Starting phenix.real_space_refine on Sat Jun 21 23:53:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnl_41422/06_2025/8tnl_41422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnl_41422/06_2025/8tnl_41422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tnl_41422/06_2025/8tnl_41422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnl_41422/06_2025/8tnl_41422.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnl_41422/06_2025/8tnl_41422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnl_41422/06_2025/8tnl_41422.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11118 atoms to isotropic. 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 96 5.16 5 C 10292 2.51 5 N 2839 2.21 5 O 3251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16478 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "C" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.89, per 1000 atoms: 0.54 Number of scatterers: 16478 At special positions: 0 Unit cell: (135.29, 137.78, 161.85, 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 96 16.00 O 3251 8.00 N 2839 7.00 C 10292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 458 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS I 368 " distance=2.05 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 465 " - pdb=" SG CYS C 469 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 458 " distance=2.03 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 268 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 66 " distance=2.03 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 129 " distance=2.03 Simple disulfide: pdb=" SG CYS I 272 " - pdb=" SG CYS I 296 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 469 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 458 " distance=2.04 Simple disulfide: pdb=" SG CYS K 42 " - pdb=" SG CYS K 268 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 66 " distance=2.03 Simple disulfide: pdb=" SG CYS K 87 " - pdb=" SG CYS K 129 " distance=2.03 Simple disulfide: pdb=" SG CYS K 272 " - pdb=" SG CYS K 296 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 469 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 28 " " NAG C 602 " - " ASN C 403 " " NAG C 603 " - " ASN C 231 " " NAG I 601 " - " ASN I 403 " " NAG I 602 " - " ASN I 28 " " NAG K 601 " - " ASN K 403 " " NAG K 602 " - " ASN K 28 " Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 2.1 seconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 60 sheets defined 19.0% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.538A pdb=" N ASP L 87 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 84 through 88' Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.010A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.127A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 358 through 377 removed outlier: 3.946A pdb=" N LYS C 372 " --> pdb=" O CYS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 448 removed outlier: 3.644A pdb=" N ILE C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'I' and resid 57 through 62 removed outlier: 4.268A pdb=" N THR I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 4.251A pdb=" N ASP I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 104 removed outlier: 3.973A pdb=" N GLU I 104 " --> pdb=" O GLN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 186 Processing helix chain 'I' and resid 359 through 377 removed outlier: 4.635A pdb=" N LYS I 372 " --> pdb=" O CYS I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 448 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 479 through 488 removed outlier: 4.175A pdb=" N TYR I 483 " --> pdb=" O ASP I 479 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU I 486 " --> pdb=" O LYS I 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 62 removed outlier: 3.771A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 removed outlier: 4.088A pdb=" N ASP K 67 " --> pdb=" O PRO K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 104 removed outlier: 3.971A pdb=" N GLU K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 187 Processing helix chain 'K' and resid 359 through 377 Processing helix chain 'K' and resid 395 through 447 Processing helix chain 'K' and resid 466 through 475 Processing helix chain 'K' and resid 483 through 490 removed outlier: 3.841A pdb=" N ALA K 487 " --> pdb=" O TYR K 483 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN K 490 " --> pdb=" O GLU K 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.643A pdb=" N LYS D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.570A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.601A pdb=" N ASP E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.640A pdb=" N LYS A 64 " --> pdb=" O PRO A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.614A pdb=" N ASP B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.682A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.514A pdb=" N THR L 5 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 58 through 59 removed outlier: 6.212A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 89 through 91 removed outlier: 3.650A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.572A pdb=" N GLY C 344 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 6 " --> pdb=" O GLY C 