : -1.25 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 209 TYR 0.014 0.001 TYR C 569 PHE 0.019 0.001 PHE C 574 TRP 0.006 0.001 TRP F 631 HIS 0.004 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00214 (31808) covalent geometry : angle 0.57915 (43104) hydrogen bonds : bond 0.03199 ( 1564) hydrogen bonds : angle 4.18988 ( 4572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 394 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 90 THR cc_start: 0.8508 (m) cc_final: 0.8277 (t) REVERT: A 141 TYR cc_start: 0.8603 (t80) cc_final: 0.8264 (t80) REVERT: A 164 ASN cc_start: 0.8777 (t0) cc_final: 0.8433 (p0) REVERT: A 192 ASN cc_start: 0.8732 (m-40) cc_final: 0.8076 (OUTLIER) REVERT: A 221 SER cc_start: 0.8837 (t) cc_final: 0.8624 (m) REVERT: A 410 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7747 (ttp80) REVERT: A 707 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7863 (tmm160) REVERT: B 164 ASN cc_start: 0.8709 (t0) cc_final: 0.8481 (p0) REVERT: B 221 SER cc_start: 0.8867 (t) cc_final: 0.8630 (m) REVERT: B 474 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8914 (tp) REVERT: C 90 THR cc_start: 0.8518 (m) cc_final: 0.8275 (t) REVERT: C 141 TYR cc_start: 0.8605 (t80) cc_final: 0.8326 (t80) REVERT: C 164 ASN cc_start: 0.8704 (t0) cc_final: 0.8382 (p0) REVERT: C 221 SER cc_start: 0.8854 (t) cc_final: 0.8624 (m) REVERT: C 451 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7478 (tt) REVERT: C 707 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7819 (tmm160) REVERT: D 164 ASN cc_start: 0.8763 (t0) cc_final: 0.8484 (p0) REVERT: D 192 ASN cc_start: 0.8636 (m-40) cc_final: 0.8131 (p0) REVERT: D 221 SER cc_start: 0.8868 (t) cc_final: 0.8645 (m) REVERT: D 474 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8915 (tp) REVERT: E 164 ASN cc_start: 0.8590 (t0) cc_final: 0.8297 (p0) REVERT: E 221 SER cc_start: 0.8828 (t) cc_final: 0.8573 (m) REVERT: F 221 SER cc_start: 0.8849 (t) cc_final: 0.8621 (m) REVERT: F 474 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (tp) REVERT: G 90 THR cc_start: 0.8541 (m) cc_final: 0.8325 (t) REVERT: G 127 LEU cc_start: 0.9218 (mt) cc_final: 0.8972 (mt) REVERT: G 164 ASN cc_start: 0.8657 (t0) cc_final: 0.8359 (p0) REVERT: G 221 SER cc_start: 0.8833 (t) cc_final: 0.8606 (m) REVERT: G 451 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7430 (tt) REVERT: H 192 ASN cc_start: 0.8697 (m-40) cc_final: 0.8124 (p0) REVERT: H 221 SER cc_start: 0.8847 (t) cc_final: 0.8611 (m) REVERT: H 451 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7248 (tt) REVERT: H 474 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8894 (tp) outliers start: 50 outliers final: 9 residues processed: 417 average time/residue: 0.5038 time to fit residues: 259.7917 Evaluate side-chains 359 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 342 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 13 optimal weight: 0.0980 chunk 105 optimal weight: 8.9990 chunk 356 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 358 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 164 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 192 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.160246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109262 restraints weight = 47079.319| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.47 r_work: 0.3224 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31808 Z= 0.109 Angle : 0.582 9.326 43104 Z= 0.279 Chirality : 0.045 0.229 5208 Planarity : 0.004 0.049 5480 Dihedral : 3.918 24.038 4328 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.93 % Allowed : 16.48 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.01 (0.13), residues: 4016 helix: 0.93 (0.12), residues: 1776 sheet: 0.16 (0.19), residues: 768 loop : -1.21 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.013 0.001 TYR G 569 PHE 0.010 0.001 PHE E 117 TRP 0.006 0.001 TRP F 631 HIS 0.004 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00239 (31808) covalent geometry : angle 0.58162 (43104) hydrogen bonds : bond 0.03221 ( 1564) hydrogen bonds : angle 4.14902 ( 4572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 393 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8544 (m) cc_final: 0.8340 (t) REVERT: A 164 ASN cc_start: 0.8738 (t0) cc_final: 0.8385 (p0) REVERT: A 221 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8623 (m) REVERT: A 707 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7856 (tmm160) REVERT: B 164 ASN cc_start: 0.8693 (t0) cc_final: 0.8381 (p0) REVERT: B 474 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8914 (tp) REVERT: C 90 THR cc_start: 0.8509 (m) cc_final: 0.8308 (t) REVERT: C 127 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8455 (mm) REVERT: C 164 ASN cc_start: 0.8737 (t0) cc_final: 0.8370 (p0) REVERT: C 221 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8623 (m) REVERT: C 414 ASN cc_start: 0.8608 (p0) cc_final: 0.8380 (p0) REVERT: C 451 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7435 (tt) REVERT: C 707 