Starting phenix.real_space_refine on Mon Mar 11 04:02:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/03_2024/6ggs_4399.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/03_2024/6ggs_4399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/03_2024/6ggs_4399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/03_2024/6ggs_4399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/03_2024/6ggs_4399.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/03_2024/6ggs_4399.pdb" } resolution = 3.94 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 ------------------------------------------------------------------------------- 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= 0.040 sd= 0.257 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 40 5.16 5 C 4270 2.51 5 N 1200 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 444": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "F ARG 488": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 466": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 466": "NH1" <-> "NH2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 466": "NH1" <-> "NH2" Residue "G ARG 488": "NH1" <-> "NH2" Residue "H ARG 444": "NH1" <-> "NH2" Residue "H ARG 466": "NH1" <-> "NH2" Residue "H ARG 488": "NH1" <-> "NH2" Residue "I ARG 444": "NH1" <-> "NH2" Residue "I ARG 466": "NH1" <-> "NH2" Residue "I ARG 488": "NH1" <-> "NH2" Residue "J ARG 444": "NH1" <-> "NH2" Residue "J ARG 466": "NH1" <-> "NH2" Residue "J ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6880 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "A" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "D" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Time building chain proxies: 4.13, per 1000 atoms: 0.60 Number of scatterers: 6880 At special positions: 0 Unit cell: (88.33, 89.54, 85.91, 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 40 16.00 O 1370 8.00 N 1200 7.00 C 4270 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: 2.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'F' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP F 439 " --> pdb=" O ALA F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER F 459 " --> pdb=" O CYS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 465 Processing helix chain 'F' and resid 473 through 478 Processing helix chain 'F' and resid 482 through 487 Processing helix chain 'F' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR F 493 " --> pdb=" O GLN F 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL F 504 " --> pdb=" O GLU F 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP A 439 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.773A pdb=" N SER A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 removed outlier: 4.120A pdb=" N TRP B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.773A pdb=" N SER B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR B 493 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP C 439 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER C 459 " --> pdb=" O CYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR C 493 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP D 439 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER D 459 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 Processing helix chain 'D' and resid 473 through 478 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR D 493 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL D 504 " --> pdb=" O GLU D 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP E 439 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 461 removed outlier: 3.773A pdb=" N SER E 459 " --> pdb=" O CYS E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 465 Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 482 through 487 Processing helix chain 'E' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR E 493 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL E 504 " --> pdb=" O GLU E 500 