Starting phenix.real_space_refine on Sun Oct 12 15:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnl_41422/10_2025/8tnl_41422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnl_41422/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tnl_41422/10_2025/8tnl_41422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnl_41422/10_2025/8tnl_41422.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tnl_41422/10_2025/8tnl_41422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnl_41422/10_2025/8tnl_41422.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.40, per 1000 atoms: 0.21 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: 1.15 Conformation dependent library (CDL) restraints added in 781.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.47 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: 2.10 Time building geometry restraints manager: 1.58 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 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.640 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- 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 : 5.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.000 ARG I 442 TYR 0.042 0.002 TYR C 186 PHE 0.021 0.002 PHE C 136 TRP 0.040 0.001 TRP H 47 HIS 0.008 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00379 (16826) covalent geometry : angle 0.84409 (22783) SS BOND : bond 0.00553 ( 25) SS BOND : angle 1.97955 ( 50) hydrogen bonds : bond 0.20802 ( 502) hydrogen bonds : angle 8.42889 ( 1329) link_NAG-ASN : bond 0.00102 ( 7) link_NAG-ASN : angle 1.09844 ( 21) *********************** 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 : 0.627 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: 0.1108 time to fit residues: 65.3367 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 : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0470 overall best weight: 1.0680 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107318 restraints weight = 27327.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108408 restraints weight = 17860.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109603 restraints weight = 13058.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110230 restraints weight = 10258.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110542 restraints weight = 9450.577| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16858 Z= 0.155 Angle : 0.621 13.648 22854 Z= 0.317 Chirality : 0.044 0.195 2483 Planarity : 0.005 0.059 2974 Dihedral : 5.791 70.997 2436 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.34 % Allowed : 9.83 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.18), residues: 2082 helix: 1.29 (0.28), residues: 333 sheet: -1.51 (0.21), residues: 601 loop : -1.44 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 484 TYR 0.021 0.002 TYR K 478 PHE 0.024 0.001 PHE K 330 TRP 0.023 0.001 TRP H 36 HIS 0.011 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00352 (16826) covalent geometry : angle 0.61651 (22783) SS BOND : bond 0.00497 ( 25) SS BOND : angle 1.73851 ( 50) hydrogen bonds : bond 0.04177 ( 502) hydrogen bonds : angle 5.86922 ( 1329) link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 0.82349 ( 21) *********************** 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 356 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.7796 (pt0) cc_final: 0.7074 (pt0) REVERT: C 311 MET cc_start: 0.9136 (ppp) cc_final: 0.8354 (ppp) REVERT: C 463 HIS cc_start: 0.6880 (p90) cc_final: 0.6568 (p-80) REVERT: C 484 ARG cc_start: 0.7785 (ptp-170) cc_final: 0.7529 (ptp-170) REVERT: K 377 ILE cc_start: 0.8204 (mm) cc_final: 0.7963 (mm) REVERT: D 14 LYS cc_start: 0.7871 (mmpt) cc_final: 0.7605 (mmmt) REVERT: B 17 GLU cc_start: 0.8235 (pt0) cc_final: 0.7613 (pm20) REVERT: B 43 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8551 (tt0) outliers start: 24 outliers final: 15 residues processed: 341 average time/residue: 0.1060 time to fit residues: 56.7878 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 : 0.584 ------------------------------------------------------------------------------- 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 2 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 189 optimal weight: 0.0270 chunk 118 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 ASN C 382 GLN I 347 HIS K 400 ASN E 43 GLN B 43 GLN B 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106860 restraints weight = 27955.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108608 restraints weight = 18595.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109116 restraints weight = 13396.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110138 restraints weight = 11136.