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB4, first strand: chain 'C' and resid 40 through 42 removed outlier: 5.685A pdb=" N ILE C 41 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.610A pdb=" N ILE C 78 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE C 77 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 90 through 92 removed outlier: 7.016A pdb=" N LYS C 91 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N TRP C 225 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AB8, first strand: chain 'C' and resid 126 through 130 removed outlier: 4.481A pdb=" N CYS C 129 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.503A pdb=" N LYS C 141 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 155 through 157 removed outlier: 3.549A pdb=" N MET C 155 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 279 removed outlier: 3.726A pdb=" N ILE C 279 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.968A pdb=" N GLY I 6 " --> pdb=" O GLY I 344 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY I 344 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS I 347 " --> pdb=" O GLY I 354 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY I 354 " --> pdb=" O HIS I 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC5, first strand: chain 'I' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AC7, first strand: chain 'I' and resid 41 through 42 removed outlier: 5.765A pdb=" N ILE I 41 " --> pdb=" O ASP I 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.255A pdb=" N ILE I 77 " --> pdb=" O ILE I 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 108 through 112 Processing sheet with id=AD1, first strand: chain 'I' and resid 140 through 142 removed outlier: 8.510A pdb=" N VAL I 170 " --> pdb=" O PRO I 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 203 through 204 Processing sheet with id=AD3, first strand: chain 'I' and resid 273 through 274 Processing sheet with id=AD4, first strand: chain 'I' and resid 451 through 453 Processing sheet with id=AD5, first strand: chain 'K' and resid 353 through 357 removed outlier: 3.986A pdb=" N CYS K 4 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN K 348 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU K 452 " --> pdb=" O GLU K 460 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 15 through 16 Processing sheet with id=AD7, first strand: chain 'K' and resid 30 through 31 Processing sheet with id=AD8, first strand: chain 'K' and resid 33 through 34 Processing sheet with id=AD9, first strand: chain 'K' and resid 41 through 42 removed outlier: 5.790A pdb=" N ILE K 41 " --> pdb=" O ASP K 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'K' and resid 48 through 50 removed outlier: 3.528A pdb=" N ILE K 78 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE K 77 " --> pdb=" O ILE K 258 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 90 through 92 removed outlier: 7.104A pdb=" N LYS K 91 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N TRP K 225 " --> pdb=" O LYS K 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 108 through 112 Processing sheet with id=AE4, first strand: chain 'K' and resid 126 through 130 removed outlier: 4.972A pdb=" N CYS K 129 " --> pdb=" O SER K 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 140 through 142 Processing sheet with id=AE6, first strand: chain 'K' and resid 155 through 160 removed outlier: 3.544A pdb=" N TYR K 159 " --> pdb=" O VAL K 234 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 272 through 274 removed outlier: 4.440A pdb=" N CYS K 272 " --> pdb=" O ILE K 279 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY K 277 " --> pdb=" O TYR K 274 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AF1, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AF2, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.769A pdb=" N TYR D 51 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 72 through 73 Processing sheet with id=AF4, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AF5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.550A pdb=" N THR E 5 " --> pdb=" O ASN E 24 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 58 through 59 removed outlier: 5.994A pdb=" N LEU E 51 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 53 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 89 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AG1, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.667A pdb=" N TYR A 50 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 58 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AG3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AG4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.219A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.705A pdb=" N GLY B 89 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 109 " --> pdb=" O GLY B 89 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1329 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: 5.01 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4721 1.33 - 1.46: 4497 1.46 - 1.59: 7470 1.59 - 1.72: 0 1.72 - 1.84: 138 Bond restraints: 16826 Sorted by residual: bond pdb=" N TYR C 186 " pdb=" CA TYR C 186 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.22e-02 