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 439 removed outlier: 4.118A pdb=" N TRP G 439 " --> pdb=" O ALA G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER G 459 " --> pdb=" O CYS G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 465 Processing helix chain 'G' and resid 473 through 478 Processing helix chain 'G' and resid 482 through 487 Processing helix chain 'G' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR G 493 " --> pdb=" O GLN G 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL G 504 " --> pdb=" O GLU G 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP H 439 " --> pdb=" O ALA H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN H 449 " --> pdb=" O GLU H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER H 459 " --> pdb=" O CYS H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 465 Processing helix chain 'H' and resid 473 through 478 Processing helix chain 'H' and resid 482 through 487 Processing helix chain 'H' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR H 493 " --> pdb=" O GLN H 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL H 504 " --> pdb=" O GLU H 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP I 439 " --> pdb=" O ALA I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN I 449 " --> pdb=" O GLU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER I 459 " --> pdb=" O CYS I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 465 Processing helix chain 'I' and resid 473 through 478 Processing helix chain 'I' and resid 482 through 487 Processing helix chain 'I' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR I 493 " --> pdb=" O GLN I 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP I 495 " --> pdb=" O LEU I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL I 504 " --> pdb=" O GLU I 500 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP J 439 " --> pdb=" O ALA J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN J 449 " --> pdb=" O GLU J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER J 459 " --> pdb=" O CYS J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 465 Processing helix chain 'J' and resid 473 through 478 Processing helix chain 'J' and resid 482 through 487 Processing helix chain 'J' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR J 493 " --> pdb=" O GLN J 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP J 495 " --> pdb=" O LEU J 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL J 504 " --> pdb=" O GLU J 500 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 600 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: 1.63 Time building geometry restraints manager: 2.69 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: 2295 1.34 - 1.45: 702 1.45 - 1.57: 3863 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 6930 Sorted by residual: bond pdb=" CG1 ILE H 496 " pdb=" CD1 ILE H 496 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CG MET C 470 " pdb=" SD MET C 470 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CG MET J 470 " pdb=" SD MET J 470 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CG1 ILE D 496 " pdb=" CD1 ILE D 496 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.54e+00 bond pdb=" CG1 ILE G 496 " pdb=" CD1 ILE G 496 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 ... (remaining 6925 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.73: 110 105.73 - 112.74: 3530 112.74 - 119.76: 2836 119.76 - 126.77: 2764 126.77 - 133.78: 60 Bond angle restraints: 9300 Sorted by residual: angle pdb=" CA LEU D 456 " pdb=" CB LEU D 456 " pdb=" CG LEU D 456 " ideal model delta sigma weight residual 116.30 127.11 -10.81 3.50e+00 8.16e-02 9.55e+00 angle pdb=" CA LEU J 456 " pdb=" CB LEU J 456 " pdb=" CG LEU J 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.53e+00 angle pdb=" CA LEU F 456 " pdb=" CB LEU F 456 " pdb=" CG LEU F 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 angle pdb=" CA LEU B 456 " pdb=" CB LEU