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7856 (tmm160) REVERT: D 127 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8737 (mm) REVERT: D 164 ASN cc_start: 0.8776 (t0) cc_final: 0.8467 (p0) REVERT: D 192 ASN cc_start: 0.8578 (m-40) cc_final: 0.8062 (p0) REVERT: D 451 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7227 (tt) REVERT: D 474 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8911 (tp) REVERT: E 164 ASN cc_start: 0.8598 (t0) cc_final: 0.8342 (p0) REVERT: E 221 SER cc_start: 0.8858 (t) cc_final: 0.8605 (m) REVERT: F 127 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8504 (mm) REVERT: F 192 ASN cc_start: 0.8663 (m-40) cc_final: 0.7887 (p0) REVERT: F 451 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7378 (tt) REVERT: F 474 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8880 (tp) REVERT: G 90 THR cc_start: 0.8540 (m) cc_final: 0.8314 (t) REVERT: G 164 ASN cc_start: 0.8654 (t0) cc_final: 0.8347 (p0) REVERT: G 221 SER cc_start: 0.8850 (t) cc_final: 0.8627 (m) REVERT: G 414 ASN cc_start: 0.8598 (p0) cc_final: 0.8372 (p0) REVERT: G 451 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7418 (tt) REVERT: H 127 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8649 (mm) REVERT: H 192 ASN cc_start: 0.8645 (m-40) cc_final: 0.8020 (p0) REVERT: H 221 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8620 (m) REVERT: H 451 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7253 (tt) REVERT: H 474 ILE cc_start: 0.9184 (tt) cc_final: 0.8911 (tp) outliers start: 67 outliers final: 14 residues processed: 412 average time/residue: 0.5544 time to fit residues: 279.3290 Evaluate side-chains 386 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 355 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 451 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 203 optimal weight: 0.6980 chunk 380 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 235 optimal weight: 0.5980 chunk 373 optimal weight: 6.9990 chunk 370 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 366 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 349 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.159430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108453 restraints weight = 46725.553| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.39 r_work: 0.3224 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31808 Z= 0.129 Angle : 0.601 9.703 43104 Z= 0.289 Chirality : 0.046 0.306 5208 Planarity : 0.004 0.050 5480 Dihedral : 3.954 23.210 4328 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.40 % Allowed : 17.38 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.05 (0.13), residues: 4016 helix: 0.90 (0.12), residues: 1776 sheet: 0.09 (0.20), residues: 728 loop : -1.16 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.013 0.001 TYR C 569 PHE 0.011 0.001 PHE D 220 TRP 0.007 0.001 TRP C 631 HIS 0.003 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00292 (31808) covalent geometry : angle 0.60118 (43104) hydrogen bonds : bond 0.03312 ( 1564) hydrogen bonds : angle 4.18038 ( 4572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 387 time to evaluate : 1.286 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: A 164 ASN cc_start: 0.8664 (t0) cc_final: 0.8457 (t0) REVERT: A 192 ASN cc_start: 0.8661 (m-40) cc_final: 0.7806 (p0) REVERT: A 221 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8601 (m) REVERT: A 414 ASN cc_start: 0.8542 (p0) cc_final: 0.8278 (p0) REVERT: A 707 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7847 (tmm160) REVERT: B 164 ASN cc_start: 0.8575 (t0) cc_final: 0.8364 (t0) REVERT: B 451 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7294 (tt) REVERT: B 474 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8906 (tp) REVERT: C 164 ASN cc_start: 0.8631 (t0) cc_final: 0.8401 (t0) REVERT: C 221 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8602 (m) REVERT: C 414 ASN cc_start: 0.8549 (p0) cc_final: 0.8303 (p0) REVERT: C 451 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7367 (tt) REVERT: C 707 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7860 (tmm160) REVERT: D 127 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8745 (mm) REVERT: D 164 ASN cc_start: 0.8653 (t0) cc_final: 0.8261 (p0) REVERT: D 192 ASN cc_start: 0.8530 (m-40) cc_final: 0.7969 (p0) REVERT: D 451 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7288 (tt) REVERT: D 474 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8897 (tp) REVERT: E 164 ASN cc_start: 0.8566 (t0) cc_final: 0.8310 (p0) REVERT: E 221 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8585 (m) REVERT: F 127 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8525 (mm) REVERT: F 192 ASN cc_start: 0.8608 (m-40) cc_final: 0.7818 (p0) REVERT: F 451 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7395 (tt) REVERT: F 474 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8895 (tp) REVERT: G 221 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8624 (m) REVERT: G 414 ASN cc_start: 0.8549 (p0) cc_final: 