Starting phenix.real_space_refine on Wed Feb 14 18:17:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/02_2024/6zg1_11191_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/02_2024/6zg1_11191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/02_2024/6zg1_11191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/02_2024/6zg1_11191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/02_2024/6zg1_11191_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/02_2024/6zg1_11191_updated.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 6232 2.51 5 N 1769 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B GLU 472": "OE1" <-> "OE2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ARG 497": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E ARG 463": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ARG 499": "NH1" <-> "NH2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "F GLU 414": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F ARG 463": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F GLU 472": "OE1" <-> "OE2" Residue "F ARG 484": "NH1" <-> "NH2" Residue "F ARG 497": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 535": "NH1" <-> "NH2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "G GLU 414": "OE1" <-> "OE2" Residue "G GLU 431": "OE1" <-> "OE2" Residue "G ARG 463": "NH1" <-> "NH2" Residue "G GLU 469": "OE1" <-> "OE2" Residue "G GLU 472": "OE1" <-> "OE2" Residue "G ARG 499": "NH1" <-> "NH2" Residue "G ARG 499": "NH1" <-> "NH2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "H GLU 400": "OE1" <-> "OE2" Residue "H GLU 414": "OE1" <-> "OE2" Residue "H GLU 416": "OE1" <-> "OE2" Residue "H GLU 431": "OE1" <-> "OE2" Residue "H ARG 463": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H GLU 469": "OE1" <-> "OE2" Residue "H GLU 472": "OE1" <-> "OE2" Residue "H ARG 484": "NH1" <-> "NH2" Residue "H ARG 497": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Residue "H GLU 520": "OE1" <-> "OE2" Residue "H ARG 543": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9931 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1164 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 143, 1164 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} bond proxies already assigned to first conformer: 1132 Chain: "B" Number of atoms: 1324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1250 Chain: "C" Number of atoms: 1232 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1206 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 142} Conformer: "B" Number of residues, atoms: 148, 1206 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 142} bond proxies already assigned to first conformer: 1199 Chain: "D" Number of atoms: 1204 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} bond proxies already assigned to first conformer: 1200 Chain: "E" Number of atoms: 1209 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 146, 1192 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} bond proxies already assigned to first conformer: 1196 Chain: "F" Number of atoms: 1211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1174 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 144, 1174 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} bond proxies already assigned to first conformer: 1152 Chain: "G" Number of atoms: 1206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 1181 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} Conformer: "B" Number of residues, atoms: 145, 1181 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 141} bond proxies already assigned to first conformer: 1174 Chain: "H" Number of atoms: 1210 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 140} Conformer: "B" Number of residues, atoms: 146, 1190 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 140} bond proxies already assigned to first conformer: 1189 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {'BME': 1, 'EDO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {'BME': 1, 'EDO': 4, 'PEG': 1, 'PGE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 16 Unusual residues: {'BME': 1, 'EDO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 35 Unusual residues: {'BME': 1, 'EDO': 6, 'PEG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BME': 1, 'EDO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BME': 1, 'EDO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BME': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BME': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" C1 BME A 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME A 602 " occ=0.60 residue: pdb=" C1 EDO B 602 " occ=0.80 ... (2 atoms not shown) pdb=" O2 EDO B 602 " occ=0.80 residue: pdb=" C1 PEG B 603 " occ=0.80 ... (5 atoms not shown) pdb=" O4 PEG B 603 " occ=0.80 residue: pdb=" C1 BME B 604 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME B 604 " occ=0.60 residue: pdb=" C1 PGE B 605 " occ=0.70 ... (8 atoms not shown) pdb=" O4 PGE B 605 " occ=0.70 residue: pdb=" C1 BME C 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME C 601 " occ=0.60 residue: pdb=" C1 PEG D 602 " occ=0.80 ... (5 atoms not shown) pdb=" O4 PEG D 602 " occ=0.80 residue: pdb=" C1 BME D 603 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME D 603 " occ=0.60 residue: pdb=" C1 EDO D 606 " occ=0.80 ... (2 atoms not shown) pdb=" O2 EDO D 606 " occ=0.80 residue: pdb=" C1 BME E 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME E 602 " occ=0.60 residue: pdb=" C1 BME F 602 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME F 602 " occ=0.60 residue: pdb=" C1 BME G 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME G 601 " occ=0.60 residue: pdb=" C1 BME H 601 " occ=0.60 ... (2 atoms not shown) pdb=" S2 BME H 601 " occ=0.60 Time building chain proxies: 10.03, per 1000 atoms: 1.01 Number of scatterers: 9931 At special positions: 0 Unit cell: (121, 119.9, 69.3, 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 64 16.00 O 1866 8.00 N 1769 7.00 C 6232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 3.5 seconds 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 0 sheets defined 65.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 427 through 435 removed outlier: 4.631A pdb=" N GLU A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 496 through 508 removed outlier: 3.733A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 removed outlier: 4.450A pdb=" N HIS A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 427 through 435 removed outlier: 4.630A pdb=" N GLU B 431 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 460 through 476 Processing helix chain 'B' and resid 487 through 494 Processing helix chain 'B' and resid 496 through 508 removed outlier: 3.669A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR B 503 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 517 removed outlier: 4.451A pdb=" N HIS B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 512 through 517' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 532 through 543 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 427 through 435 removed outlier: 4.601A pdb=" N GLU C 431 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.517A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 508 removed outlier: 3.523A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR C 503 " --> pdb=" O GLN C 500 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 507 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 517 removed outlier: 4.455A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 532 through 544 removed outlier: 3.973A pdb=" N GLU C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 427 through 435 removed outlier: 4.582A pdb=" N GLU D 431 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 460 through 476 Processing helix chain 'D' and resid 487 through 494 Processing helix chain 'D' and resid 496 through 508 removed outlier: 3.867A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR D 503 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER D 507 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 517 removed outlier: 4.715A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 532 through 543 Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 414 through 423 Processing helix chain 'E' and resid 427 through 435 removed outlier: 4.683A pdb=" N GLU E 431 " --> pdb=" O LYS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 448 through 453 Processing helix chain 'E' and resid 460 through 476 Processing helix chain 'E' and resid 487 through 494 Processing helix chain 'E' and resid 496 through 508 removed outlier: 3.621A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR E 503 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER E 507 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 517 removed outlier: 4.548A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 532 through 543 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 414 through 423 Processing helix chain 'F' and resid 427 through 435 removed outlier: 4.566A pdb=" N GLU F 431 " --> pdb=" O LYS F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 444 Processing helix chain 'F' and resid 448 through 453 Processing helix chain 'F' and resid 460 through 476 Processing helix chain 'F' and resid 487 through 494 Processing helix chain 'F' and resid 496 through 508 removed outlier: 3.735A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR F 503 " --> pdb=" O GLN F 500 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER F 507 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 517 removed outlier: 4.470A pdb=" N HIS F 516 " --> pdb=" O SER F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 525 Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 427 through 435 removed outlier: 4.634A pdb=" N GLU G 431 " --> pdb=" O LYS G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'G' and resid 448 through 453 Processing helix chain 'G' and resid 460 through 476 Processing helix chain 'G' and resid 487 through 494 Processing helix chain 'G' and resid 496 through 508 removed outlier: 3.714A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR G 503 " --> pdb=" O GLN G 500 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 506 " --> pdb=" O TYR G 503 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 507 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 517 removed outlier: 4.382A pdb=" N HIS G 516 " --> pdb=" O ARG G 512 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG G 517 " --> pdb=" O SER G 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 512 through 517' Processing helix chain 'G' and resid 520 through 525 Processing helix chain 'G' and resid 532 through 543 Processing helix chain 'H' and resid 409 through 411 No H-bonds generated for 'chain 'H' and resid 409 through 411' Processing helix chain 'H' and resid 414 through 423 Processing helix chain 'H' and resid 427 through 435 removed outlier: 4.665A pdb=" N GLU H 431 " --> pdb=" O LYS H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 444 Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 460 through 476 Processing helix chain 'H' and resid 487 through 494 Processing helix chain 'H' and resid 496 through 508 removed outlier: 3.672A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR H 503 " --> pdb=" O GLN H 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 506 " --> pdb=" O TYR H 503 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER H 507 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 517 removed outlier: 4.435A pdb=" N HIS H 516 " --> pdb=" O ARG H 512 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG H 517 " --> pdb=" O SER H 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 512 through 517' Processing helix chain 'H' and resid 520 through 525 Processing helix chain 'H' and resid 532 through 544 removed outlier: 3.656A pdb=" N GLU H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 846 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: 2.51 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1912 1.32 - 1.46: 3330 1.46 - 1.59: 4810 1.59 - 1.72: 0 1.72 - 1.85: 80 Bond restraints: 10132 Sorted by residual: bond pdb=" C LEU F 406 " pdb=" O LEU F 406 " ideal model delta sigma weight residual 1.234 1.218 0.016 5.00e-03 4.00e+04 1.08e+01 bond pdb=" CA SER H 480 " pdb=" CB SER H 480 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.56e-02 4.11e+03 8.85e+00 bond pdb=" CG ASP H 439 " pdb=" OD2 ASP H 439 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.82e+00 bond pdb=" CA GLY C 504 " pdb=" C GLY C 504 " ideal model delta sigma weight residual 1.515 1.548 -0.033 1.15e-02 7.56e+03 8.30e+00 bond pdb=" CG ASP G 439 " pdb=" OD2 ASP G 439 " ideal model delta sigma weight residual 1.249 1.194 0.055 1.90e-02 2.77e+03 8.30e+00 ... (remaining 10127 not shown) Histogram of bond angle deviations from ideal: 96.31 - 104.00: 98 104.00 - 111.69: 3719 111.69 - 119.39: 4805 119.39 - 127.08: 4935 127.08 - 134.77: 107 Bond angle restraints: 13664 Sorted by residual: angle pdb=" CB GLU D 414 " pdb=" CG GLU D 414 " pdb=" CD GLU D 414 " ideal model delta sigma weight residual 112.60 130.88 -18.28 1.70e+00 3.46e-01 1.16e+02 angle pdb=" C CYS B 508 " pdb=" CA CYS B 508 " pdb=" CB CYS B 508 " ideal model delta sigma weight residual 110.01 96.31 13.70 1.80e+00 3.09e-01 5.79e+01 angle pdb=" CB GLU C 431 " pdb=" CG GLU C 431 " pdb=" CD GLU C 431 " ideal model delta sigma weight residual 112.60 125.45 -12.85 1.70e+00 3.46e-01 5.71e+01 angle pdb=" N MET A 545 " pdb=" CA MET A 545 " pdb=" C MET A 545 " ideal model delta sigma weight residual 113.50 105.29 8.21 1.23e+00 6.61e-01 4.46e+01 angle pdb=" CB BGLU B 472 " pdb=" CG BGLU B 472 " pdb=" CD BGLU B 472 " ideal model delta sigma weight residual 112.60 123.46 -10.86 1.70e+00 3.46e-01 4.08e+01 ... (remaining 13659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5974 35.95 - 71.90: 219 71.90 - 107.85: 35 107.85 - 143.80: 1 143.80 - 179.75: 2 Dihedral angle restraints: 6231 sinusoidal: 2661 harmonic: 3570 Sorted by residual: dihedral pdb=" CD BARG H 465 " pdb=" NE BARG H 465 " pdb=" CZ BARG