Starting phenix.real_space_refine on Sat Jul 20 03:46:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/07_2024/6zg1_11191.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/07_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_11191/07_2024/6zg1_11191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/07_2024/6zg1_11191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/07_2024/6zg1_11191.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg1_11191/07_2024/6zg1_11191.cif" } 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-5388/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: 10.25, per 1000 atoms: 1.03 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: 4.35 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... Secondary structure from input PDB file: 105 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.547A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.733A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.731A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 4.450A pdb=" N HIS A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 544 Processing helix chain 'B' and resid 394 through 398 removed outlier: 3.655A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.669A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.634A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 4.451A pdb=" N HIS B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 544 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 476 Processing helix chain 'C' and resid 486 through 495 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 500 removed outlier: 3.523A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.667A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.455A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 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 408 through 412 Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 477 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.515A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.867A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.757A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 518 removed outlier: 4.715A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 544 removed outlier: 3.527A pdb=" N GLU D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 459 through 476 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.509A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.621A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.683A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 4.548A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 544 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 436 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 459 through 477 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.521A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.735A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.704A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 removed outlier: 4.441A pdb=" N HIS F 516 " --> pdb=" O ARG F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 544 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 459 through 476 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.524A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.714A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.716A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 516 removed outlier: 4.382A pdb=" N HIS G 516 " --> pdb=" O ARG G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 544 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 439 through 445 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 459 through 477 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.515A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.672A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.667A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 516 removed outlier: 4.435A pdb=" N HIS H 516 " --> pdb=" O ARG H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.656A pdb=" N GLU H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1327 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: 2.81 Time building geometry restraints manager: 4.63 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: 4080 2.94 - 3.43: 10012 3.43 - 3.92: 17293 3.92 - 4.41: 20364 4.41 - 4.90: 31927 Nonbonded interactions: 83676 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 83671 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: 0.220 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 36.780 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 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:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- 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= 0.624 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 : 1.128 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: 0.3075 time to fit residues: 240.8797 Evaluate side-chains 386 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 374 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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: 7.