6.72e+03 9.59e+00 bond pdb=" N GLN B 95 " pdb=" CA GLN B 95 " ideal model delta sigma weight residual 1.454 1.483 -0.028 1.17e-02 7.31e+03 5.81e+00 bond pdb=" N ARG H 38 " pdb=" CA ARG H 38 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.18e-02 7.18e+03 5.75e+00 bond pdb=" N LYS K 379 " pdb=" CA LYS K 379 " ideal model delta sigma weight residual 1.453 1.481 -0.029 1.31e-02 5.83e+03 4.82e+00 bond pdb=" C GLN B 47 " pdb=" N SER B 48 " ideal model delta sigma weight residual 1.328 1.359 -0.031 1.44e-02 4.82e+03 4.59e+00 ... (remaining 16821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 22518 3.17 - 6.34: 228 6.34 - 9.51: 29 9.51 - 12.68: 5 12.68 - 15.84: 3 Bond angle restraints: 22783 Sorted by residual: angle pdb=" C GLY B 16 " pdb=" N GLU B 17 " pdb=" CA GLU B 17 " ideal model delta sigma weight residual 122.56 130.81 -8.25 1.58e+00 4.01e-01 2.72e+01 angle pdb=" CA MET K 470 " pdb=" CB MET K 470 " pdb=" CG MET K 470 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 angle pdb=" N GLU K 449 " pdb=" CA GLU K 449 " pdb=" C GLU K 449 " ideal model delta sigma weight residual 114.39 107.39 7.00 1.45e+00 4.76e-01 2.33e+01 angle pdb=" N THR I 477 " pdb=" CA THR I 477 " pdb=" C THR I 477 " ideal model delta sigma weight residual 114.56 109.03 5.53 1.27e+00 6.20e-01 1.90e+01 angle pdb=" CA MET C 470 " pdb=" CB MET C 470 " pdb=" CG MET C 470 " ideal model delta sigma weight residual 114.10 122.30 -8.20 2.00e+00 2.50e-01 1.68e+01 ... (remaining 22778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 9089 18.01 - 36.02: 837 36.02 - 54.02: 154 54.02 - 72.03: 34 72.03 - 90.04: 20 Dihedral angle restraints: 10134 sinusoidal: 4128 harmonic: 6006 Sorted by residual: dihedral pdb=" CB CYS I 272 " pdb=" SG CYS I 272 " pdb=" SG CYS I 296 " pdb=" CB CYS I 296 " ideal model delta sinusoidal sigma weight residual 93.00 11.70 81.30 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS C 20 " pdb=" SG CYS C 20 " pdb=" SG CYS I 368 " pdb=" CB CYS I 368 " ideal model delta sinusoidal sigma weight residual 93.00 22.70 70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sinusoidal sigma weight residual -86.00 -155.45 69.45 1 1.00e+01 1.00e-02 6.23e+01 ... (remaining 10131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2229 0.078 - 0.156: 237 0.156 - 0.235: 14 0.235 - 0.313: 2 0.313 - 0.391: 1 Chirality restraints: 2483 Sorted by residual: chirality pdb=" CB ILE C 280 " pdb=" CA ILE C 280 " pdb=" CG1 ILE C 280 " pdb=" CG2 ILE C 280 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CB VAL I 234 " pdb=" CA VAL I 234 " pdb=" CG1 VAL I 234 " pdb=" CG2 VAL I 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA GLU K 424 " pdb=" N GLU K 424 " pdb=" C GLU K 424 " pdb=" CB GLU K 424 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2480 not shown) Planarity restraints: 2981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I 88 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO I 89 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO I 89 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 89 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 63 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO C 64 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 296 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO C 297 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 297 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 297 " -0.038 5.00e-02 4.00e+02 ... (remaining 2978 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1567 2.75 - 3.29: 14809 3.29 - 3.83: 27515 3.83 - 4.36: 31003 4.36 - 4.90: 55060 Nonbonded interactions: 129954 Sorted by model distance: nonbonded pdb=" OH TYR H 32 " pdb=" O LEU H 98 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU C 111 " pdb=" OH TYR A 52 " model vdw 2.246 3.040 nonbonded pdb=" OG SER C 434 " pdb=" O LEU K 323 " model vdw 2.247 3.040 nonbonded pdb=" O LEU C 323 " pdb=" OG SER I 434 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR I 18 " pdb=" OE1 GLN I 426 " model vdw 2.280 3.040 ... (remaining 129949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = (chain 'C' and (resid 1 through 490 or resid 601 through 602)) selection = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 37.230 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 0.004 0.053 16858 Z= 0.188 Angle : 0.848 15.844 22854 Z= 0.443 Chirality : 0.048 0.391 2483 Planarity : 0.007 0.080 2974 Dihedral : 14.390 90.041 6237 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.17), residues: 2082 helix: 0.08 (0.25), residues: 333 sheet: -1.44 (0.23), residues: 565 loop : -1.66 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 47 HIS 0.008 0.001 HIS H 101 PHE 0.021 0.002 PHE C 136 TYR 0.042 0.002 TYR C 186 ARG 0.012 0.000 ARG I 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 7) link_NAG-ASN : angle 1.09844 ( 21) hydrogen bonds : bond 0.20802 ( 502) hydrogen bonds : angle 8.42889 ( 1329) SS BOND : bond 0.00553 ( 25) SS BOND : angle 1.97955 ( 50) covalent geometry : bond 0.00379 (16826) covalent geometry : angle 0.84409 (22783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.5492 (pt0) cc_final: 0.5231 (pt0) REVERT: L 63 VAL cc_start: 0.7774 (t) cc_final: 0.7572 (t) REVERT: I 348 GLN cc_start: 0.8024 (tp40) cc_final: 0.7321 (tp40) REVERT: K 377 ILE cc_start: 0.8276 (mm) cc_final: 0.7990 (mm) REVERT: D 96 TYR cc_start: 0.7367 (m-10) cc_final: 0.7100 (m-10) REVERT: B 2 ILE cc_start: 0.7527 (mt) cc_final: 0.7261 (mt) REVERT: B 63 VAL cc_start: 0.7807 (t) cc_final: 0.7604 (t) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.2508 time to fit residues: 146.5396 Evaluate side-chains 305 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.0040 chunk 187 optimal weight: 4.