Starting phenix.real_space_refine on Thu Mar 14 22:56:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptv_13641/03_2024/7ptv_13641_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptv_13641/03_2024/7ptv_13641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptv_13641/03_2024/7ptv_13641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptv_13641/03_2024/7ptv_13641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptv_13641/03_2024/7ptv_13641_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptv_13641/03_2024/7ptv_13641_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 30 5.16 5 C 6374 2.51 5 N 1678 2.21 5 O 1910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 655": "OD1" <-> "OD2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 482": "OD1" <-> "OD2" Residue "B TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 655": "OD1" <-> "OD2" Residue "B PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9996 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 4945 Classifications: {'peptide': 645} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 603} Chain: "B" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 4945 Classifications: {'peptide': 645} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 603} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.57, per 1000 atoms: 0.56 Number of scatterers: 9996 At special positions: 0 Unit cell: (88.29, 98.1, 110.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 4 15.00 O 1910 8.00 N 1678 7.00 C 6374 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=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 14 sheets defined 31.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 98 through 101 No H-bonds generated for 'chain 'A' and resid 98 through 101' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.800A pdb=" N GLN A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 352 through 362 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 439 through 442 removed outlier: 3.929A pdb=" N GLY A 442 " --> pdb=" O SER A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 461 through 467 Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 525 through 559 removed outlier: 5.200A pdb=" N LYS A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) Proline residue: A 534 - end of helix removed outlier: 3.914A pdb=" N ILE A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 593 removed outlier: 3.652A pdb=" N LEU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP A 589 " --> pdb=" O TYR A 585 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP A 590 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE A 593 " --> pdb=" O TRP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 621 removed outlier: 4.039A pdb=" N TYR A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 669 through 683 removed outlier: 3.650A pdb=" N ASP A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 203 through 220 removed outlier: 3.800A pdb=" N GLN B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 No H-bonds generated for 'chain 'B' and resid 284 through 287' Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 352 through 362 Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'B' and resid 439 through 442 removed outlier: 3.930A pdb=" N GLY B 442 " --> pdb=" O SER B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 461 through 467 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 525 through 559 removed outlier: 5.200A pdb=" N LYS B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) Proline residue: B 534 - end of helix removed outlier: 3.915A pdb=" N ILE B 548 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 593 removed outlier: 3.651A pdb=" N LEU B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE B 587 " --> pdb=" O ASN B 583 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN B 588 " --> pdb=" O THR B 584 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP B 589 " --> pdb=" O TYR B 585 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP B 590 " --> pdb=" O GLY B 586 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE B 593 " --> pdb=" O TRP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 621 removed outlier: 4.038A pdb=" N TYR B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR B 618 " --> pdb=" O LYS B 614 " (cutoff:3.500A) Proline residue: B 619 - end of helix Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 669 through 683 removed outlier: 3.650A pdb=" N ASP B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 690 No H-bonds generated for 'chain 'B' and resid 688 through 690' Processing sheet with id= A, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.123A pdb=" N VAL A 346 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 130 Processing sheet with id= C, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= D, first strand: chain 'A' and resid 337 through 341 removed outlier: 