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110472 restraints weight = 9890.778| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16858 Z= 0.122 Angle : 0.574 13.835 22854 Z= 0.291 Chirality : 0.043 0.198 2483 Planarity : 0.004 0.054 2974 Dihedral : 5.488 71.740 2436 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.62 % Allowed : 12.84 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.18), residues: 2082 helix: 1.79 (0.28), residues: 333 sheet: -1.51 (0.21), residues: 601 loop : -1.32 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 442 TYR 0.014 0.001 TYR I 478 PHE 0.025 0.001 PHE K 330 TRP 0.018 0.001 TRP H 47 HIS 0.008 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00280 (16826) covalent geometry : angle 0.56884 (22783) SS BOND : bond 0.00422 ( 25) SS BOND : angle 1.66116 ( 50) hydrogen bonds : bond 0.03784 ( 502) hydrogen bonds : angle 5.39084 ( 1329) link_NAG-ASN : bond 0.00119 ( 7) link_NAG-ASN : angle 0.84445 ( 21) *********************** 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 342 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 313 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.7880 (pt0) cc_final: 0.7313 (pt0) REVERT: L 84 GLU cc_start: 0.7172 (mp0) cc_final: 0.6917 (mp0) REVERT: C 311 MET cc_start: 0.9058 (ppp) cc_final: 0.8359 (ppp) REVERT: C 484 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7412 (ptp-170) REVERT: I 444 LYS cc_start: 0.8223 (tttp) cc_final: 0.8010 (ttpt) REVERT: I 463 HIS cc_start: 0.6407 (p-80) cc_final: 0.6110 (p90) REVERT: K 367 ASP cc_start: 0.7834 (t70) cc_final: 0.7620 (t0) REVERT: K 377 ILE cc_start: 0.8151 (mm) cc_final: 0.7941 (mm) REVERT: D 14 LYS cc_start: 0.7833 (mmpt) cc_final: 0.7593 (mmpt) REVERT: E 17 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: E 84 GLU cc_start: 0.7087 (mp0) cc_final: 0.6795 (mp0) REVERT: A 111 GLN cc_start: 0.8103 (tp40) cc_final: 0.7898 (mm-40) outliers start: 29 outliers final: 21 residues processed: 324 average time/residue: 0.1172 time to fit residues: 59.3111 Evaluate side-chains 312 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 290 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 114 LEU 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 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 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain K residue 4 CYS 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 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 A residue 21 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 205 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS I 263 GLN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.129945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098569 restraints weight = 28000.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100460 restraints weight = 19332.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100938 restraints weight = 13682.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101802 restraints weight = 11443.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102141 restraints weight = 10313.826| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 16858 Z= 0.300 Angle : 0.701 12.242 22854 Z= 0.360 Chirality : 0.047 0.231 2483 Planarity : 0.005 0.062 2974 Dihedral : 5.888 71.605 2436 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.96 % Allowed : 13.40 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.18), residues: 2082 helix: 1.66 (0.29), residues: 333 sheet: -1.79 (0.20), residues: 589 loop : -1.38 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.022 0.002 TYR D 34 PHE 0.024 0.002 PHE K 330 TRP 0.023 0.002 TRP H 47 HIS 0.011 0.002 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00694 (16826) covalent geometry : angle 0.69104 (22783) SS BOND : bond 0.00813 ( 25) SS BOND : angle 2.42300 ( 50) hydrogen bonds : bond 0.04074 ( 502) hydrogen bonds : angle 5.40853 ( 1329) link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.55000 ( 21) *********************** 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 366 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 313 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8457 (m-10) cc_final: 0.8134 (m-80) REVERT: H 89 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8024 (t0) REVERT: H 90 THR cc_start: 0.7671 (m) cc_final: 0.7328 (m) REVERT: L 40 TRP cc_start: 0.8531 (m100) cc_final: 0.8031 (m100) REVERT: L 84 GLU cc_start: 0.7421 (mp0) cc_final: 0.7099 (mp0) REVERT: C 311 MET cc_start: 0.9209 (ppp) cc_final: 0.8556 (ppp) REVERT: C 463 HIS cc_start: 0.6664 (p90) cc_final: 0.6385 (p-80) REVERT: C 484 ARG cc_start: 0.7891 (ptp-170) cc_final: 0.7479 (ptp-170) REVERT: C 488 MET cc_start: 0.7033 (tmm) cc_final: 0.6647 (tmm) REVERT: I 463 HIS cc_start: 0.6293 (p-80) cc_final: 0.6070 (p-80) REVERT: K 377 