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN C 174 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 ASN K 349 ASN K 400 ASN ** K 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 95 GLN ** 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 = 0.3736 r_free = 0.3736 target = 0.138394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108329 restraints weight = 27646.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109524 restraints weight = 18250.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110430 restraints weight = 13133.738| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16858 Z= 0.138 Angle : 0.615 14.527 22854 Z= 0.313 Chirality : 0.043 0.196 2483 Planarity : 0.005 0.058 2974 Dihedral : 5.806 70.930 2436 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.28 % Allowed : 9.66 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 2082 helix: 1.29 (0.28), residues: 333 sheet: -1.53 (0.21), residues: 601 loop : -1.44 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 36 HIS 0.012 0.001 HIS C 174 PHE 0.025 0.001 PHE K 330 TYR 0.022 0.002 TYR I 478 ARG 0.003 0.000 ARG I 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 7) link_NAG-ASN : angle 0.76936 ( 21) hydrogen bonds : bond 0.04299 ( 502) hydrogen bonds : angle 5.96494 ( 1329) SS BOND : bond 0.00421 ( 25) SS BOND : angle 1.66168 ( 50) covalent geometry : bond 0.00310 (16826) covalent geometry : angle 0.61086 (22783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 338 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.7730 (pt0) cc_final: 0.6958 (pt0) REVERT: C 311 MET cc_start: 0.9073 (ppp) cc_final: 0.8297 (ppp) REVERT: C 463 HIS cc_start: 0.6906 (p90) cc_final: 0.6652 (p-80) REVERT: C 484 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7558 (ptp-170) REVERT: I 463 HIS cc_start: 0.7215 (t70) cc_final: 0.6997 (p-80) REVERT: K 377 ILE cc_start: 0.8217 (mm) cc_final: 0.7977 (mm) REVERT: K 436 MET cc_start: 0.7614 (tpt) cc_final: 0.7279 (tpt) REVERT: D 38 ILE cc_start: 0.9190 (mm) cc_final: 0.8984 (mm) REVERT: B 17 GLU cc_start: 0.8100 (pt0) cc_final: 0.7477 (pm20) REVERT: B 43 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8554 (tt0) outliers start: 23 outliers final: 15 residues processed: 346 average time/residue: 0.2505 time to fit residues: 134.6793 Evaluate side-chains 308 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 292 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain B residue 43 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 117 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN K 400 ASN E 43 GLN B 43 GLN B 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105654 restraints weight = 27678.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107279 restraints weight = 18197.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107802 restraints weight = 13344.050| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16858 Z= 0.153 Angle : 0.603 13.723 22854 Z= 0.305 Chirality : 0.044 0.208 2483 Planarity : 0.004 0.053 2974 Dihedral : 5.564 71.737 2436 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.40 % Allowed : 11.56 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2082 helix: 1.71 (0.28), residues: 333 sheet: -1.53 (0.21), residues: 597 loop : -1.32 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 47 HIS 0.008 0.001 HIS D 54 PHE 0.024 0.001 PHE K 330 TYR 0.014 0.002 TYR C 483 ARG 0.003 0.000 ARG C 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 7) link_NAG-ASN : angle 0.93995 ( 21) hydrogen bonds : bond 0.03844 ( 502) hydrogen bonds : angle 5.43264 ( 1329) SS BOND : bond 0.00584 ( 25) SS BOND : angle 2.01814 ( 50) covalent geometry : bond 0.00352 (16826) covalent geometry : angle 0.59589 (22783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 84 GLU cc_start: 0.7226 (mp0) cc_final: 0.6945 (mp0) REVERT: C 311 MET cc_start: 0.9087 (ppp) cc_final: 0.8413 (ppp) REVERT: C 463 HIS cc_start: 0.7099 (p90) cc_final: 0.6651 (p90) REVERT: C 484 ARG cc_start: 0.7801 (ptp-170) cc_final: 0.7419 (ptp-170) REVERT: I 444 LYS cc_start: 0.8223 (tttp) cc_final: 0.8020 (ttpt) REVERT: I 463 HIS cc_start: 0.7054 (t70) cc_final: 0.6815 (p-80) REVERT: I 483 TYR cc_start: 0.7962 (m-80) cc_final: 0.7432 (m-80) REVERT: K 377 ILE cc_start: 0.8152 (mm) cc_final: 0.7918 (mm) REVERT: K 444 LYS cc_start: 0.8534 (tptm) cc_final: 0.8286 (tttm) REVERT: D 14 LYS cc_start: 0.7867 (mmpt) cc_final: 0.7639 (mmpt) REVERT: D 109 ASP cc_start: 0.8133 (p0) cc_final: 0.7913 (p0) REVERT: E 17 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: E 84 GLU cc_start: 0.7126 (mp0) cc_final: 0.6811 (mp0) REVERT: A 111 GLN cc_start: 0.8168 (tp40) cc_final: 0.7967 (mm-40) REVERT: B 40 TRP cc_start: 0.8438 (m100) cc_final: 0.8038 (m100) REVERT: B 43 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8279 (tt0) outliers start: 43 outliers final: 31 residues processed: 328 average time/residue: 0.3103 time to fit residues: 156.6547 Evaluate side-chains 323 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 43 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 101 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS K 400 ASN K 480 HIS B 43 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105644 restraints weight = 27692.