B 456 " pdb=" CG LEU B 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 angle pdb=" CA LEU G 456 " pdb=" CB LEU G 456 " pdb=" CG LEU G 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 ... (remaining 9295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 3950 15.35 - 30.69: 360 30.69 - 46.04: 70 46.04 - 61.39: 20 61.39 - 76.74: 20 Dihedral angle restraints: 4420 sinusoidal: 1900 harmonic: 2520 Sorted by residual: dihedral pdb=" CA GLU C 472 " pdb=" C GLU C 472 " pdb=" N ASP C 473 " pdb=" CA ASP C 473 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU F 472 " pdb=" C GLU F 472 " pdb=" N ASP F 473 " pdb=" CA ASP F 473 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN H 489 " pdb=" C GLN H 489 " pdb=" N LEU H 490 " pdb=" CA LEU H 490 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 513 0.040 - 0.081: 370 0.081 - 0.121: 157 0.121 - 0.162: 30 0.162 - 0.202: 30 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CA GLU A 472 " pdb=" N GLU A 472 " pdb=" C GLU A 472 " pdb=" CB GLU A 472 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU C 472 " pdb=" N GLU C 472 " pdb=" C GLU C 472 " pdb=" CB GLU C 472 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU G 472 " pdb=" N GLU G 472 " pdb=" C GLU G 472 " pdb=" CB GLU G 472 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1097 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL J 477 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C VAL J 477 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL J 477 " 0.007 2.00e-02 2.50e+03 pdb=" N SER J 478 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 477 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C VAL H 477 " 0.019 2.00e-02 2.50e+03 pdb=" O VAL H 477 " -0.007 2.00e-02 2.50e+03 pdb=" N SER H 478 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 477 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C VAL B 477 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL B 477 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 478 " 0.007 2.00e-02 2.50e+03 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 113 2.63 - 3.20: 6291 3.20 - 3.76: 11306 3.76 - 4.33: 16042 4.33 - 4.90: 23335 Nonbonded interactions: 57087 Sorted by model distance: nonbonded pdb=" OD1 ASP A 461 " pdb=" NE ARG D 444 " model vdw 2.060 2.520 nonbonded pdb=" OD1 ASP F 461 " pdb=" NE ARG I 444 " model vdw 2.060 2.520 nonbonded pdb=" OD1 ASP G 461 " pdb=" NE ARG J 444 " model vdw 2.061 2.520 nonbonded pdb=" OD1 ASP B 461 " pdb=" NE ARG E 444 " model vdw 2.061 2.520 nonbonded pdb=" OD1 ASP E 461 " pdb=" NE ARG H 444 " model vdw 2.061 2.520 ... (remaining 57082 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.006 0.049 6930 Z= 0.365 Angle : 1.154 10.815 9300 Z= 0.572 Chirality : 0.065 0.202 1100 Planarity : 0.004 0.012 1190 Dihedral : 14.099 76.735 2760 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.27 % Allowed : 7.59 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.91 (0.16), residues: 840 helix: -4.95 (0.07), residues: 530 sheet: None (None), residues: 0 loop : -3.50 (0.26), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP F 439 PHE 0.010 0.003 PHE J 501 TYR 0.005 0.002 TYR H 474 ARG 0.010 0.003 ARG I 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 399 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.7854 (t60) cc_final: 0.7337 (t60) REVERT: F 443 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8441 (mtpp) REVERT: F 453 GLU cc_start: 0.8492 (pp20) cc_final: 0.8076 (pp20) REVERT: F 457 ASN cc_start: 0.9153 (m110) cc_final: 0.8674 (m-40) REVERT: F 458 GLN cc_start: 0.8384 (pt0) cc_final: 0.8105 (pt0) REVERT: F 515 MET cc_start: 0.7086 (pp-130) cc_final: 0.6851 (pp-130) REVERT: A 439 TRP cc_start: 0.7645 (t60) cc_final: 0.6837 (t60) REVERT: A 453 GLU cc_start: 0.8477 (pp20) cc_final: 0.8013 (pp20) REVERT: A 457 ASN cc_start: 0.9084 (m110) cc_final: 0.8771 (m-40) REVERT: A 458 GLN cc_start: 0.8530 (pt0) cc_final: 0.8034 (pt0) REVERT: A 500 GLU