ILE cc_start: 0.8159 (mm) cc_final: 0.7950 (mm) REVERT: D 14 LYS cc_start: 0.7790 (mmpt) cc_final: 0.7530 (mmpt) REVERT: E 84 GLU cc_start: 0.7345 (mp0) cc_final: 0.6997 (mp0) REVERT: A 47 TRP cc_start: 0.8898 (t60) cc_final: 0.8208 (t60) REVERT: B 33 ASN cc_start: 0.8131 (p0) cc_final: 0.7817 (m-40) REVERT: B 40 TRP cc_start: 0.8543 (m100) cc_final: 0.8082 (m100) REVERT: B 43 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8653 (tt0) outliers start: 53 outliers final: 39 residues processed: 343 average time/residue: 0.1142 time to fit residues: 61.6391 Evaluate side-chains 323 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 ASP 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 102 THR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 139 GLU 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 235 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 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 388 ASP Chi-restraints excluded: chain D residue 18 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 400 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103423 restraints weight = 27806.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105047 restraints weight = 18579.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105858 restraints weight = 13544.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106634 restraints weight = 10990.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106967 restraints weight = 10030.869| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16858 Z= 0.118 Angle : 0.583 12.356 22854 Z= 0.297 Chirality : 0.043 0.229 2483 Planarity : 0.004 0.056 2974 Dihedral : 5.522 71.826 2436 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.74 % Allowed : 15.19 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.18), residues: 2082 helix: 1.99 (0.29), residues: 333 sheet: -1.66 (0.21), residues: 593 loop : -1.24 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.016 0.001 TYR C 483 PHE 0.025 0.001 PHE K 330 TRP 0.016 0.001 TRP H 47 HIS 0.010 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00271 (16826) covalent geometry : angle 0.57653 (22783) SS BOND : bond 0.00495 ( 25) SS BOND : angle 1.87376 ( 50) hydrogen bonds : bond 0.03509 ( 502) hydrogen bonds : angle 5.03580 ( 1329) link_NAG-ASN : bond 0.00117 ( 7) link_NAG-ASN : angle 1.05400 ( 21) *********************** 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 367 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 318 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8391 (m-10) cc_final: 0.8073 (m-80) REVERT: H 89 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8047 (t0) REVERT: H 90 THR cc_start: 0.7552 (m) cc_final: 0.7178 (m) REVERT: L 6 GLN cc_start: 0.7875 (pt0) cc_final: 0.7466 (pt0) REVERT: L 40 TRP cc_start: 0.8411 (m100) cc_final: 0.7901 (m100) REVERT: L 84 GLU cc_start: 0.7423 (mp0) cc_final: 0.7108 (mp0) REVERT: C 311 MET cc_start: 0.9159 (ppp) cc_final: 0.8509 (ppp) REVERT: C 463 HIS cc_start: 0.6676 (p90) cc_final: 0.6431 (p-80) REVERT: C 484 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7473 (ptp-170) REVERT: C 488 MET cc_start: 0.6966 (tmm) cc_final: 0.6558 (tmm) REVERT: I 463 HIS cc_start: 0.6571 (p-80) cc_final: 0.6329 (p-80) REVERT: K 483 TYR cc_start: 0.8044 (m-80) cc_final: 0.7598 (m-10) REVERT: D 14 LYS cc_start: 0.7735 (mmpt) cc_final: 0.7487 (mmpt) REVERT: E 17 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: E 84 GLU cc_start: 0.7297 (mp0) cc_final: 0.6989 (mp0) REVERT: B 33 ASN cc_start: 0.8072 (p0) cc_final: 0.7726 (m-40) REVERT: B 40 TRP cc_start: 0.8395 (m100) cc_final: 0.7954 (m100) outliers start: 49 outliers final: 38 residues processed: 344 average time/residue: 0.1096 time to fit residues: 59.9510 Evaluate side-chains 339 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 102 THR Chi-restraints excluded: chain C residue 3 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 268 CYS Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 143 LEU 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 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 293 VAL 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 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 67 ILE 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 29 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 42 optimal weight: 0.0570 chunk 119 optimal weight: 0.9980 chunk 169 optimal weight: 0.4980 chunk 173 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 239 ASN I 313 ASN 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 = 0.3690 r_free = 0.3690 target = 0.134610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103505 restraints weight = 27750.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105113 restraints weight = 18437.