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107137 restraints weight = 18504.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107695 restraints weight = 13335.912| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16858 Z= 0.133 Angle : 0.575 13.780 22854 Z= 0.289 Chirality : 0.043 0.215 2483 Planarity : 0.004 0.054 2974 Dihedral : 5.427 72.130 2436 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.29 % Allowed : 13.18 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2082 helix: 2.00 (0.29), residues: 333 sheet: -1.57 (0.21), residues: 589 loop : -1.26 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.007 0.001 HIS D 54 PHE 0.025 0.001 PHE K 330 TYR 0.017 0.001 TYR A 59 ARG 0.002 0.000 ARG K 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 7) link_NAG-ASN : angle 0.89860 ( 21) hydrogen bonds : bond 0.03532 ( 502) hydrogen bonds : angle 5.16143 ( 1329) SS BOND : bond 0.00472 ( 25) SS BOND : angle 1.79596 ( 50) covalent geometry : bond 0.00307 (16826) covalent geometry : angle 0.56931 (22783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 332 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 89 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7986 (t0) REVERT: H 90 THR cc_start: 0.7635 (m) cc_final: 0.7287 (m) REVERT: L 6 GLN cc_start: 0.7826 (pt0) cc_final: 0.7372 (pt0) REVERT: L 40 TRP cc_start: 0.8453 (m100) cc_final: 0.7941 (m100) REVERT: L 84 GLU cc_start: 0.7317 (mp0) cc_final: 0.7029 (mp0) REVERT: C 311 MET cc_start: 0.9013 (ppp) cc_final: 0.8390 (ppp) REVERT: C 484 ARG cc_start: 0.7835 (ptp-170) cc_final: 0.7436 (ptp-170) REVERT: C 488 MET cc_start: 0.6886 (tmm) cc_final: 0.6510 (tmm) REVERT: I 348 GLN cc_start: 0.7800 (tp40) cc_final: 0.7538 (tp-100) REVERT: I 465 CYS cc_start: 0.5279 (OUTLIER) cc_final: 0.5077 (t) REVERT: I 483 TYR cc_start: 0.8029 (m-80) cc_final: 0.7813 (m-80) REVERT: K 367 ASP cc_start: 0.7863 (t70) cc_final: 0.7649 (t0) REVERT: K 444 LYS cc_start: 0.8528 (tptm) cc_final: 0.8303 (tttm) REVERT: E 79 LYS cc_start: 0.7780 (mppt) cc_final: 0.7422 (mptt) REVERT: E 84 GLU cc_start: 0.7256 (mp0) cc_final: 0.6936 (mp0) REVERT: A 111 GLN cc_start: 0.8194 (tp40) cc_final: 0.7891 (mm-40) REVERT: B 40 TRP cc_start: 0.8400 (m100) cc_final: 0.7986 (m100) REVERT: B 43 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8383 (tt0) outliers start: 41 outliers final: 34 residues processed: 349 average time/residue: 0.3208 time to fit residues: 175.6304 Evaluate side-chains 332 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain I residue 465 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 43 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 119 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 177 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 0.0040 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS I 239 ASN K 400 ASN B 43 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.104186 restraints weight = 28068.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105556 restraints weight = 20010.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106215 restraints weight = 13343.580| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16858 Z= 0.129 Angle : 0.587 13.713 22854 Z= 0.292 Chirality : 0.043 0.229 2483 Planarity : 0.004 0.056 2974 Dihedral : 5.386 72.611 2436 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.74 % Allowed : 13.96 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2082 helix: 2.05 (0.29), residues: 333 sheet: -1.58 (0.22), residues: 559 loop : -1.20 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS D 54 PHE 0.025 0.001 PHE K 330 TYR 0.021 0.001 TYR C 483 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 7) link_NAG-ASN : angle 0.89709 ( 21) hydrogen bonds : bond 0.03430 ( 502) hydrogen bonds : angle 5.03343 ( 1329) SS BOND : bond 0.00623 ( 25) SS BOND : angle 1.89828 ( 50) covalent geometry : bond 0.00299 (16826) covalent geometry : angle 0.58007 (22783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 325 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 89 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7910 (t0) REVERT: H 90 THR cc_start: 0.7563 (m) cc_final: 0.7201 (m) REVERT: L 6 GLN cc_start: 0.7866 (pt0) cc_final: 0.7385 (pt0) REVERT: L 40 TRP cc_start: 0.8443 (m100) cc_final: 0.7909 (m100) REVERT: L 84 GLU cc_start: 0.7390 (mp0) cc_final: 0.7060 (mp0) REVERT: C 311 MET cc_start: 0.8950 (ppp) cc_final: 0.8330 (ppp) REVERT: C 424 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7521 (mt-10) REVERT: C 484 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.7441 (ptp-170) REVERT: C 488 MET cc_start: 0.6909 (tmm) cc_final: 0.6524 (tmm) REVERT: I 130 ARG cc_start: 0.7869 (mmm160) cc_final: 0.7388 (mmm160) REVERT: I 348 GLN cc_start: 0.7770 (tp40) cc_final: 0.7497 (tp-100) REVERT: K 367 ASP cc_start: 0.7954 (t70) cc_final: 0.7745 (t0) REVERT: K 444 LYS cc_start: 0.8541 (tptm) cc_final: 0.8280 (tttm) REVERT: D 60 TYR cc_start: 0.8380 (m-10) cc_final: 0.8153 (m-10) REVERT: E 84 GLU cc_start: 0.7353 (mp0) cc_final: 0.7016 (mp0) REVERT: A 111 GLN cc_start: 0.8233 (tp40) cc_final: 0.7942 (mm-40) REVERT: B 40 TRP cc_start: 0.8409 (m100) cc_final: 0.7965 (m100) outliers start: 49 outliers final: 46 residues processed: 347 average time/residue: 0.2574 time to fit residues: 140.6700 Evaluate side-chains 353 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 458 CYS Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 239 ASN Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 268 CYS Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 159 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS I 239 ASN I 313 ASN K 400 ASN A 39 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104042 restraints weight = 27754.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105628 restraints weight = 18646.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106492 restraints weight = 12947.866| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16858 Z= 0.129 Angle : 0.585 13.833 22854 Z= 0.291 Chirality : 0.043 0.242 2483 Planarity : 0.004 0.057 2974 Dihedral : 5.378 72.976 2436 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.96 % Allowed : 14.74 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2082 helix: 2.13 (0.29), residues: 333 sheet: -1.55 (0.22), residues: 559 loop : -1.18 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS D 54 PHE 0.026 0.001 PHE K 330 TYR 0.015 0.001 TYR H 52 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 7) link_NAG-ASN : angle 0.91907 ( 21) hydrogen bonds : bond 0.03381 ( 502) hydrogen bonds : angle 4.93023 ( 1329) SS BOND : bond 0.00603 ( 25) SS BOND : angle 1.86532 ( 50) covalent geometry : bond 0.00298 (16826) covalent geometry : angle 0.57868 (22783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 315 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 THR cc_start: 0.7486 (m) cc_final: 0.7096 (m) REVERT: L 6 GLN cc_start: 0.7828 (pt0) cc_final: 0.7363 (pt0) REVERT: L 40 TRP cc_start: 0.8423 (m100) cc_final: 0.7880 (m100) REVERT: L 84 GLU cc_start: 0.7429 (mp0) cc_final: 0.7088 (mp0) REVERT: C 311 MET cc_start: 0.8911 (ppp) cc_final: 0.8289 (ppp) REVERT: C 484 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.7452 (ptp-170) REVERT: C 488 MET cc_start: 0.6923 (tmm) cc_final: 0.6528 (tmm) REVERT: I 130 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7368 (mmm160) REVERT: I 348 GLN cc_start: 0.7776 (tp40) cc_final: 0.7454 (tp-100) REVERT: K 367 ASP cc_start: 0.7983 (t70) cc_final: 0.7773 (t0) REVERT: E 84 GLU cc_start: 0.7355 (mp0) cc_final: 0.7047 (mp0) REVERT: A 111 GLN cc_start: 0.8183 (tp40) cc_final: 0.7889 (mm-40) REVERT: B 40 TRP cc_start: 0.8419 (m100) cc_final: 0.7925 (m100) outliers start: 53 outliers final: 46 residues processed: 338 average time/residue: 0.2718 time to fit residues: 145.0696 Evaluate side-chains 349 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 303 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain I residue 463 HIS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 268 CYS Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 14 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 239 ASN K 400 ASN D 54 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102160 restraints weight = 27670.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103875 restraints weight = 18874.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104399 restraints weight = 13416.788| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16858 Z= 0.188 Angle : 0.629 13.314 22854 Z= 0.315 Chirality : 0.044 0.259 2483 Planarity : 0.004 0.057 2974 Dihedral : 5.496 73.035 2436 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.90 % Allowed : 15.35 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2082 helix: 2.02 (0.29), residues: 333 sheet: -1.54 (0.21), residues: 593 loop : -1.22 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.008 0.001 HIS C 347 PHE 0.025 0.002 PHE K 330 TYR 0.021 0.002 TYR I 440 ARG 0.003 0.000 ARG K 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 7) link_NAG-ASN : angle 1.15816 ( 21) hydrogen bonds : bond 0.03507 ( 502) hydrogen bonds : angle 4.94650 ( 1329) SS BOND : bond 0.00664 ( 25) SS BOND : angle 2.10386 ( 50) covalent geometry : bond 0.00438 (16826) covalent geometry : angle 0.62162 (22783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 313 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 THR cc_start: 0.7426 (m) cc_final: 0.7077 (m) REVERT: L 6 GLN cc_start: 0.7901 (pt0) cc_final: 0.7426 (pt0) REVERT: L 40 TRP cc_start: 0.8462 (m100) cc_final: 0.7977 (m100) REVERT: L 84 GLU cc_start: 0.7445 (mp0) cc_final: 0.7135 (mp0) REVERT: C 311 MET cc_start: 0.8995 (ppp) cc_final: 0.8441 (ppp) REVERT: C 484 ARG cc_start: 0.7906 (ptp-170) cc_final: 0.7448 (ptp-170) REVERT: C 488 MET cc_start: 0.6966 (tmm) cc_final: 0.6531 (tmm) REVERT: I 130 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7689 (mmm160) REVERT: I 348 GLN cc_start: 0.7788 (tp40) cc_final: 0.7466 (tp-100) REVERT: E 84 GLU cc_start: 0.7337 (mp0) cc_final: 0.7049 (mp0) REVERT: A 47 TRP cc_start: 0.8854 (t60) cc_final: 0.8303 (t60) REVERT: A 111 GLN cc_start: 0.8290 (tp40) cc_final: 0.7883 (mm-40) REVERT: B 33 ASN cc_start: 0.8121 (p0) cc_final: 0.7772 (m-40) REVERT: B 40 TRP cc_start: 0.8463 (m100) cc_final: 0.8028 (m100) outliers start: 52 outliers final: 46 residues processed: 342 average time/residue: 0.2505 time to fit residues: 134.8631 Evaluate side-chains 350 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 239 ASN Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 268 CYS Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 ASN I 463 HIS K 400 ASN K 450 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104332 restraints weight = 27648.