0.8266 (p0) REVERT: G 451 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7349 (tt) REVERT: H 127 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8707 (mm) REVERT: H 164 ASN cc_start: 0.8664 (t0) cc_final: 0.8383 (p0) REVERT: H 192 ASN cc_start: 0.8606 (m-40) cc_final: 0.7976 (p0) REVERT: H 474 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8930 (tp) outliers start: 83 outliers final: 21 residues processed: 429 average time/residue: 0.5179 time to fit residues: 274.3784 Evaluate side-chains 404 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 365 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 303 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 182 optimal weight: 0.0870 chunk 135 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 342 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 chunk 354 optimal weight: 0.2980 chunk 193 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.160907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108185 restraints weight = 47121.283| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.37 r_work: 0.3251 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31808 Z= 0.105 Angle : 0.603 10.079 43104 Z= 0.287 Chirality : 0.046 0.332 5208 Planarity : 0.004 0.050 5480 Dihedral : 3.790 21.404 4328 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.02 % Allowed : 18.33 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.11 (0.13), residues: 4016 helix: 0.95 (0.12), residues: 1792 sheet: 0.20 (0.20), residues: 720 loop : -1.00 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 139 TYR 0.014 0.001 TYR G 569 PHE 0.011 0.001 PHE E 117 TRP 0.006 0.001 TRP C 631 HIS 0.003 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00224 (31808) covalent geometry : angle 0.60312 (43104) hydrogen bonds : bond 0.03116 ( 1564) hydrogen bonds : angle 4.09206 ( 4572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 391 time to evaluate : 1.233 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: A 164 ASN cc_start: 0.8662 (t0) cc_final: 0.8387 (p0) REVERT: A 414 ASN cc_start: 0.8488 (p0) cc_final: 0.8210 (p0) REVERT: A 707 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7833 (tmm160) REVERT: B 451 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7310 (tt) REVERT: B 474 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8891 (tp) REVERT: C 164 ASN cc_start: 0.8608 (t0) cc_final: 0.8355 (p0) REVERT: C 414 ASN cc_start: 0.8443 (p0) cc_final: 0.8154 (p0) REVERT: C 451 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7332 (tt) REVERT: C 707 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7809 (tmm160) REVERT: D 127 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8733 (mm) REVERT: D 192 ASN cc_start: 0.8532 (m-40) cc_final: 0.7979 (p0) REVERT: D 451 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7316 (tt) REVERT: D 474 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8902 (tp) REVERT: E 221 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8577 (m) REVERT: F 127 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8581 (mm) REVERT: F 164 ASN cc_start: 0.8439 (t0) cc_final: 0.8239 (p0) REVERT: F 192 ASN cc_start: 0.8551 (m-40) cc_final: 0.7844 (p0) REVERT: F 451 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7380 (tt) REVERT: F 474 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8893 (tp) REVERT: G 164 ASN cc_start: 0.8549 (t0) cc_final: 0.8249 (p0) REVERT: G 414 ASN cc_start: 0.8414 (p0) cc_final: 0.8160 (p0) REVERT: G 451 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7328 (tt) REVERT: H 127 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (mm) REVERT: H 192 ASN cc_start: 0.8583 (m-40) cc_final: 0.7957 (p0) REVERT: H 474 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8894 (tp) outliers start: 70 outliers final: 23 residues processed: 427 average time/residue: 0.5023 time to fit residues: 262.9288 Evaluate side-chains 407 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 369 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 298 optimal weight: 0.0670 chunk 377 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.159369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109538 restraints weight = 46911.088| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.30 r_work: 0.3221 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31808 Z= 0.146 Angle : 0.638 14.959 43104 Z= 0.304 Chirality : 0.047 0.337 5208 Planarity : 0.004 0.052 5480 Dihedral : 3.961 21.067 4328 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.99 % Allowed : 18.53 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.07 (0.13), residues: 4016 helix: 0.88 (0.12), residues: 1792 sheet: 0.10 (0.20), residues: 728 loop : -0.92 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 139 TYR 0.015 0.001 TYR D 141 PHE 0.011 0.001 PHE D 220 TRP 0.008 0.001 TRP C 631 HIS 0.003 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00335 (31808) covalent geometry : angle 0.63830 (43104) hydrogen bonds : bond 0.03401 ( 1564) hydrogen bonds : angle 