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105640 restraints weight = 13510.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106509 restraints weight = 11275.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106913 restraints weight = 10145.204| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16858 Z= 0.132 Angle : 0.583 13.022 22854 Z= 0.292 Chirality : 0.043 0.240 2483 Planarity : 0.004 0.061 2974 Dihedral : 5.470 72.414 2436 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.85 % Allowed : 15.91 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.19), residues: 2082 helix: 2.05 (0.29), residues: 333 sheet: -1.59 (0.21), residues: 593 loop : -1.19 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.018 0.001 TYR I 440 PHE 0.024 0.001 PHE K 330 TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00307 (16826) covalent geometry : angle 0.57627 (22783) SS BOND : bond 0.00504 ( 25) SS BOND : angle 1.84413 ( 50) hydrogen bonds : bond 0.03397 ( 502) hydrogen bonds : angle 4.91564 ( 1329) link_NAG-ASN : bond 0.00067 ( 7) link_NAG-ASN : angle 1.03737 ( 21) *********************** 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 362 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8399 (m-10) cc_final: 0.8086 (m-80) REVERT: H 90 THR cc_start: 0.7490 (m) cc_final: 0.7151 (m) REVERT: L 6 GLN cc_start: 0.7916 (pt0) cc_final: 0.7214 (pt0) REVERT: L 40 TRP cc_start: 0.8397 (m100) cc_final: 0.7881 (m100) REVERT: L 84 GLU cc_start: 0.7422 (mp0) cc_final: 0.7101 (mp0) REVERT: C 311 MET cc_start: 0.9125 (ppp) cc_final: 0.8456 (ppp) REVERT: C 463 HIS cc_start: 0.6737 (p90) cc_final: 0.6415 (p-80) REVERT: C 484 ARG cc_start: 0.7872 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: C 488 MET cc_start: 0.7010 (tmm) cc_final: 0.6586 (tmm) REVERT: I 239 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7634 (t0) REVERT: I 463 HIS cc_start: 0.6887 (p-80) cc_final: 0.6608 (p-80) REVERT: K 311 MET cc_start: 0.8992 (ppp) cc_final: 0.8305 (ppp) REVERT: K 483 TYR cc_start: 0.8045 (m-80) cc_final: 0.7506 (m-10) REVERT: E 17 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: E 84 GLU cc_start: 0.7317 (mp0) cc_final: 0.7028 (mp0) REVERT: A 47 TRP cc_start: 0.8845 (t60) cc_final: 0.8308 (t60) REVERT: B 33 ASN cc_start: 0.8027 (p0) cc_final: 0.7668 (m-40) REVERT: B 40 TRP cc_start: 0.8391 (m100) cc_final: 0.7936 (m100) outliers start: 51 outliers final: 40 residues processed: 339 average time/residue: 0.1078 time to fit residues: 58.1881 Evaluate side-chains 343 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR 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 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 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 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 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 A residue 21 THR 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 184 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 400 ASN D 54 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.133010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102030 restraints weight = 27695.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103581 restraints weight = 18715.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104383 restraints weight = 13494.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105136 restraints weight = 11012.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105491 restraints weight = 10057.982| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16858 Z= 0.170 Angle : 0.609 12.886 22854 Z= 0.306 Chirality : 0.044 0.254 2483 Planarity : 0.004 0.061 2974 Dihedral : 5.510 72.767 2436 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.85 % Allowed : 16.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.19), residues: 2082 helix: 2.01 (0.29), residues: 333 sheet: -1.61 (0.21), residues: 593 loop : -1.20 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.021 0.002 TYR C 483 PHE 0.024 0.001 PHE K 330 TRP 0.016 0.001 TRP H 47 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00397 (16826) covalent geometry : angle 0.60227 (22783) SS BOND : bond 0.00602 ( 25) SS BOND : angle 1.90485 ( 50) hydrogen bonds : bond 0.03463 ( 502) hydrogen bonds : angle 4.90131 ( 1329) link_NAG-ASN : bond 0.00053 ( 7) link_NAG-ASN : angle 1.19030 ( 21) *********************** 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 363 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 312 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8435 (m-10) cc_final: 0.8174 (m-10) REVERT: H 90 THR cc_start: 0.7456 (m) cc_final: 0.7098 (m) REVERT: L 6 GLN cc_start: 0.7946 (pt0) cc_final: 0.7236 (pt0) REVERT: L 40 TRP cc_start: 0.8420 (m100) cc_final: 