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105971 restraints weight = 18547.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106512 restraints weight = 13469.700| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16858 Z= 0.127 Angle : 0.604 13.769 22854 Z= 0.299 Chirality : 0.043 0.276 2483 Planarity : 0.004 0.057 2974 Dihedral : 5.410 73.273 2436 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.62 % Allowed : 15.80 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 2082 helix: 2.25 (0.29), residues: 327 sheet: -1.51 (0.21), residues: 593 loop : -1.17 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.009 0.001 HIS D 54 PHE 0.027 0.001 PHE K 330 TYR 0.017 0.001 TYR I 440 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 7) link_NAG-ASN : angle 0.99069 ( 21) hydrogen bonds : bond 0.03333 ( 502) hydrogen bonds : angle 4.84003 ( 1329) SS BOND : bond 0.00558 ( 25) SS BOND : angle 1.93644 ( 50) covalent geometry : bond 0.00295 (16826) covalent geometry : angle 0.59769 (22783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 THR cc_start: 0.7413 (m) cc_final: 0.7056 (m) REVERT: L 6 GLN cc_start: 0.7853 (pt0) cc_final: 0.7102 (pt0) REVERT: L 40 TRP cc_start: 0.8362 (m100) cc_final: 0.7818 (m100) REVERT: L 84 GLU cc_start: 0.7433 (mp0) cc_final: 0.7124 (mp0) REVERT: C 311 MET cc_start: 0.9104 (ppp) cc_final: 0.8492 (ppp) REVERT: C 484 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7689 (ptp-170) REVERT: C 488 MET cc_start: 0.6985 (tmm) cc_final: 0.6557 (tmm) REVERT: I 130 ARG cc_start: 0.7893 (mmm160) cc_final: 0.7690 (mmm160) REVERT: I 348 GLN cc_start: 0.7753 (tp40) cc_final: 0.7408 (tp-100) REVERT: E 17 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: E 84 GLU cc_start: 0.7341 (mp0) cc_final: 0.7064 (mp0) REVERT: A 47 TRP cc_start: 0.8805 (t60) cc_final: 0.8294 (t60) REVERT: A 111 GLN cc_start: 0.8193 (tp40) cc_final: 0.7846 (mm-40) REVERT: B 17 GLU cc_start: 0.7906 (pt0) cc_final: 0.7412 (pm20) REVERT: B 33 ASN cc_start: 0.8117 (p0) cc_final: 0.7727 (m-40) REVERT: B 40 TRP cc_start: 0.8413 (m100) cc_final: 0.7984 (m100) outliers start: 47 outliers final: 41 residues processed: 344 average time/residue: 0.2465 time to fit residues: 134.6903 Evaluate side-chains 355 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 268 CYS Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 97 CYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 3 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 190 optimal weight: 0.7980 chunk 136 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 ASN K 400 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105842 restraints weight = 27703.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107424 restraints weight = 18510.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108017 restraints weight = 13434.260| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16858 Z= 0.107 Angle : 0.595 14.477 22854 Z= 0.291 Chirality : 0.042 0.285 2483 Planarity : 0.004 0.062 2974 Dihedral : 5.328 73.842 2436 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.74 % Allowed : 15.91 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 2082 helix: 2.34 (0.28), residues: 327 sheet: -1.44 (0.21), residues: 591 loop : -1.11 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.009 0.001 HIS D 54 PHE 0.025 0.001 PHE K 330 TYR 0.020 0.001 TYR C 478 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 7) link_NAG-ASN : angle 0.90069 ( 21) hydrogen bonds : bond 0.03252 ( 502) hydrogen bonds : angle 4.75538 ( 1329) SS BOND : bond 0.00456 ( 25) SS BOND : angle 1.85652 ( 50) covalent geometry : bond 0.00246 (16826) covalent geometry : angle 0.58875 (22783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 328 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 90 THR cc_start: 0.7409 (m) cc_final: 0.7045 (m) REVERT: L 6 GLN cc_start: 0.7827 (pt0) cc_final: 0.7055 (pt0) REVERT: L 40 TRP cc_start: 0.8311 (m100) cc_final: 0.7705 (m100) REVERT: L 84 GLU cc_start: 0.7429 (mp0) cc_final: 0.7115 (mp0) REVERT: C 311 MET cc_start: 0.8985 (ppp) cc_final: 0.8235 (ppp) REVERT: C 348 GLN cc_start: 0.8034 (tp40) cc_final: 0.7675 (mm110) REVERT: C 484 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7670 (ptp-170) REVERT: C 488 MET cc_start: 0.7043 (tmm) cc_final: 0.6628 (tmm) REVERT: I 5 LEU cc_start: 0.7668 (mt) cc_final: 0.7351 (mt) REVERT: I 130 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7577 (mmm160) REVERT: I 239 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7477 (t0) REVERT: I 348 GLN