H 465 " pdb=" NH1BARG H 465 " ideal model delta sinusoidal sigma weight residual 0.00 -179.75 179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG A 465 " pdb=" NE BARG A 465 " pdb=" CZ BARG A 465 " pdb=" NH1BARG A 465 " ideal model delta sinusoidal sigma weight residual 0.00 178.20 -178.20 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C ARG B 497 " pdb=" N ARG B 497 " pdb=" CA ARG B 497 " pdb=" CB ARG B 497 " ideal model delta harmonic sigma weight residual -122.60 -140.37 17.77 0 2.50e+00 1.60e-01 5.06e+01 ... (remaining 6228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1187 0.134 - 0.268: 282 0.268 - 0.402: 12 0.402 - 0.536: 1 0.536 - 0.670: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CA ARG B 497 " pdb=" N ARG B 497 " pdb=" C ARG B 497 " pdb=" CB ARG B 497 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA GLU H 544 " pdb=" N GLU H 544 " pdb=" C GLU H 544 " pdb=" CB GLU H 544 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA GLU H 416 " pdb=" N GLU H 416 " pdb=" C GLU H 416 " pdb=" CB GLU H 416 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 1481 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 476 " 0.046 2.00e-02 2.50e+03 2.83e-02 1.41e+01 pdb=" CG PHE E 476 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 476 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE E 476 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 476 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE E 476 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E 476 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 466 " 0.041 2.00e-02 2.50e+03 2.70e-02 1.27e+01 pdb=" CG PHE F 466 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE F 466 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE F 466 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE F 466 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 466 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE F 466 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 476 " 0.040 2.00e-02 2.50e+03 2.67e-02 1.25e+01 pdb=" CG PHE C 476 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 476 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 476 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 476 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE C 476 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 476 " 0.008 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4139 2.94 - 3.43: 10065 3.43 - 3.92: 17407 3.92 - 4.41: 20520 4.41 - 4.90: 31935 Nonbonded interactions: 84066 Sorted by model distance: nonbonded pdb=" N TYR D 479 " pdb=" O1 PEG D 602 " model vdw 2.449 2.520 nonbonded pdb=" NH2 ARG D 465 " pdb=" O1 EDO D 601 " model vdw 2.457 2.520 nonbonded pdb=" OD1 ASP G 489 " pdb=" NH1BARG G 499 " model vdw 2.457 2.520 nonbonded pdb=" OG SER F 459 " pdb=" NE2 GLN G 436 " model vdw 2.458 2.520 nonbonded pdb=" N MET A 545 " pdb=" N LEU A 546 " model vdw 2.478 2.560 ... (remaining 84061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'B' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'C' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'D' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'E' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'F' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'G' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) selection = (chain 'H' and (resid 404 through 410 or resid 412 through 422 or resid 424 thro \ ugh 426 or resid 428 through 430 or resid 433 or resid 436 through 464 or resid \ 466 through 471 or resid 473 through 479 or resid 481 or resid 483 through 488 o \ r resid 490 through 492 or resid 494 through 498 or resid 500 through 515 or res \ id 518 through 520 or resid 522 through 534 or resid 536 through 542 or resid 54 \ 5)) } 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=0.40 max=1.00 mean=0.97 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.370 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 37.120 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 0.010 0.086 10132 Z= 0.629 Angle : 1.608 18.276 13664 Z= 1.047 Chirality : 0.105 0.670 1484 Planarity : 0.007 0.047 1767 Dihedral : 18.790 179.752 3943 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.98 % Favored : 97.93 % Rotamer: Outliers : 5.94 % Allowed : 6.58 % Favored : 87.49 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1201 helix: -1.21 (0.16), residues: 768 sheet: None (None), residues: 0 loop : -0.26 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP C 420 HIS 0.015 0.004 HIS E 534 PHE 0.046 0.009 PHE E 476 TYR 0.041 0.009 TYR D 429 ARG 0.020 0.002 ARG F 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 593 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.4846 (OUTLIER) cc_final: 0.4344 (mm) REVERT: A 411 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.6796 (t) REVERT: A 424 ILE cc_start: 0.7374 (pt) cc_final: 0.6991 (pt) REVERT: B 411 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6697 (t) REVERT: C 447 THR cc_start: 0.7912 (p) cc_final: 0.7700 (p) REVERT: D 424 ILE cc_start: 0.7058 (pt) cc_final: 0.6572 (pt) REVERT: D 473 LEU cc_start: 0.7961 (tp) cc_final: 0.7751 (tp) REVERT: D 476 PHE cc_start: 0.7518 (m-80) cc_final: 0.7314 (m-10) REVERT: E 431 GLU cc_start: 0.7646 (tp30) cc_final: 0.7418 (tt0) REVERT: E 486 ASN cc_start: 0.7796 (t0) cc_final: 0.7479 (t0) REVERT: F 447 THR cc_start: 0.8171 (p) cc_final: 0.7719 (p) REVERT: F 524 LEU cc_start: 0.7482 (tp) cc_final: 0.7228 (tt) REVERT: G 411 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7446 (t) REVERT: G 424 ILE cc_start: 0.7777 (pt) cc_final: 0.7364 (pt) REVERT: H 431 GLU cc_start: 0.8665 (tt0) cc_final: 0.8236 (tm-30) outliers start: 54 outliers final: 8 residues processed: 618 average time/residue: 0.3077 time to fit residues: 242.8075 Evaluate side-chains 386 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 374 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain H residue 416 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0060 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 418 GLN B 423 GLN B 500 GLN B 530 HIS C 423 GLN B C 530 HIS C 547 HIS D 418 GLN D 516 HIS E 500 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS E 534 HIS F 422 GLN ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS G 422 GLN G 436 GLN H 423 GLN H 452 GLN H 500 GLN H 530 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10132 Z= 0.250 Angle : 0.831 10.889 13664 Z= 0.423 Chirality : 0.044 0.163 1484 Planarity : 0.005 0.068 1767 Dihedral : 10.265 178.737 1481 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.47 % Allowed : 24.11 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1201 helix: -0.32 (0.18), residues: 763 sheet: None (None), residues: 0 loop : -0.05 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 490 HIS 0.010 0.002 HIS E 530 PHE 0.019 0.002 PHE B 476 TYR 0.030 0.003 TYR E 501 ARG 0.010 0.001 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 424 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.4934 (OUTLIER) cc_final: 0.4554 (mm) REVERT: A 411 SER cc_start: 0.7655 (m) cc_final: 0.7250 (t) REVERT: B 476 PHE cc_start: 0.6832 (m-80) cc_final: 0.6497 (m-80) REVERT: B 505 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7548 (mt) REVERT: B 525 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8282 (mp0) REVERT: D 472 GLU cc_start: 0.7524 (tp30) cc_final: 0.7181 (tp30) REVERT: G 414 GLU cc_start: 0.8193 (mp0) cc_final: 0.7970 (mm-30) REVERT: G 447 THR cc_start: 0.8170 (p) cc_final: 0.7947 (p) REVERT: G 476 PHE cc_start: 0.8560 (m-80) cc_final: 0.8281 (m-10) REVERT: G 522 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7188 (mt0) REVERT: H 545 MET cc_start: 0.5338 (ptt) cc_final: 0.4721 (ptt) outliers start: 38 outliers final: 22 residues processed: 443 average time/residue: 0.2606 time to fit residues: 150.8097 Evaluate side-chains 368 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 344 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 530 HIS Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 530 HIS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN C 436 GLN C 500 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 530 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10132 Z= 0.245 Angle : 0.805 11.456 13664 Z= 0.406 Chirality : 0.045 0.173 1484 Planarity : 0.005 0.049 1767 Dihedral : 9.653 179.936 1464 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.02 % Allowed : 28.40 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1201 helix: -0.21 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.19 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 490 HIS 0.019 0.002 HIS B 530 PHE 0.014 0.001 PHE C 476 TYR 0.023 0.003 TYR B 479 ARG 0.011 0.001 ARG E 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 372 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.5053 (OUTLIER) cc_final: 0.4785 (mm) REVERT: A 411 SER cc_start: 0.7759 (m) cc_final: 0.7257 (t) REVERT: B 423 GLN cc_start: 0.8547 (tp40) cc_final: 0.8338 (tp-100) REVERT: C 468 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7087 (tmm-80) REVERT: D 408 SER cc_start: 0.8205 (m) cc_final: 0.8000 (p) REVERT: D 540 THR cc_start: 0.8113 (m) cc_final: 0.7911 (m) REVERT: D 544 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8314 (mp0) REVERT: G 414 GLU cc_start: 0.8284 (mp0) cc_final: 0.8041 (mm-30) REVERT: G 468 