4.19933 ( 4572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 381 time to evaluate : 1.272 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: A 164 ASN cc_start: 0.8613 (t0) cc_final: 0.8344 (p0) REVERT: A 414 ASN cc_start: 0.8485 (p0) cc_final: 0.8268 (p0) REVERT: A 707 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7921 (tmm160) REVERT: B 451 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7307 (tt) REVERT: B 474 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8896 (tp) REVERT: C 164 ASN cc_start: 0.8567 (t0) cc_final: 0.8324 (p0) REVERT: C 192 ASN cc_start: 0.8639 (m-40) cc_final: 0.8147 (OUTLIER) REVERT: C 414 ASN cc_start: 0.8471 (p0) cc_final: 0.8243 (p0) REVERT: C 451 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7330 (tt) REVERT: C 707 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7895 (tmm160) REVERT: D 46 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8743 (pp) REVERT: D 127 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8763 (mm) REVERT: D 192 ASN cc_start: 0.8526 (m-40) cc_final: 0.7952 (p0) REVERT: D 451 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7316 (tt) REVERT: D 474 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8900 (tp) REVERT: E 221 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8612 (m) REVERT: F 127 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8613 (mm) REVERT: F 164 ASN cc_start: 0.8393 (t0) cc_final: 0.8139 (p0) REVERT: F 192 ASN cc_start: 0.8551 (m-40) cc_final: 0.7823 (p0) REVERT: F 451 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7390 (tt) REVERT: F 474 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8903 (tp) REVERT: G 451 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7348 (tt) REVERT: H 127 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8757 (mm) REVERT: H 192 ASN cc_start: 0.8576 (m-40) cc_final: 0.7918 (p0) REVERT: H 474 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8923 (tp) outliers start: 69 outliers final: 25 residues processed: 414 average time/residue: 0.5446 time to fit residues: 277.2935 Evaluate side-chains 411 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 371 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 325 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 282 optimal weight: 0.0020 chunk 256 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 312 optimal weight: 0.7980 chunk 384 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.159656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107964 restraints weight = 47102.872| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.51 r_work: 0.3212 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31808 Z= 0.132 Angle : 0.638 14.130 43104 Z= 0.302 Chirality : 0.047 0.334 5208 Planarity : 0.004 0.053 5480 Dihedral : 3.924 20.320 4328 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.59 % Allowed : 19.54 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.15 (0.13), residues: 4016 helix: 0.94 (0.12), residues: 1792 sheet: 0.27 (0.20), residues: 728 loop : -0.95 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.017 0.001 TYR G 141 PHE 0.010 0.001 PHE E 117 TRP 0.007 0.001 TRP C 631 HIS 0.003 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00299 (31808) covalent geometry : angle 0.63811 (43104) hydrogen bonds : bond 0.03328 ( 1564) hydrogen bonds : angle 4.18435 ( 4572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 376 time to evaluate : 1.204 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: A 164 ASN cc_start: 0.8619 (t0) cc_final: 0.8352 (p0) REVERT: A 414 ASN cc_start: 0.8504 (p0) cc_final: 0.8302 (p0) REVERT: B 127 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8871 (mm) REVERT: B 451 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7360 (tt) REVERT: B 474 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8896 (tp) REVERT: C 192 ASN cc_start: 0.8611 (m-40) cc_final: 0.7920 (p0) REVERT: C 451 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7376 (tt) REVERT: C 707 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7888 (tmm160) REVERT: D 46 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8655 (pp) REVERT: D 127 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8727 (mm) REVERT: D 192 ASN cc_start: 0.8552 (m-40) cc_final: 0.7897 (p0) REVERT: D 451 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7382 (tt) REVERT: D 474 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8903 (tp) REVERT: E 164 ASN cc_start: 0.8400 (t0) cc_final: 0.8146 (p0) REVERT: E 221 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8621 (m) REVERT: F 127 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8594 (mm) REVERT: F 164 ASN cc_start: 0.8398 (t0) cc_final: 0.8129 (p0) REVERT: F 451 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7409 (tt) REVERT: F 474 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8892 (tp) REVERT: G 451 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7327 (tt) REVERT: H 46 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8749 (pt) REVERT: H 127 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8720 (mm) REVERT: H 164 ASN cc_start: 0.8536 (t0) cc_final: 0.8300 (p0) REVERT: H 192 ASN cc_start: 0.8557 (m-40) cc_final: 0.7857 (p0) REVERT: H 474 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8933 (tp) outliers start: 55 outliers final: 25 residues processed: 403 average time/residue: 0.5360 time to fit residues: 266.2108 Evaluate side-chains 404 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 362 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 398 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 329 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 369 optimal weight: 0.0980 chunk 342 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 352 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.160699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108744 restraints weight = 47018.745| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.45 r_work: 0.3247 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31808 Z= 0.114 Angle : 0.636 14.202 43104 Z= 0.300 Chirality : 0.047 0.334 5208 Planarity : 0.004 0.054 5480 Dihedral : 3.819 19.600 4328 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.44 % Allowed : 20.06 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.13), residues: 4016 helix: 1.07 (0.12), residues: 1784 sheet: 0.25 (0.20), residues: 712 loop : -0.87 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.017 0.001 TYR E 141 PHE 0.010 0.001 PHE H 117 TRP 0.006 0.001 TRP C 631 HIS 0.003 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00252 (31808) covalent geometry : angle 0.63643 (43104) hydrogen bonds : bond 0.03240 ( 1564) hydrogen bonds : angle 4.14187 ( 4572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8032 Ramachandran restraints generated. 4016 Oldfield, 0 Emsley, 4016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 370 time to evaluate : 1.170 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: A 164 ASN cc_start: 0.8544 (t0) cc_final: 0.8294 (p0) REVERT: B 127 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8900 (mm) REVERT: B 474 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8920 (tp) REVERT: C 451 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7348 (tt) REVERT: C 707 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7834 (tmm160) REVERT: D 43 PHE cc_start: 0.8773 (m-10) cc_final: 0.8569 (m-10) REVERT: D 46 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (pp) REVERT: D 127 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8684 (mm) REVERT: D 192 ASN cc_start: 0.8543 (m-40) cc_final: 0.7883 (p0) REVERT: D 474 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8909 (tp) REVERT: E 164 ASN cc_start: 0.8428 (t0) cc_final: 0.8123 (p0) REVERT: E 221 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8587 (m) REVERT: F 122 ARG cc_start: 0.8914 (ttp-170) cc_final: 0.8666 (ttp-170) REVERT: F 127 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8599 (mm) REVERT: F 164 ASN cc_start: 0.8336 (t0) cc_final: 0.8078 (p0) REVERT: F 474 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8909 (tp) REVERT: G 451 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7295 (tt) REVERT: H 46 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8711 (pt) REVERT: H 127 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8725 (mm) REVERT: H 164 ASN cc_start: 0.8529 (t0) cc_final: 0.8209 (p0) REVERT: H 192 ASN cc_start: 0.8553 (m-40) cc_final: 0.7702 (m-40) REVERT: H 474 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8937 (tp) outliers start: 50 outliers final: 21 residues processed: 398 average time/residue: 0.5062 time to fit residues: 249.3636 Evaluate side-chains 398 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 363 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 36 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 376 optimal weight: 0.4980 chunk 170 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 294 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108269 restraints weight = 47021.078| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.46 r_work: 0.3185 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31808 Z= 0.173 Angle : 0.671 13.882 43104 Z= 0.321 Chirality : 0.048 0.392 5208 Planarity : 0.004 0.053 5480 Dihedral : 4.077 19.891 4328 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.18 % Allowed : 20.44 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.13 (0.13), residues: 4016 helix: 0.90 (0.12), residues: 1792 sheet: 0.16 (0.20), residues: 728 loop : -0.86 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 122 TYR 0.020 0.001 TYR G 141 PHE 0.012 0.001 PHE F 220 TRP 0.009 0.001 TRP G 631 HIS 0.003 0.001 HIS H 571 Details of bonding type rmsd covalent geometry : bond 0.00404 (31808) covalent geometry : angle 0.67108 (43104) hydrogen bonds : bond 0.03564 ( 1564) hydrogen bonds : angle 4.28418 ( 4572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13043.09 seconds wall clock time: 222 minutes 7.84 seconds (13327.84 seconds total)