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 452 GLN H 500 GLN ** H 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5110 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= 0.264 Angle : 0.846 10.679 13664 Z= 0.431 Chirality : 0.044 0.185 1484 Planarity : 0.005 0.070 1767 Dihedral : 10.234 178.904 1481 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.84 % Allowed : 24.57 % Favored : 71.60 % 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: 0.34 (0.24), residues: 1201 helix: 0.04 (0.18), residues: 770 sheet: None (None), residues: 0 loop : 0.98 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 490 HIS 0.010 0.002 HIS E 530 PHE 0.020 0.002 PHE B 476 TYR 0.026 0.003 TYR E 501 ARG 0.009 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 453 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 422 time to evaluate : 1.033 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: A 405 ILE cc_start: 0.4965 (OUTLIER) cc_final: 0.4571 (mm) REVERT: A 411 SER cc_start: 0.7657 (m) cc_final: 0.7263 (t) REVERT: B 476 PHE cc_start: 0.6778 (m-80) cc_final: 0.6474 (m-80) REVERT: B 517 ARG cc_start: 0.9006 (mtp85) cc_final: 0.8796 (ttt-90) REVERT: D 421 LEU cc_start: 0.7950 (mt) cc_final: 0.7733 (mt) REVERT: D 431 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7264 (tm-30) REVERT: D 472 GLU cc_start: 0.7549 (tp30) cc_final: 0.7190 (tp30) REVERT: E 414 GLU cc_start: 0.7601 (mp0) cc_final: 0.7351 (mp0) REVERT: F 447 THR cc_start: 0.8227 (p) cc_final: 0.7956 (p) REVERT: G 414 GLU cc_start: 0.8247 (mp0) cc_final: 0.8031 (mm-30) REVERT: G 476 PHE cc_start: 0.8553 (m-80) cc_final: 0.8280 (m-10) REVERT: G 543 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8218 (mtm110) REVERT: H 545 MET cc_start: 0.5508 (ptt) cc_final: 0.4777 (ptt) outliers start: 31 outliers final: 17 residues processed: 439 average time/residue: 0.2515 time to fit residues: 144.3811 Evaluate side-chains 360 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 342 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 530 HIS 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 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: 0.0770 chunk 31 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS E 500 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10132 Z= 0.246 Angle : 0.826 10.777 13664 Z= 0.412 Chirality : 0.045 0.192 1484 Planarity : 0.004 0.051 1767 Dihedral : 9.527 179.853 1464 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.29 % Allowed : 27.76 % Favored : 68.95 % 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: 0.49 (0.25), residues: 1201 helix: 0.18 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 0.98 (0.34), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 490 HIS 0.018 0.002 HIS B 530 PHE 0.010 0.001 PHE A 476 TYR 0.023 0.003 TYR B 479 ARG 0.006 0.001 ARG B 517 *********************** 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 406 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 381 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.5254 (OUTLIER) cc_final: 0.4998 (mm) REVERT: A 411 SER cc_start: 0.7634 (m) cc_final: 0.7239 (t) REVERT: A 476 PHE cc_start: 0.8354 (m-10) cc_final: 0.8114 (m-10) REVERT: A 478 ASN cc_start: 0.7761 (t0) cc_final: 0.7552 (t0) REVERT: C 468 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7212 (tmm-80) REVERT: C 507 SER cc_start: 0.8479 (m) cc_final: 0.8215 (p) REVERT: C 522 GLN cc_start: 0.6632 (mt0) cc_final: 0.6394 (mt0) REVERT: D 408 SER cc_start: 0.8189 (m) cc_final: 0.7917 (p) REVERT: F 414 GLU cc_start: 0.8432 (mp0) cc_final: 0.8077 (mm-30) REVERT: F 457 MET cc_start: 0.6070 (mtt) cc_final: 0.5849 (ttm) REVERT: G 468 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7539 (ttp80) REVERT: H 545 MET cc_start: 0.5351 (ptt) cc_final: 0.4824 (ptt) outliers start: 25 outliers final: 14 residues processed: 395 average time/residue: 0.2612 time to fit residues: 135.9764 Evaluate side-chains 346 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 329 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 470 LEU Chi-restraints excluded: chain A residue 518 VAL 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 457 MET 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 545 MET Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain G residue 468 ARG 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: 5.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10132 Z= 0.269 Angle : 0.830 14.056 13664 Z= 0.413 Chirality : 0.046 0.227 1484 Planarity : 0.005 0.054 1767 Dihedral : 9.342 179.771 1464 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.29 % Allowed : 28.40 % Favored : 67.31 % 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: 0.31 (0.25), residues: 1201 helix: 0.08 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.82 (0.34), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 490 HIS 0.019 0.002 HIS H 530 PHE 0.034 0.002 PHE B 476 TYR 0.019 0.002 TYR A 503 ARG 0.010 0.001 ARG A 512 *********************** 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 399 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 363 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.5641 (OUTLIER) cc_final: 0.5439 (mm) REVERT: A 411 SER cc_start: 0.7734 (m) cc_final: 0.7335 (t) REVERT: A 447 THR cc_start: 0.8536 (p) cc_final: 