cc_start: 0.6342 (mp0) cc_final: 0.6043 (mp0) REVERT: A 515 MET cc_start: 0.7258 (pp-130) cc_final: 0.6731 (pp-130) REVERT: B 443 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8583 (mtpp) REVERT: B 447 ILE cc_start: 0.8607 (tt) cc_final: 0.8391 (tt) REVERT: B 453 GLU cc_start: 0.8600 (pp20) cc_final: 0.8090 (pp20) REVERT: B 457 ASN cc_start: 0.9177 (m110) cc_final: 0.8732 (m110) REVERT: B 458 GLN cc_start: 0.8635 (pt0) cc_final: 0.8227 (pt0) REVERT: B 482 THR cc_start: 0.8265 (t) cc_final: 0.7988 (t) REVERT: B 515 MET cc_start: 0.7310 (pp-130) cc_final: 0.6797 (pp-130) REVERT: C 439 TRP cc_start: 0.8076 (t60) cc_final: 0.7601 (t60) REVERT: C 443 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8332 (mtpp) REVERT: C 453 GLU cc_start: 0.8445 (pp20) cc_final: 0.7971 (pp20) REVERT: C 457 ASN cc_start: 0.9178 (m110) cc_final: 0.8945 (m-40) REVERT: C 473 ASP cc_start: 0.8418 (p0) cc_final: 0.7779 (p0) REVERT: C 515 MET cc_start: 0.7031 (pp-130) cc_final: 0.6807 (pp-130) REVERT: D 439 TRP cc_start: 0.8126 (t60) cc_final: 0.7515 (t60) REVERT: D 443 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8496 (mtpp) REVERT: D 453 GLU cc_start: 0.8430 (pp20) cc_final: 0.8020 (pp20) REVERT: D 457 ASN cc_start: 0.9228 (m110) cc_final: 0.8776 (m-40) REVERT: D 461 ASP cc_start: 0.8391 (t70) cc_final: 0.7975 (t70) REVERT: D 473 ASP cc_start: 0.8356 (p0) cc_final: 0.8079 (p0) REVERT: D 515 MET cc_start: 0.7345 (pp-130) cc_final: 0.6835 (pp-130) REVERT: E 439 TRP cc_start: 0.8012 (t60) cc_final: 0.7513 (t60) REVERT: E 443 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8427 (mtpp) REVERT: E 453 GLU cc_start: 0.8454 (pp20) cc_final: 0.7940 (pp20) REVERT: E 457 ASN cc_start: 0.9099 (m110) cc_final: 0.8701 (m-40) REVERT: E 474 TYR cc_start: 0.7435 (t80) cc_final: 0.7157 (t80) REVERT: E 515 MET cc_start: 0.7228 (pp-130) cc_final: 0.6522 (pp-130) REVERT: G 439 TRP cc_start: 0.8114 (t60) cc_final: 0.7490 (t60) REVERT: G 443 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8539 (mtpp) REVERT: G 447 ILE cc_start: 0.8654 (tt) cc_final: 0.8451 (tt) REVERT: G 458 GLN cc_start: 0.8563 (pt0) cc_final: 0.8120 (pt0) REVERT: G 515 MET cc_start: 0.7146 (pp-130) cc_final: 0.6766 (pp-130) REVERT: H 439 TRP cc_start: 0.8004 (t60) cc_final: 0.7528 (t60) REVERT: H 457 ASN cc_start: 0.9074 (m110) cc_final: 0.8322 (t0) REVERT: H 458 GLN cc_start: 0.8873 (pt0) cc_final: 0.8385 (pt0) REVERT: H 515 MET cc_start: 0.7211 (pp-130) cc_final: 0.6426 (pp-130) REVERT: I 439 TRP cc_start: 0.7832 (t60) cc_final: 0.7192 (t60) REVERT: I 443 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8453 (mtpp) REVERT: I 457 ASN cc_start: 0.8943 (m110) cc_final: 0.8015 (t0) REVERT: I 458 GLN cc_start: 0.8856 (pt0) cc_final: 0.8642 (pt0) REVERT: I 474 TYR cc_start: 0.7834 (t80) cc_final: 0.7549 (t80) REVERT: I 515 MET cc_start: 0.7162 (pp-130) cc_final: 0.6416 (pp-130) REVERT: J 443 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8283 (mtpp) REVERT: J 457 ASN cc_start: 0.9117 (m110) cc_final: 0.8299 (t0) REVERT: J 458 GLN cc_start: 0.8737 (pt0) cc_final: 0.8220 (pt0) REVERT: J 515 MET cc_start: 0.7266 (pp-130) cc_final: 0.6831 (pp-130) outliers start: 10 outliers final: 0 residues processed: 399 average time/residue: 0.2036 time to fit residues: 105.1749 Evaluate side-chains 335 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 489 GLN A 437 GLN A 489 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 438 GLN B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN G 489 GLN ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 489 GLN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 GLN J 489 GLN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6930 Z= 0.168 Angle : 0.780 9.852 9300 Z= 0.373 Chirality : 0.042 0.210 1100 Planarity : 0.003 0.016 1190 Dihedral : 6.175 16.923 900 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.81 % Allowed : 16.84 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.31 (0.21), residues: 