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7489 (ttp80) REVERT: G 543 ARG cc_start: 0.8304 (mtt180) cc_final: 0.8077 (mtm110) REVERT: H 486 ASN cc_start: 0.8432 (t0) cc_final: 0.8120 (t0) REVERT: H 522 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7747 (mm-40) REVERT: H 545 MET cc_start: 0.5323 (ptt) cc_final: 0.4859 (ptt) outliers start: 33 outliers final: 12 residues processed: 390 average time/residue: 0.2568 time to fit residues: 131.8975 Evaluate side-chains 355 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 340 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 523 LEU Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 109 optimal weight: 0.0980 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN C 534 HIS ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10132 Z= 0.238 Angle : 0.802 12.702 13664 Z= 0.400 Chirality : 0.044 0.238 1484 Planarity : 0.005 0.058 1767 Dihedral : 9.436 179.869 1464 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.84 % Allowed : 27.95 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1201 helix: -0.39 (0.18), residues: 761 sheet: None (None), residues: 0 loop : -0.29 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 490 HIS 0.021 0.001 HIS H 530 PHE 0.036 0.002 PHE B 476 TYR 0.016 0.002 TYR E 501 ARG 0.010 0.001 ARG G 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 377 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5520 (mm) REVERT: A 411 SER cc_start: 0.7717 (m) cc_final: 0.7305 (t) REVERT: A 454 ASP cc_start: 0.6584 (OUTLIER) cc_final: 0.6318 (t0) REVERT: B 423 GLN cc_start: 0.8479 (tp40) cc_final: 0.8270 (tp-100) REVERT: B 464 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8538 (ttmt) REVERT: C 468 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7250 (tmm-80) REVERT: D 447 THR cc_start: 0.8230 (p) cc_final: 0.7997 (p) REVERT: D 449 GLU cc_start: 0.6964 (pp20) cc_final: 0.6443 (pp20) REVERT: D 454 ASP cc_start: 0.6656 (t0) cc_final: 0.6361 (t0) REVERT: G 468 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7484 (ttp80) REVERT: H 486 ASN cc_start: 0.8418 (t0) cc_final: 0.8080 (t0) outliers start: 31 outliers final: 18 residues processed: 395 average time/residue: 0.2592 time to fit residues: 136.0986 Evaluate side-chains 362 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 340 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10132 Z= 0.291 Angle : 0.823 12.641 13664 Z= 0.413 Chirality : 0.046 0.205 1484 Planarity : 0.005 0.129 1767 Dihedral : 9.228 179.463 1464 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.47 % Allowed : 30.23 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.24), residues: 1201 helix: -0.52 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.28 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 490 HIS 0.005 0.001 HIS H 530 PHE 0.028 0.001 PHE A 476 TYR 0.026 0.003 TYR H 501 ARG 0.007 0.001 ARG H 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 359 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6499 (t0) REVERT: A 476 PHE cc_start: 0.8470 (m-10) cc_final: 0.8157 (m-10) REVERT: B 464 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8705 (ttmt) REVERT: C 468 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7381 (tmm-80) REVERT: G 418 GLN cc_start: 0.8060 (mm110) cc_final: 0.7860 (tp40) REVERT: G 468 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7586 (ttp80) REVERT: G 521 GLN cc_start: 0.8510 (pp30) cc_final: 0.8092 (pp30) REVERT: G 522 GLN cc_start: 0.7751 (tp40) cc_final: 0.7257 (tp40) REVERT: G 540 THR cc_start: 0.8908 (p) cc_final: 0.8700 (p) REVERT: H 545 MET cc_start: 0.5786 (ptt) cc_final: 0.5330 (ptt) outliers start: 39 outliers final: 26 residues processed: 378 average time/residue: 0.2454 time to fit residues: 123.6906 Evaluate side-chains 360 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 331 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.0370 chunk 105 optimal weight: 1.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 422 GLN D 452 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 GLN ** G 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 418 GLN H 452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10132 Z= 0.248 Angle : 0.857 12.275 13664 Z= 0.420 Chirality : 0.045 0.199 1484 Planarity : 0.004 0.035 1767 Dihedral : 8.946 179.850 1462 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.92 % Allowed : 33.33 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1201 helix: -0.56 (0.18), residues: 747 sheet: None (None), residues: 0 loop : -0.27 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 490 HIS 0.028 0.001 HIS H 530 PHE 0.023 0.001 PHE A 476 TYR 0.024 0.002 TYR H 501 ARG 0.009 0.001 ARG F 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 