0.8095 (p) REVERT: A 476 PHE cc_start: 0.8266 (m-10) cc_final: 0.8041 (m-10) REVERT: A 478 ASN cc_start: 0.7901 (t0) cc_final: 0.7653 (t0) REVERT: B 464 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8521 (ttmt) REVERT: C 468 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7313 (tmm-80) REVERT: C 507 SER cc_start: 0.8577 (m) cc_final: 0.8307 (p) REVERT: D 448 GLU cc_start: 0.7030 (pm20) cc_final: 0.6796 (pt0) REVERT: D 454 ASP cc_start: 0.6747 (t0) cc_final: 0.6541 (t0) REVERT: G 468 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7667 (ttp80) REVERT: H 486 ASN cc_start: 0.8531 (t0) cc_final: 0.8210 (t0) REVERT: H 545 MET cc_start: 0.5457 (ptt) cc_final: 0.4870 (ptt) outliers start: 36 outliers final: 25 residues processed: 385 average time/residue: 0.2570 time to fit residues: 131.3786 Evaluate side-chains 367 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 339 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 470 LEU 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 538 ILE Chi-restraints excluded: chain D residue 457 MET 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 461 ILE Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 495 ASP Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.0010 chunk 45 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS ** G 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 418 GLN H 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10132 Z= 0.255 Angle : 0.835 16.384 13664 Z= 0.410 Chirality : 0.046 0.213 1484 Planarity : 0.004 0.034 1767 Dihedral : 9.129 179.897 1464 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.65 % Allowed : 30.05 % Favored : 66.30 % 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: 0.27 (0.25), residues: 1201 helix: 0.08 (0.19), residues: 769 sheet: None (None), residues: 0 loop : 0.73 (0.34), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 490 HIS 0.030 0.002 HIS F 530 PHE 0.023 0.001 PHE B 476 TYR 0.016 0.002 TYR G 479 ARG 0.009 0.001 ARG D 543 *********************** 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 406 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 377 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5544 (mm) REVERT: A 411 SER cc_start: 0.7710 (m) cc_final: 0.7272 (t) REVERT: A 476 PHE cc_start: 0.8200 (m-10) cc_final: 0.7903 (m-10) REVERT: A 478 ASN cc_start: 0.8037 (t0) cc_final: 0.7835 (t0) REVERT: A 544 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 464 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8610 (ttmt) REVERT: C 468 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7188 (tmm-80) REVERT: C 507 SER cc_start: 0.8547 (m) cc_final: 0.8293 (p) REVERT: C 521 GLN cc_start: 0.8325 (pp30) cc_final: 0.8037 (pp30) REVERT: F 479 TYR cc_start: 0.6109 (m-80) cc_final: 0.5826 (m-80) REVERT: G 468 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7693 (ttp80) REVERT: H 486 ASN cc_start: 0.8519 (t0) cc_final: 0.8206 (t0) REVERT: H 545 MET cc_start: 0.5234 (ptt) cc_final: 0.4793 (ptt) outliers start: 29 outliers final: 19 residues processed: 395 average time/residue: 0.2450 time to fit residues: 128.7100 Evaluate side-chains 362 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 340 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP 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 437 GLN Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 441 ASP Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 chunk 105 optimal weight: 0.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN F 530 HIS H 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10132 Z= 0.270 Angle : 0.876 13.734 13664 Z= 0.431 Chirality : 0.046 0.194 1484 Planarity : 0.005 0.050 1767 Dihedral : 9.006 179.984 1464 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.56 % Allowed : 30.96 % Favored : 65.48 % 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: 0.10 (0.25), residues: 1201 helix: -0.07 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 0.69 (0.35), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 490 HIS 0.028 0.002 HIS E 530 PHE 0.022 0.001 PHE B 476 TYR 0.040 0.003 TYR C 501 ARG 0.011 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 385 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 357 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7648 (m) cc_final: 0.7263 (t) REVERT: A 476 PHE cc_start: 0.8261 (m-10) cc_final: 0.7938 (m-10) REVERT: B 464 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8628 (ttmt) REVERT: C 468 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7229 (ttp80) REVERT: D 469 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7230 (mm-30) REVERT: F 479 TYR cc_start: 0.6395 (m-80) cc_final: 0.6169 (m-80) REVERT: F 524 LEU cc_start: 0.7576 (tt) cc_final: 0.7314 (pp) REVERT: G 424 ILE cc_start: 0.7477 (pt) cc_final: 0.7206 (pt) REVERT: G 468 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7693 (ttp80) REVERT: H 413 LYS cc_start: 0.8554 (tmtt) cc_final: 0.8317 (tppp) REVERT: H 486 ASN cc_start: 0.8522 (t0) cc_final: 0.8215 (t0) REVERT: H 545 MET cc_start: 0.5606 (ptt) cc_final: 0.5132 (ptt) outliers start: 28 outliers final: 15 residues processed: 373 average time/residue: 0.2478 time to fit residues: 123.8378 