3.590A pdb=" N THR A 329 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 317 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 331 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL A 315 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 393 through 395 Processing sheet with id= F, first strand: chain 'A' and resid 425 through 428 removed outlier: 3.623A pdb=" N GLY A 426 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER A 400 " --> pdb=" O MET A 567 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N MET A 567 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR A 402 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU A 565 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 491 through 493 Processing sheet with id= H, first strand: chain 'B' and resid 651 through 653 removed outlier: 6.123A pdb=" N VAL B 346 " --> pdb=" O ARG B 652 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 126 through 130 Processing sheet with id= J, first strand: chain 'B' and resid 271 through 273 Processing sheet with id= K, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.590A pdb=" N THR B 329 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 317 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 331 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL B 315 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 393 through 395 Processing sheet with id= M, first strand: chain 'B' and resid 425 through 428 removed outlier: 3.623A pdb=" N GLY B 426 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER B 400 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N MET B 567 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR B 402 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 565 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 491 through 493 272 hydrogen bonds defined for protein. 774 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: 2.76 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3225 1.34 - 1.45: 1512 1.45 - 1.57: 5465 1.57 - 1.68: 10 1.68 - 1.80: 48 Bond restraints: 10260 Sorted by residual: bond pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.660 1.571 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" O3P FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.660 1.572 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O5B FAD A 901 " pdb=" PA FAD A 901 " ideal model delta sigma weight residual 1.634 1.559 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5B FAD B 901 " pdb=" PA FAD B 901 " ideal model delta sigma weight residual 1.634 1.559 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O5' FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.637 1.572 0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 10255 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.13: 333 106.13 - 113.13: 5424 113.13 - 120.13: 3856 120.13 - 127.12: 4281 127.12 - 134.12: 138 Bond angle restraints: 14032 Sorted by residual: angle pdb=" CA GLN A 551 " pdb=" CB GLN A 551 " pdb=" CG GLN A 551 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA GLN B 551 " pdb=" CB GLN B 551 " pdb=" CG GLN B 551 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CB GLN B 551 " pdb=" CG GLN B 551 " pdb=" CD GLN B 551 " ideal model delta sigma weight residual 112.60 118.43 -5.83 1.70e+00 3.46e-01 1.17e+01 angle pdb=" CB GLN A 551 " pdb=" CG GLN A 551 " pdb=" CD GLN A 551 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.70e+00 3.46e-01 1.17e+01 angle pdb=" CA LYS A 303 " pdb=" CB LYS A 303 " pdb=" CG LYS A 303 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 ... (remaining 14027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 5436 16.71 - 33.42: 455 33.42 - 50.13: 105 50.13 - 66.84: 40 66.84 - 83.55: 8 Dihedral angle restraints: 6044 sinusoidal: 2342 harmonic: 3702 Sorted by residual: dihedral pdb=" CA HIS B 319 " pdb=" C HIS B 319 " pdb=" N PHE B 320 " pdb=" CA PHE B 320 " ideal model delta harmonic sigma weight residual -180.00 -143.51 -36.49 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA HIS A 319 " pdb=" C HIS A 319 " pdb=" N PHE A 320 " pdb=" CA PHE A 320 " ideal model delta harmonic sigma weight residual -180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA VAL B 144 " pdb=" C VAL B 144 " pdb=" N ALA B 145 " pdb=" CA ALA B 145 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 874 0.041 - 0.082: 471 0.082 - 0.122: 177 0.122 - 0.163: 38 0.163 - 0.204: 4 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CA TYR A 161 " pdb=" N TYR A 161 " pdb=" C TYR A 161 " pdb=" CB TYR A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA TYR B 161 " pdb=" N TYR B 161 " pdb=" C TYR B 161 " pdb=" CB TYR B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2B FAD A 901 " pdb=" C1B FAD A 901 " pdb=" C3B FAD A 901 " pdb=" O2B FAD A 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 1561 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 