0.7920 (m100) REVERT: L 84 GLU cc_start: 0.7467 (mp0) cc_final: 0.7153 (mp0) REVERT: C 311 MET cc_start: 0.9173 (ppp) cc_final: 0.8486 (ppp) REVERT: C 463 HIS cc_start: 0.6924 (p90) cc_final: 0.6493 (p-80) REVERT: C 484 ARG cc_start: 0.7931 (ptp-170) cc_final: 0.7462 (ptp-170) REVERT: C 488 MET cc_start: 0.7024 (tmm) cc_final: 0.6601 (tmm) REVERT: I 463 HIS cc_start: 0.6864 (p-80) cc_final: 0.6532 (p-80) REVERT: K 311 MET cc_start: 0.9037 (ppp) cc_final: 0.8346 (ppp) REVERT: K 483 TYR cc_start: 0.8010 (m-80) cc_final: 0.7415 (m-10) REVERT: E 17 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: E 84 GLU cc_start: 0.7364 (mp0) cc_final: 0.7072 (mp0) REVERT: A 13 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7388 (mmtt) REVERT: B 33 ASN cc_start: 0.7989 (p0) cc_final: 0.7615 (m-40) REVERT: B 40 TRP cc_start: 0.8444 (m100) cc_final: 0.7987 (m100) REVERT: B 43 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8587 (tt0) outliers start: 51 outliers final: 44 residues processed: 342 average time/residue: 0.1100 time to fit residues: 59.6333 Evaluate side-chains 346 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR 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 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 264 VAL Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 304 SER 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 127 SER 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 377 ILE 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 A residue 21 THR Chi-restraints excluded: chain A residue 67 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 400 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103950 restraints weight = 27883.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105459 restraints weight = 18609.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106293 restraints weight = 13588.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107077 restraints weight = 11012.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107438 restraints weight = 10034.688| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16858 Z= 0.125 Angle : 0.609 13.250 22854 Z= 0.303 Chirality : 0.043 0.274 2483 Planarity : 0.004 0.062 2974 Dihedral : 5.450 73.265 2436 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.96 % Allowed : 16.53 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 2082 helix: 2.14 (0.29), residues: 333 sheet: -1.54 (0.21), residues: 593 loop : -1.17 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.020 0.001 TYR C 483 PHE 0.023 0.001 PHE K 330 TRP 0.015 0.001 TRP A 36 HIS 0.009 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00292 (16826) covalent geometry : angle 0.60160 (22783) SS BOND : bond 0.00558 ( 25) SS BOND : angle 2.10208 ( 50) hydrogen bonds : bond 0.03393 ( 502) hydrogen bonds : angle 4.80552 ( 1329) link_NAG-ASN : bond 0.00091 ( 7) link_NAG-ASN : angle 0.99059 ( 21) *********************** 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 372 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8414 (m-10) cc_final: 0.8118 (m-80) REVERT: H 90 THR cc_start: 0.7412 (m) cc_final: 0.7059 (m) REVERT: L 6 GLN cc_start: 0.7896 (pt0) cc_final: 0.7185 (pt0) REVERT: L 40 TRP cc_start: 0.8357 (m100) cc_final: 0.7839 (m100) REVERT: L 84 GLU cc_start: 0.7457 (mp0) cc_final: 0.7152 (mp0) REVERT: C 311 MET cc_start: 0.9095 (ppp) cc_final: 0.8444 (ppp) REVERT: C 463 HIS cc_start: 0.6996 (p90) cc_final: 0.6571 (p-80) REVERT: C 484 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.7689 (ptp-170) REVERT: C 488 MET cc_start: 0.7096 (tmm) cc_final: 0.6656 (tmm) REVERT: I 155 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7799 (pmm) REVERT: I 463 HIS cc_start: 0.6906 (p-80) cc_final: 0.6579 (p-80) REVERT: K 311 MET cc_start: 0.8985 (ppp) cc_final: 0.8308 (ppp) REVERT: D 17 GLU cc_start: 0.8145 (tt0) cc_final: 0.7894 (tt0) REVERT: E 17 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: E 84 GLU cc_start: 0.7382 (mp0) cc_final: 0.7087 (mp0) REVERT: A 13 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7371 (mmtt) REVERT: B 17 GLU cc_start: 0.7869 (pt0) cc_final: 0.7388 (pm20) REVERT: B 33 ASN cc_start: 0.7982 (p0) cc_final: 0.7592 (m-40) REVERT: B 40 TRP cc_start: 0.8393 (m100) cc_final: 0.7936 (m100) outliers start: 53 outliers final: 46 residues processed: 346 average time/residue: 0.1103 time to fit residues: 60.2184 Evaluate side-chains 354 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 155 MET Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 273 TYR Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 456 THR 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 127 SER 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 380 THR 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 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 116 THR Chi-restraints excluded: chain B residue 27 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 70 optimal weight: 0.0470 chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 400 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104892 restraints weight = 27608.