366 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6427 (t0) REVERT: C 468 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7315 (tmm-80) REVERT: D 544 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8442 (mp0) REVERT: F 479 TYR cc_start: 0.6451 (m-80) cc_final: 0.6144 (m-80) REVERT: G 468 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7443 (ttp80) REVERT: G 543 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7753 (mtm110) REVERT: H 517 ARG cc_start: 0.8908 (mtp180) cc_final: 0.8703 (tpt-90) REVERT: H 522 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7448 (tp-100) REVERT: H 545 MET cc_start: 0.5922 (ptt) cc_final: 0.5467 (ptt) outliers start: 22 outliers final: 13 residues processed: 380 average time/residue: 0.2451 time to fit residues: 124.6694 Evaluate side-chains 355 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 339 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain H residue 452 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 79 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 0.0010 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10132 Z= 0.259 Angle : 0.848 12.683 13664 Z= 0.418 Chirality : 0.046 0.241 1484 Planarity : 0.004 0.036 1767 Dihedral : 8.768 179.915 1462 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.65 % Allowed : 33.52 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1201 helix: -0.57 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -0.33 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 490 HIS 0.004 0.001 HIS H 530 PHE 0.010 0.001 PHE C 498 TYR 0.052 0.003 TYR H 501 ARG 0.007 0.001 ARG C 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 358 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6362 (t0) REVERT: B 535 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7357 (mtm110) REVERT: C 468 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7433 (tmm-80) REVERT: C 526 ASP cc_start: 0.6681 (t0) cc_final: 0.6438 (t0) REVERT: F 479 TYR cc_start: 0.6502 (m-80) cc_final: 0.6204 (m-80) REVERT: F 483 ASP cc_start: 0.6207 (t0) cc_final: 0.5889 (t0) REVERT: F 521 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8858 (tp-100) REVERT: G 468 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7622 (ttp80) REVERT: G 525 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8617 (mp0) REVERT: H 418 GLN cc_start: 0.7436 (mm-40) cc_final: 0.6746 (mm-40) outliers start: 19 outliers final: 11 residues processed: 369 average time/residue: 0.2454 time to fit residues: 121.9296 Evaluate side-chains 351 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 337 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain H residue 495 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10132 Z= 0.253 Angle : 0.864 11.786 13664 Z= 0.425 Chirality : 0.045 0.228 1484 Planarity : 0.004 0.030 1767 Dihedral : 8.531 179.926 1460 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.92 % Allowed : 33.52 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1201 helix: -0.60 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -0.28 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 490 HIS 0.005 0.001 HIS H 530 PHE 0.034 0.001 PHE A 476 TYR 0.046 0.002 TYR B 501 ARG 0.007 0.001 ARG F 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 369 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6473 (t0) REVERT: C 468 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7394 (tmm-80) REVERT: C 520 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 526 ASP cc_start: 0.6649 (t0) cc_final: 0.6414 (t0) REVERT: F 479 TYR cc_start: 0.6476 (m-80) cc_final: 0.6237 (m-80) REVERT: F 483 ASP cc_start: 0.6281 (t0) cc_final: 0.5912 (t0) REVERT: F 524 LEU cc_start: 0.8059 (tt) cc_final: 0.7572 (pp) REVERT: G 468 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7598 (ttp80) REVERT: G 474 LYS cc_start: 0.8809 (mttp) cc_final: 0.8582 (mttp) REVERT: G 545 MET cc_start: 0.6703 (mmm) cc_final: 0.6081 (ppp) REVERT: H 418 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6812 (mm-40) REVERT: H 486 ASN cc_start: 0.8467 (t0) cc_final: 0.8255 (t0) REVERT: H 517 ARG cc_start: 0.9133 (mtp180) cc_final: 0.8794 (ttt-90) REVERT: H 545 MET cc_start: 0.6270 (ptt) cc_final: 0.5754 (ptt) outliers start: 22 outliers final: 13 residues processed: 378 average time/residue: 0.2407 time to fit residues: 122.0169 Evaluate side-chains 356 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 340 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN H 530 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.7562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10132 Z= 0.291 Angle : 0.869 12.542 13664 Z= 0.432 Chirality : 0.046 0.209 1484 Planarity : 0.004 0.030 1767 Dihedral : 8.488 179.713 1460 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.29 % Allowed : 33.79 % Favored : 62.