128 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO A 129 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 128 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 129 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 525 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 526 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " 0.028 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2574 2.79 - 3.32: 9118 3.32 - 3.84: 16555 3.84 - 4.37: 20217 4.37 - 4.90: 33957 Nonbonded interactions: 82421 Sorted by model distance: nonbonded pdb=" O ASN A 157 " pdb=" NH2 ARG A 281 " model vdw 2.259 2.520 nonbonded pdb=" O ASN B 157 " pdb=" NH2 ARG B 281 " model vdw 2.260 2.520 nonbonded pdb=" NH2 ARG A 213 " pdb=" O GLU A 241 " model vdw 2.304 2.520 nonbonded pdb=" NH2 ARG B 213 " pdb=" O GLU B 241 " model vdw 2.305 2.520 nonbonded pdb=" OD2 ASP B 192 " pdb=" OH TYR B 288 " model vdw 2.312 2.440 ... (remaining 82416 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.810 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.008 0.089 10260 Z= 0.499 Angle : 0.803 9.268 14032 Z= 0.422 Chirality : 0.055 0.204 1564 Planarity : 0.005 0.063 1812 Dihedral : 14.239 83.554 3700 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.05 % Allowed : 1.12 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.22), residues: 1286 helix: -0.54 (0.24), residues: 420 sheet: -0.23 (0.37), residues: 172 loop : -1.52 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 668 HIS 0.008 0.001 HIS A 343 PHE 0.019 0.002 PHE A 367 TYR 0.034 0.002 TYR B 161 ARG 0.003 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.632 Fit side-chains REVERT: A 343 HIS cc_start: 0.8284 (m-70) cc_final: 0.8078 (m170) REVERT: A 398 GLN cc_start: 0.6857 (pp30) cc_final: 0.6620 (pp30) REVERT: A 551 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: A 641 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8638 (p) REVERT: B 518 THR cc_start: 0.8851 (p) cc_final: 0.8585 (t) outliers start: 22 outliers final: 1 residues processed: 145 average time/residue: 0.2074 time to fit residues: 43.9160 Evaluate side-chains 112 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN B 142 ASN B 206 ASN B 387 GLN B 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10260 Z= 0.177 Angle : 0.570 7.935 14032 Z= 0.294 Chirality : 0.047 0.133 1564 Planarity : 0.004 0.055 1812 Dihedral : 8.973 89.581 1498 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.68 % Allowed : 8.47 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.33 (0.23), residues: 1286 helix: -0.25 (0.26), residues: 416 sheet: -0.47 (0.35), residues: 180 loop : -1.38 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 127 HIS 0.004 0.001 HIS B 319 PHE 0.013 0.001 PHE A 228 TYR 0.017 0.001 TYR B 75 ARG 0.002 0.000 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.131 Fit side-chains REVERT: A 212 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (mmm) REVERT: A 548 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7640 (mm) REVERT: A 641 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 329 THR cc_start: 0.8821 (p) cc_final: 0.8617 (p) REVERT: B 518 THR cc_start: 0.8886 (p) cc_final: 0.8622 (t) outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 0.1880 time to fit residues: 34.2044 Evaluate side-chains 120 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 0.0470 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10260 Z= 0.184 Angle : 0.549 6.942 14032 Z= 0.282 Chirality : 0.047 0.135 1564 Planarity : 0.004 0.052 1812 Dihedral : 8.365 76.773 1495 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.05 % Allowed : 10.80 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1286 helix: -0.05 (0.26), residues: 414 sheet: -0.06 (0.37), residues: 172 loop : -1.33 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 668 HIS 0.004 0.001 HIS B 319 PHE 0.011 0.001 PHE A 228 TYR 0.017 0.001 TYR B 75 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8291 (mmm) REVERT: A 226 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7747 (t) REVERT: A 641 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8551 (p) REVERT: B 161 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: B 519 ASP cc_start: 0.7257 (t0) cc_final: 0.6985 (t0) outliers start: 22 outliers final: 16 residues processed: 123 average time/residue: 0.1965 time to fit residues: 35.9644 Evaluate side-chains 122 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 60 optimal weight: 0.0270 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10260 Z= 0.181 Angle : 0.538 6.350 14032 Z= 0.277 Chirality : 0.047 0.232 1564 Planarity : 0.004 0.051 1812 Dihedral : 8.200 78.703 1495 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.26 % Allowed : 11.08 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % 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: -0.98 (0.24), residues: 1286 helix: 0.05 (0.26), residues: 