cc_start: 0.7773 (tp40) cc_final: 0.7402 (tp-100) REVERT: K 483 TYR cc_start: 0.7914 (m-10) cc_final: 0.7577 (m-10) REVERT: E 17 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: E 84 GLU cc_start: 0.7321 (mp0) cc_final: 0.7078 (mp0) REVERT: A 13 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7311 (mmtt) REVERT: B 33 ASN cc_start: 0.8108 (p0) cc_final: 0.7718 (m-40) REVERT: B 40 TRP cc_start: 0.8376 (m100) cc_final: 0.7926 (m100) outliers start: 49 outliers final: 42 residues processed: 353 average time/residue: 0.2318 time to fit residues: 128.8124 Evaluate side-chains 357 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 313 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 239 ASN Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 268 CYS Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 59 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 4 optimal weight: 0.0010 chunk 192 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 239 ASN K 400 ASN K 450 ASN K 480 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103867 restraints weight = 28032.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105384 restraints weight = 19185.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105947 restraints weight = 13673.130| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16858 Z= 0.150 Angle : 0.629 14.183 22854 Z= 0.310 Chirality : 0.043 0.290 2483 Planarity : 0.004 0.062 2974 Dihedral : 5.437 74.263 2436 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.68 % Allowed : 16.47 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 2082 helix: 2.26 (0.29), residues: 327 sheet: -1.42 (0.21), residues: 593 loop : -1.13 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 36 HIS 0.010 0.001 HIS I 463 PHE 0.023 0.001 PHE K 330 TYR 0.019 0.002 TYR C 478 ARG 0.004 0.000 ARG K 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 7) link_NAG-ASN : angle 1.05356 ( 21) hydrogen bonds : bond 0.03361 ( 502) hydrogen bonds : angle 4.79432 ( 1329) SS BOND : bond 0.00565 ( 25) SS BOND : angle 2.05226 ( 50) covalent geometry : bond 0.00350 (16826) covalent geometry : angle 0.62219 (22783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 THR cc_start: 0.7411 (m) cc_final: 0.7039 (m) REVERT: L 6 GLN cc_start: 0.7955 (pt0) cc_final: 0.7159 (pt0) REVERT: L 40 TRP cc_start: 0.8354 (m100) cc_final: 0.7839 (m100) REVERT: L 84 GLU cc_start: 0.7444 (mp0) cc_final: 0.7123 (mp0) REVERT: C 311 MET cc_start: 0.9062 (ppp) cc_final: 0.8412 (ppp) REVERT: C 348 GLN cc_start: 0.8064 (tp40) cc_final: 0.7708 (mm110) REVERT: C 484 ARG cc_start: 0.7991 (ptp-170) cc_final: 0.7705 (ptp-170) REVERT: C 488 MET cc_start: 0.7123 (tmm) cc_final: 0.6724 (tmm) REVERT: I 5 LEU cc_start: 0.7824 (mt) cc_final: 0.7500 (mt) REVERT: I 130 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7599 (mmm160) REVERT: I 348 GLN cc_start: 0.7754 (tp40) cc_final: 0.7381 (tp-100) REVERT: K 155 MET cc_start: 0.8022 (mtp) cc_final: 0.7750 (mtp) REVERT: K 483 TYR cc_start: 0.7937 (m-10) cc_final: 0.7582 (m-10) REVERT: E 79 LYS cc_start: 0.7840 (mppt) cc_final: 0.7640 (mppt) REVERT: E 84 GLU cc_start: 0.7351 (mp0) cc_final: 0.7076 (mp0) REVERT: A 13 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7352 (mmtt) REVERT: B 17 GLU cc_start: 0.7884 (pt0) cc_final: 0.7376 (pm20) REVERT: B 33 ASN cc_start: 0.8012 (p0) cc_final: 0.7660 (m-40) REVERT: B 40 TRP cc_start: 0.8453 (m100) cc_final: 0.7992 (m100) outliers start: 48 outliers final: 44 residues processed: 342 average time/residue: 0.3086 time to fit residues: 169.6115 Evaluate side-chains 356 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 239 ASN Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 377 ILE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 268 CYS Chi-restraints excluded: chain K residue 293 VAL Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 388 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 146 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 239 ASN K 400 ASN ** K 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104459 restraints weight = 27841.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105812 restraints weight = 19150.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106743 restraints weight = 13677.202| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16858 Z= 0.133 Angle : 0.626 14.488 22854 Z= 0.306 Chirality : 0.043 0.288 2483 Planarity : 0.004 0.062 2974 Dihedral : 5.427 74.453 2436 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.85 % Allowed : 16.58 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 2082 helix: 2.37 (0.29), residues: 327 sheet: -1.40 (0.21), residues: 595 loop : -1.14 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.009 0.001 HIS I 463 PHE 0.024 0.001 PHE K 330 TYR 0.020 0.001 TYR C 478 ARG 0.010 0.000 ARG I 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 7) link_NAG-ASN : angle 0.97722 ( 21) hydrogen bonds : bond 0.03347 ( 502) hydrogen bonds : angle 4.78470 ( 1329) SS BOND : bond 0.00585 ( 25) SS BOND : angle 1.99617 ( 50) covalent geometry : bond 0.00311 (16826) covalent geometry : angle 0.61881 (22783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7938.89 seconds wall clock time: 144 minutes 32.03 seconds (8672.03 seconds total)