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105696 restraints weight = 17702.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106386 restraints weight = 13409.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108145 restraints weight = 11667.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108208 restraints weight = 10055.151| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16858 Z= 0.117 Angle : 0.614 13.936 22854 Z= 0.303 Chirality : 0.043 0.285 2483 Planarity : 0.004 0.062 2974 Dihedral : 5.436 74.222 2436 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.90 % Allowed : 16.47 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.19), residues: 2082 helix: 2.32 (0.29), residues: 327 sheet: -1.50 (0.21), residues: 593 loop : -1.18 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 484 TYR 0.019 0.001 TYR C 483 PHE 0.022 0.001 PHE K 330 TRP 0.014 0.001 TRP H 47 HIS 0.009 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00272 (16826) covalent geometry : angle 0.60636 (22783) SS BOND : bond 0.00586 ( 25) SS BOND : angle 2.07880 ( 50) hydrogen bonds : bond 0.03339 ( 502) hydrogen bonds : angle 4.74194 ( 1329) link_NAG-ASN : bond 0.00113 ( 7) link_NAG-ASN : angle 0.91682 ( 21) *********************** 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 378 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 326 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8378 (m-10) cc_final: 0.8093 (m-10) REVERT: L 6 GLN cc_start: 0.7889 (pt0) cc_final: 0.7168 (pt0) REVERT: L 38 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8384 (tt) REVERT: L 40 TRP cc_start: 0.8319 (m100) cc_final: 0.7806 (m100) REVERT: L 79 LYS cc_start: 0.7850 (mptt) cc_final: 0.7607 (mptt) REVERT: L 84 GLU cc_start: 0.7440 (mp0) cc_final: 0.7146 (mp0) REVERT: C 311 MET cc_start: 0.9052 (ppp) cc_final: 0.8443 (ppp) REVERT: C 463 HIS cc_start: 0.6989 (p90) cc_final: 0.6587 (p-80) REVERT: C 484 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7700 (ptp-170) REVERT: C 488 MET cc_start: 0.7104 (tmm) cc_final: 0.6712 (tmm) REVERT: I 5 LEU cc_start: 0.7735 (mt) cc_final: 0.7344 (mt) REVERT: I 155 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7695 (pmm) REVERT: I 463 HIS cc_start: 0.6967 (p-80) cc_final: 0.6618 (p-80) REVERT: I 484 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7726 (ptt90) REVERT: K 155 MET cc_start: 0.8001 (mtp) cc_final: 0.7713 (mtp) REVERT: K 162 THR cc_start: 0.8330 (p) cc_final: 0.8024 (t) REVERT: K 311 MET cc_start: 0.8970 (ppp) cc_final: 0.8292 (ppp) REVERT: D 17 GLU cc_start: 0.8159 (tt0) cc_final: 0.7944 (tt0) REVERT: E 17 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 13 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7382 (mmtt) REVERT: B 33 ASN cc_start: 0.7976 (p0) cc_final: 0.7584 (m-40) REVERT: B 40 TRP cc_start: 0.8386 (m100) cc_final: 0.7906 (m100) REVERT: B 43 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8569 (tt0) outliers start: 52 outliers final: 44 residues processed: 351 average time/residue: 0.1047 time to fit residues: 58.5092 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 : 0.629 ------------------------------------------------------------------------------- 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 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 155 MET Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 273 TYR Chi-restraints excluded: chain I residue 293 VAL Chi-restraints excluded: chain I residue 456 THR 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 127 SER 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 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 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 116 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 43 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 147 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102984 restraints weight = 27843.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104486 restraints weight = 18933.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105314 restraints weight = 13590.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106089 restraints weight = 11102.