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1201 helix: -0.53 (0.19), residues: 733 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 490 HIS 0.027 0.002 HIS H 530 PHE 0.013 0.001 PHE F 466 TYR 0.029 0.003 TYR C 501 ARG 0.008 0.001 ARG H 484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 361 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7392 (tmm-80) REVERT: F 479 TYR cc_start: 0.6600 (m-80) cc_final: 0.6382 (m-80) REVERT: F 483 ASP cc_start: 0.6694 (t0) cc_final: 0.6256 (t0) REVERT: F 524 LEU cc_start: 0.8260 (tt) cc_final: 0.7963 (tp) REVERT: G 431 GLU cc_start: 0.9010 (tt0) cc_final: 0.8699 (tp30) REVERT: G 468 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7611 (ttp80) REVERT: G 545 MET cc_start: 0.6764 (mmm) cc_final: 0.6154 (ppp) REVERT: H 418 GLN cc_start: 0.7619 (mm-40) cc_final: 0.6933 (mm-40) REVERT: H 486 ASN cc_start: 0.8519 (t0) cc_final: 0.8296 (t0) REVERT: H 545 MET cc_start: 0.6645 (ptt) cc_final: 0.6240 (ptt) outliers start: 26 outliers final: 20 residues processed: 374 average time/residue: 0.2535 time to fit residues: 129.6449 Evaluate side-chains 366 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 344 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain H residue 452 GLN Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 530 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 89 optimal weight: 0.0010 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 0.0370 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 0.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN E 422 GLN G 500 GLN ** G 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN H 530 HIS H 534 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10132 Z= 0.265 Angle : 0.946 16.165 13664 Z= 0.457 Chirality : 0.045 0.214 1484 Planarity : 0.004 0.035 1767 Dihedral : 8.493 179.923 1460 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.28 % Allowed : 35.25 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1201 helix: -0.58 (0.19), residues: 727 sheet: None (None), residues: 0 loop : -0.33 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 490 HIS 0.022 0.002 HIS H 530 PHE 0.040 0.002 PHE A 476 TYR 0.023 0.003 TYR G 501 ARG 0.009 0.001 ARG H 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 364 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7392 (ttp80) REVERT: F 479 TYR cc_start: 0.6575 (m-80) cc_final: 0.6347 (m-80) REVERT: F 483 ASP cc_start: 0.6446 (t0) cc_final: 0.5974 (t0) REVERT: F 524 LEU cc_start: 0.8181 (tt) cc_final: 0.7671 (pp) REVERT: G 414 GLU cc_start: 0.8370 (mp0) cc_final: 0.8146 (mp0) REVERT: G 468 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7665 (ttp80) REVERT: G 469 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7356 (mm-30) REVERT: G 476 PHE cc_start: 0.8157 (m-10) cc_final: 0.7953 (m-10) REVERT: G 544 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8488 (mm-30) REVERT: G 545 MET cc_start: 0.6778 (mmm) cc_final: 0.6167 (ppp) REVERT: H 418 GLN cc_start: 0.7506 (mm-40) cc_final: 0.6864 (mm-40) REVERT: H 486 ASN cc_start: 0.8384 (t0) cc_final: 0.8043 (t0) REVERT: H 545 MET cc_start: 0.6540 (ptt) cc_final: 0.6071 (ptt) outliers start: 15 outliers final: 8 residues processed: 373 average time/residue: 0.2332 time to fit residues: 118.1024 Evaluate side-chains 352 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 342 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain H residue 452 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 534 HIS ** 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 = 0.4159 r_free = 0.4159 target = 0.127863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089829 restraints weight = 177980.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.097127 restraints weight = 41979.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.102518 restraints weight = 21050.425| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10132 Z= 0.285 Angle : 0.925 16.904 13664 Z= 0.452 Chirality : 0.046 0.226 1484 Planarity : 0.004 0.057 1767 Dihedral : 8.458 179.888 1460 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.19 % Allowed : 35.71 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1201 helix: -0.59 (0.19), residues: 725 sheet: None (None), residues: 0 loop : -0.40 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 490 HIS 0.008 0.001 HIS A 534 PHE 0.028 0.001 PHE B 476 TYR 0.036 0.003 TYR G 501 ARG 0.008 0.001 ARG H 484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.44 seconds wall clock time: 54 minutes 56.48 seconds (3296.48 seconds total)