Evaluate side-chains 356 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 339 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS H 452 GLN ** H 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10132 Z= 0.264 Angle : 0.896 12.409 13664 Z= 0.437 Chirality : 0.045 0.216 1484 Planarity : 0.004 0.055 1767 Dihedral : 8.714 179.966 1462 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.20 % Allowed : 32.15 % Favored : 64.66 % 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: -0.01 (0.26), residues: 1201 helix: -0.11 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 0.55 (0.36), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 490 HIS 0.008 0.001 HIS F 530 PHE 0.018 0.001 PHE B 476 TYR 0.039 0.002 TYR C 501 ARG 0.008 0.001 ARG F 484 *********************** 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 382 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 357 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7582 (m) cc_final: 0.7244 (t) REVERT: A 454 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6510 (t0) REVERT: A 476 PHE cc_start: 0.8207 (m-10) cc_final: 0.7978 (m-10) REVERT: C 468 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7244 (ttp80) REVERT: C 521 GLN cc_start: 0.8025 (pp30) cc_final: 0.7599 (pp30) REVERT: D 470 LEU cc_start: 0.7815 (tt) cc_final: 0.7583 (tt) REVERT: E 429 TYR cc_start: 0.7637 (m-80) cc_final: 0.7423 (m-10) REVERT: F 479 TYR cc_start: 0.6379 (m-80) cc_final: 0.6110 (m-80) REVERT: F 483 ASP cc_start: 0.6335 (t0) cc_final: 0.6041 (t0) REVERT: F 524 LEU cc_start: 0.7773 (tt) cc_final: 0.7572 (pp) REVERT: G 468 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7687 (ttp80) REVERT: G 474 LYS cc_start: 0.8873 (mttt) cc_final: 0.8659 (mttp) REVERT: G 544 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7610 (mp0) REVERT: H 413 LYS cc_start: 0.8488 (tmtt) cc_final: 0.8282 (tppp) REVERT: H 418 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6888 (mm-40) REVERT: H 486 ASN cc_start: 0.8540 (t0) cc_final: 0.8245 (t0) REVERT: H 545 MET cc_start: 0.5931 (ptt) cc_final: 0.5657 (ptt) outliers start: 25 outliers final: 17 residues processed: 370 average time/residue: 0.2307 time to fit residues: 114.9458 Evaluate side-chains 362 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 342 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER 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 447 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain E residue 431 GLU 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 F residue 507 SER Chi-restraints excluded: chain F residue 530 HIS 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 495 ASP Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 99 optimal weight: 0.0570 chunk 104 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- 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 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS ** H 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.7295 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= 0.275 Angle : 0.900 13.793 13664 Z= 0.439 Chirality : 0.046 0.282 1484 Planarity : 0.004 0.039 1767 Dihedral : 8.503 179.882 1460 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.29 % Allowed : 32.69 % Favored : 64.02 % 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: 0.01 (0.26), residues: 1201 helix: -0.09 (0.19), residues: 765 sheet: None (None), residues: 0 loop : 0.55 (0.36), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 490 HIS 0.022 0.001 HIS F 530 PHE 0.021 0.001 PHE D 476 TYR 0.037 0.003 TYR C 501 ARG 0.009 0.001 ARG G 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 385 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 359 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7606 (m) cc_final: 0.7267 (t) REVERT: A 421 LEU cc_start: 0.7774 (mt) cc_final: 0.7337 (mt) REVERT: C 468 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7309 (ttp80) REVERT: D 470 LEU cc_start: 0.7912 (tt) cc_final: 0.7653 (tt) REVERT: E 429 TYR cc_start: 0.7792 (m-80) cc_final: 0.7492 (m-10) REVERT: F 479 TYR cc_start: 0.6432 (m-80) cc_final: 0.6204 (m-80) REVERT: F 524 LEU cc_start: 0.7762 (tt) cc_final: 0.7495 (pp) REVERT: G 468 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7740 (ttp80) REVERT: H 418 GLN cc_start: 0.7579 (mm-40) cc_final: 0.6926 (mm-40) REVERT: H 486 ASN cc_start: 0.8482 (t0) cc_final: 0.8209 (t0) REVERT: H 545 MET cc_start: 0.5880 (ptt) cc_final: 0.5652 (ptt) outliers start: 26 outliers final: 20 residues processed: 370 average time/residue: 0.2403 time to fit residues: 119.8276 Evaluate side-chains 362 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 340 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LYS 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 447 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 474 LYS 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 F residue 403 ARG Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 530 HIS 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 495 ASP Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 HIS ** G 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.7494 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= 