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106450 restraints weight = 10125.894| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16858 Z= 0.159 Angle : 0.648 14.724 22854 Z= 0.319 Chirality : 0.044 0.294 2483 Planarity : 0.004 0.063 2974 Dihedral : 5.517 74.409 2436 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.96 % Allowed : 17.31 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.19), residues: 2082 helix: 2.13 (0.29), residues: 333 sheet: -1.48 (0.21), residues: 593 loop : -1.17 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 484 TYR 0.018 0.002 TYR A 33 PHE 0.022 0.002 PHE K 330 TRP 0.014 0.001 TRP H 47 HIS 0.009 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00374 (16826) covalent geometry : angle 0.63969 (22783) SS BOND : bond 0.00644 ( 25) SS BOND : angle 2.18905 ( 50) hydrogen bonds : bond 0.03414 ( 502) hydrogen bonds : angle 4.74384 ( 1329) link_NAG-ASN : bond 0.00052 ( 7) link_NAG-ASN : angle 1.06372 ( 21) ********************** 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 369 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 316 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8432 (m-10) cc_final: 0.8189 (m-10) REVERT: L 6 GLN cc_start: 0.7923 (pt0) cc_final: 0.7224 (pt0) REVERT: L 38 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8437 (tt) REVERT: L 40 TRP cc_start: 0.8344 (m100) cc_final: 0.7823 (m100) REVERT: L 79 LYS cc_start: 0.7872 (mptt) cc_final: 0.7667 (mppt) REVERT: L 84 GLU cc_start: 0.7465 (mp0) cc_final: 0.7170 (mp0) REVERT: C 311 MET cc_start: 0.9122 (ppp) cc_final: 0.8474 (ppp) REVERT: C 463 HIS cc_start: 0.6976 (p90) cc_final: 0.6595 (p-80) REVERT: C 484 ARG cc_start: 0.8067 (ptp-170) cc_final: 0.7776 (ptp-170) REVERT: C 488 MET cc_start: 0.7130 (tmm) cc_final: 0.6737 (tmm) REVERT: I 5 LEU cc_start: 0.7758 (mt) cc_final: 0.7385 (mt) REVERT: I 155 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.7934 (pmm) REVERT: I 463 HIS cc_start: 0.6965 (p-80) cc_final: 0.6613 (p-80) REVERT: I 484 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7694 (ptt90) REVERT: K 155 MET cc_start: 0.8065 (mtp) cc_final: 0.7788 (mtp) REVERT: K 311 MET cc_start: 0.9038 (ppp) cc_final: 0.8350 (ppp) REVERT: K 483 TYR cc_start: 0.7880 (m-10) cc_final: 0.7483 (m-10) REVERT: E 17 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 13 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7378 (mmtt) REVERT: A 47 TRP cc_start: 0.8818 (t60) cc_final: 0.8302 (t60) REVERT: B 17 GLU cc_start: 0.7886 (pt0) cc_final: 0.7398 (pm20) REVERT: B 33 ASN cc_start: 0.8021 (p0) cc_final: 0.7618 (m-40) REVERT: B 40 TRP cc_start: 0.8444 (m100) cc_final: 0.7950 (m100) REVERT: B 43 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8611 (tt0) outliers start: 53 outliers final: 46 residues processed: 341 average time/residue: 0.1097 time to fit residues: 59.0446 Evaluate side-chains 360 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 155 MET Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 194 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 304 SER Chi-restraints excluded: chain I residue 456 THR 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 127 SER 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 377 ILE Chi-restraints excluded: chain K residue 380 THR 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 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 116 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 43 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 173 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 400 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104558 restraints weight = 27780.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105971 restraints weight = 18879.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106849 restraints weight = 13610.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107622 restraints weight = 11029.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108001 restraints weight = 10060.525| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16858 Z= 0.123 Angle : 0.634 14.161 22854 Z= 0.309 Chirality : 0.043 0.287 2483 Planarity : 0.004 0.062 2974 Dihedral : 5.451 74.804 2436 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.62 % Allowed : 17.64 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.19), residues: 2082 helix: 2.37 (0.29), residues: 327 sheet: -1.43 (0.21), residues: 593 loop : -1.17 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 484 TYR 0.016 0.001 TYR I 343 PHE 0.021 0.001 PHE K 330 TRP 0.013 0.001 TRP H 47 HIS 0.009 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00289 (16826) covalent geometry : angle 0.62759 (22783) SS BOND : bond 0.00633 ( 25) SS BOND : angle 1.99659 ( 50) hydrogen bonds : bond 0.03334 ( 502) hydrogen bonds : angle 4.69303 ( 1329) link_NAG-ASN : bond 0.00106 ( 7) link_NAG-ASN : angle 0.94903 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2819.00 seconds wall clock time: 49 minutes 35.16 seconds (2975.16 seconds total)