414 sheet: -0.05 (0.38), residues: 174 loop : -1.24 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.019 0.001 HIS A 319 PHE 0.011 0.001 PHE A 228 TYR 0.018 0.001 TYR B 75 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.163 Fit side-chains REVERT: A 212 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8323 (mmm) REVERT: A 226 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7719 (t) REVERT: A 641 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8541 (p) REVERT: B 161 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: B 519 ASP cc_start: 0.7282 (t0) cc_final: 0.6917 (t0) outliers start: 35 outliers final: 24 residues processed: 128 average time/residue: 0.1822 time to fit residues: 35.3042 Evaluate side-chains 130 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN B 319 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10260 Z= 0.271 Angle : 0.594 8.214 14032 Z= 0.304 Chirality : 0.049 0.270 1564 Planarity : 0.005 0.053 1812 Dihedral : 8.183 80.963 1495 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.63 % Allowed : 12.10 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.98 (0.23), residues: 1286 helix: -0.01 (0.26), residues: 414 sheet: 0.08 (0.39), residues: 172 loop : -1.24 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.009 0.001 HIS A 319 PHE 0.013 0.001 PHE A 228 TYR 0.019 0.001 TYR B 75 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 106 time to evaluate : 1.144 Fit side-chains REVERT: A 212 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8327 (mmm) REVERT: A 226 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (t) REVERT: A 227 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7726 (t0) REVERT: A 641 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8593 (p) REVERT: B 161 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: B 227 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7640 (t70) REVERT: B 519 ASP cc_start: 0.7293 (t0) cc_final: 0.6889 (t0) outliers start: 39 outliers final: 26 residues processed: 130 average time/residue: 0.1780 time to fit residues: 35.0810 Evaluate side-chains 134 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 72 optimal weight: 0.0070 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.0470 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10260 Z= 0.142 Angle : 0.519 8.242 14032 Z= 0.268 Chirality : 0.046 0.208 1564 Planarity : 0.004 0.049 1812 Dihedral : 8.091 83.912 1495 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.17 % Allowed : 13.04 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.95 (0.24), residues: 1286 helix: 0.02 (0.26), residues: 426 sheet: -0.02 (0.39), residues: 172 loop : -1.20 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.011 0.001 HIS A 319 PHE 0.008 0.001 PHE A 228 TYR 0.018 0.001 TYR B 75 ARG 0.003 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8395 (mmm) REVERT: A 226 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7694 (t) REVERT: A 551 GLN cc_start: 0.7346 (mp10) cc_final: 0.6971 (mp10) REVERT: A 641 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8530 (p) REVERT: B 161 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: B 215 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6985 (pp) REVERT: B 519 ASP cc_start: 0.7518 (t0) cc_final: 0.7122 (t0) outliers start: 34 outliers final: 17 residues processed: 133 average time/residue: 0.1862 time to fit residues: 37.5578 Evaluate side-chains 128 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10260 Z= 0.212 Angle : 0.566 9.891 14032 Z= 0.287 Chirality : 0.048 0.219 1564 Planarity : 0.004 0.050 1812 Dihedral : 7.871 82.295 1493 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.45 % Allowed : 13.04 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1286 helix: -0.01 (0.26), residues: 426 sheet: 0.04 (0.39), residues: 172 loop : -1.16 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.010 0.001 HIS A 319 PHE 0.017 0.001 PHE A 499 TYR 0.019 0.001 TYR B 75 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5859 (m-10) REVERT: A 212 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8414 (mmm) REVERT: A 551 GLN cc_start: 0.7361 (mp10) cc_final: 0.7134 (mp10) REVERT: A 641 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8562 (p) REVERT: B 161 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: B 227 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7651 (t70) REVERT: B 519 ASP cc_start: 0.7544 (t0) cc_final: 0.7103 (t0) outliers start: 37 outliers final: 25 residues processed: 131 average time/residue: 0.1814 time to fit residues: 36.2836 Evaluate side-chains 132 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0050 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10260 Z= 0.146 Angle : 0.522 9.591 14032 Z= 0.267 Chirality : 0.046 0.182 1564 Planarity : 0.004 0.049 1812 Dihedral : 7.744 84.703 1493 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.26 % Allowed : 13.31 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.91 (0.24), residues: 1286 helix: 0.08 (0.26), residues: 426 sheet: -0.02 (0.37), residues: 188 loop : -1.21 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS A 319 PHE 0.019 0.001 PHE A 499 TYR 0.020 0.001 TYR B 75 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5802 (m-10) REVERT: A 212 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8420 (mmm) REVERT: A 551 GLN cc_start: 0.7490 (mp10) cc_final: 0.7082 (mp10) REVERT: A 629 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: B 146 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.7598 (t-90) REVERT: B 161 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: B 226 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7123 (t) REVERT: B 519 ASP cc_start: 0.7547 (t0) cc_final: 0.7104 (t0) REVERT: B 654 THR cc_start: 0.8898 (p) cc_final: 0.8632 (m) outliers start: 35 outliers final: 26 residues processed: 130 average time/residue: 0.1736 time to fit residues: 34.8212 Evaluate side-chains 133 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 69 optimal weight: 0.0370 chunk 50 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10260 Z= 0.167 Angle : 0.537 9.856 14032 Z= 0.272 Chirality : 0.047 0.196 1564 Planarity : 0.004 0.049 1812 Dihedral : 7.525 85.488 1492 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.26 % Allowed : 13.69 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.84 (0.24), residues: 1286 helix: 0.08 (0.26), residues: 426 sheet: 0.05 (0.37), residues: 202 loop : -1.16 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.008 0.001 HIS A 319 PHE 0.025 0.001 PHE A 699 TYR 0.019 0.001 TYR B 75 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6167 (m-10) REVERT: A 212 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8346 (mmm) REVERT: A 551 GLN cc_start: 0.7569 (mp10) cc_final: 0.7176 (mp10) REVERT: A 629 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: B 161 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.7045 (m-10) REVERT: B 226 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7103 (t) REVERT: B 227 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7656 (t70) REVERT: B 519 ASP cc_start: 0.7546 (t0) cc_final: 0.7039 (t0) REVERT: B 654 THR cc_start: 0.8932 (p) cc_final: 0.8658 (m) outliers start: 35 outliers final: 26 residues processed: 130 average time/residue: 0.1752 time to fit residues: 34.6751 Evaluate side-chains 133 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 127 optimal weight: 0.0570 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10260 Z= 0.177 Angle : 0.544 9.849 14032 Z= 0.276 Chirality : 0.047 0.260 1564 Planarity : 0.004 0.050 1812 Dihedral : 7.452 86.736 1492 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.54 % Allowed : 13.50 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.86 (0.24), residues: 1286 helix: 0.06 (0.26), residues: 426 sheet: 0.05 (0.36), residues: 202 loop : -1.18 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.005 0.001 HIS A 319 PHE 0.020 0.001 PHE A 499 TYR 0.019 0.001 TYR B 75 ARG 0.001 0.000 ARG B 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6589 (m-10) REVERT: A 212 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8363 (mmm) REVERT: A 551 GLN cc_start: 0.7591 (mp10) cc_final: 0.7196 (mp10) REVERT: A 629 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: B 161 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: B 226 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.7056 (t) REVERT: B 227 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7645 (t70) REVERT: B 519 ASP cc_start: 0.7576 (t0) cc_final: 0.7048 (t0) outliers start: 38 outliers final: 30 residues processed: 132 average time/residue: 0.1892 time to fit residues: 38.1839 Evaluate side-chains 139 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 14 optimal weight: 0.0030 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 89 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 overall best weight: 0.2828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.078168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.069161 restraints weight = 20207.080| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.93 r_work: 0.2644 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10260 Z= 0.141 Angle : 0.513 9.621 14032 Z= 0.261 Chirality : 0.046 0.212 1564 Planarity : 0.004 0.050 1812 Dihedral : 7.189 89.190 1492 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.17 % Allowed : 13.87 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1286 helix: 0.13 (0.26), residues: 426 sheet: 0.01 (0.36), residues: 202 loop : -1.10 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.004 0.001 HIS A 319 PHE 0.021 0.001 PHE A 499 TYR 0.019 0.001 TYR B 75 ARG 0.001 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.95 seconds wall clock time: 37 minutes 10.99 seconds (2230.99 seconds total)