0.281 Angle : 0.923 13.854 13664 Z= 0.451 Chirality : 0.047 0.246 1484 Planarity : 0.004 0.038 1767 Dihedral : 8.468 179.818 1460 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.47 % Allowed : 34.06 % Favored : 63.47 % 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: -0.01 (0.26), residues: 1201 helix: -0.10 (0.19), residues: 764 sheet: None (None), residues: 0 loop : 0.53 (0.36), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 490 HIS 0.020 0.001 HIS F 530 PHE 0.022 0.001 PHE B 476 TYR 0.037 0.003 TYR B 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 377 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 360 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7653 (m) cc_final: 0.7283 (t) REVERT: A 454 ASP cc_start: 0.6959 (m-30) cc_final: 0.6645 (t0) REVERT: A 476 PHE cc_start: 0.8118 (m-10) cc_final: 0.7844 (m-10) REVERT: C 468 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7384 (ttp80) REVERT: C 517 ARG cc_start: 0.8308 (mtp85) cc_final: 0.8078 (mtp180) REVERT: D 470 LEU cc_start: 0.7953 (tt) cc_final: 0.7747 (tt) REVERT: E 429 TYR cc_start: 0.7770 (m-80) cc_final: 0.7478 (m-10) REVERT: F 479 TYR cc_start: 0.6546 (m-80) cc_final: 0.6300 (m-80) REVERT: G 411 SER cc_start: 0.8075 (m) cc_final: 0.7802 (t) REVERT: G 468 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7727 (ttp80) REVERT: H 418 GLN cc_start: 0.7604 (mm-40) cc_final: 0.6966 (mm-40) REVERT: H 486 ASN cc_start: 0.8472 (t0) cc_final: 0.8211 (t0) outliers start: 17 outliers final: 13 residues processed: 370 average time/residue: 0.2311 time to fit residues: 116.3824 Evaluate side-chains 357 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 342 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 437 GLN 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 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 0.0010 overall best weight: 0.5366 ------------------------------------------------------------------------------- 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 522 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS B ** F 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 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.7654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10132 Z= 0.280 Angle : 0.961 14.363 13664 Z= 0.461 Chirality : 0.047 0.253 1484 Planarity : 0.004 0.036 1767 Dihedral : 8.418 179.969 1460 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.19 % Allowed : 35.25 % Favored : 62.56 % 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: -0.00 (0.26), residues: 1201 helix: -0.10 (0.19), residues: 763 sheet: None (None), residues: 0 loop : 0.54 (0.36), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 490 HIS 0.007 0.001 HIS C 534 PHE 0.020 0.001 PHE A 476 TYR 0.029 0.003 TYR C 501 ARG 0.007 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 380 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 366 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 SER cc_start: 0.7612 (m) cc_final: 0.7263 (t) REVERT: A 454 ASP cc_start: 0.6938 (m-30) cc_final: 0.6623 (t0) REVERT: A 476 PHE cc_start: 0.8106 (m-10) cc_final: 0.7903 (m-10) REVERT: C 468 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7337 (ttp80) REVERT: D 470 LEU cc_start: 0.7979 (tt) cc_final: 0.7723 (tt) REVERT: E 429 TYR cc_start: 0.7736 (m-80) cc_final: 0.7459 (m-10) REVERT: F 525 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8481 (mm-30) REVERT: G 411 SER cc_start: 0.8072 (m) cc_final: 0.7849 (t) REVERT: G 414 GLU cc_start: 0.8587 (mp0) cc_final: 0.8383 (mp0) REVERT: G 525 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8564 (mp0) REVERT: H 418 GLN cc_start: 0.7592 (mm-40) cc_final: 0.6861 (mm-40) REVERT: H 486 ASN cc_start: 0.8346 (t0) cc_final: 0.8106 (t0) REVERT: H 545 MET cc_start: 0.6167 (ptt) cc_final: 0.5807 (ptt) outliers start: 14 outliers final: 11 residues processed: 375 average time/residue: 0.2161 time to fit residues: 110.9482 Evaluate side-chains 365 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 353 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 447 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 467 PHE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.131210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092036 restraints weight = 179375.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.099750 restraints weight = 41224.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.105297 restraints weight = 20497.769| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 10132 Z= 0.348 Angle : 1.165 59.200 13664 Z= 0.631 Chirality : 0.055 1.170 1484 Planarity : 0.004 0.037 1767 Dihedral : 8.453 179.937 1460 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 2.19 % Allowed : 34.98 % Favored : 62.83 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.03 (0.26), residues: 1201 helix: -0.12 (0.19), residues: 763 sheet: None (None), residues: 0 loop : 0.53 (0.36), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 490 HIS 0.006 0.001 HIS C 534 PHE 0.017 0.001 PHE A 476 TYR 0.026 0.003 TYR C 501 ARG 0.010 0.001 ARG C 484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.39 seconds wall clock time: 53 minutes 12.63 seconds (3192.63 seconds total)