840 helix: -4.32 (0.11), residues: 520 sheet: None (None), residues: 0 loop : -1.66 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 439 PHE 0.006 0.003 PHE E 501 TYR 0.005 0.001 TYR D 474 ARG 0.002 0.000 ARG J 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 341 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8537 (tptp) REVERT: F 451 MET cc_start: 0.8052 (tpp) cc_final: 0.7846 (tpt) REVERT: F 457 ASN cc_start: 0.9326 (m110) cc_final: 0.8917 (m-40) REVERT: F 461 ASP cc_start: 0.8648 (t70) cc_final: 0.7744 (t70) REVERT: F 474 TYR cc_start: 0.6889 (t80) cc_final: 0.6236 (t80) REVERT: F 515 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6555 (pp-130) REVERT: A 437 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6337 (mt0) REVERT: A 441 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 443 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8541 (tptp) REVERT: A 457 ASN cc_start: 0.9204 (m110) cc_final: 0.8861 (m-40) REVERT: A 458 GLN cc_start: 0.8280 (pt0) cc_final: 0.8064 (pt0) REVERT: A 461 ASP cc_start: 0.8831 (t70) cc_final: 0.8095 (t70) REVERT: A 469 ILE cc_start: 0.9015 (tp) cc_final: 0.8796 (tt) REVERT: A 500 GLU cc_start: 0.6542 (mp0) cc_final: 0.6301 (mp0) REVERT: A 515 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6789 (pp-130) REVERT: B 457 ASN cc_start: 0.9151 (m110) cc_final: 0.8743 (m-40) REVERT: B 469 ILE cc_start: 0.8778 (tp) cc_final: 0.8452 (tt) REVERT: B 482 THR cc_start: 0.7986 (t) cc_final: 0.7636 (t) REVERT: B 515 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6872 (pp-130) REVERT: C 457 ASN cc_start: 0.9241 (m110) cc_final: 0.8982 (m-40) REVERT: C 458 GLN cc_start: 0.8250 (pt0) cc_final: 0.7481 (pt0) REVERT: C 466 ARG cc_start: 0.8337 (mpp-170) cc_final: 0.8088 (mtm-85) REVERT: C 469 ILE cc_start: 0.8799 (tp) cc_final: 0.8502 (tt) REVERT: D 443 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8157 (mmtt) REVERT: D 444 ARG cc_start: 0.8772 (ttt180) cc_final: 0.8571 (ttt180) REVERT: D 450 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8183 (tm-30) REVERT: D 457 ASN cc_start: 0.9419 (m110) cc_final: 0.9076 (m-40) REVERT: D 461 ASP cc_start: 0.8746 (t70) cc_final: 0.7815 (t70) REVERT: D 469 ILE cc_start: 0.8836 (tp) cc_final: 0.8511 (tt) REVERT: D 473 ASP cc_start: 0.8472 (p0) cc_final: 0.8166 (p0) REVERT: D 474 TYR cc_start: 0.7002 (t80) cc_final: 0.6284 (t80) REVERT: D 515 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6609 (pp-130) REVERT: E 441 GLN cc_start: 0.7714 (mp10) cc_final: 0.7352 (mp10) REVERT: E 443 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8480 (mmmt) REVERT: E 458 GLN cc_start: 0.8035 (pt0) cc_final: 0.7770 (pt0) REVERT: E 461 ASP cc_start: 0.8747 (t70) cc_final: 0.8431 (t70) REVERT: E 500 GLU cc_start: 0.7136 (mp0) cc_final: 0.6868 (mp0) REVERT: E 515 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6621 (pp-130) REVERT: G 443 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8583 (tptp) REVERT: G 458 GLN cc_start: 0.8421 (pt0) cc_final: 0.8087 (pt0) REVERT: G 515 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6942 (pp-130) REVERT: H 444 ARG cc_start: 0.8786 (ttt180) cc_final: 0.8479 (ttt180) REVERT: H 515 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6441 (pp-130) REVERT: I 443 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8309 (tptp) REVERT: I 450 GLN cc_start: 0.8745 (tm-30) cc_final: 0.7938 (tm-30) REVERT: I 451 MET cc_start: 0.8422 (tpp) cc_final: 0.8094 (tpt) REVERT: I 473 ASP cc_start: 0.8421 (p0) cc_final: 0.7891 (p0) REVERT: I 482 THR cc_start: 0.7889 (t) cc_final: 0.7602 (t) REVERT: I 515 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6510 (pp-130) REVERT: J 441 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7984 (mp10) REVERT: J 443 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8435 (tptp) REVERT: J 469 ILE cc_start: 0.8608 (tp) cc_final: 0.8066 (tt) REVERT: J 473 ASP cc_start: 0.8529 (p0) cc_final: 0.8306 (p0) REVERT: J 515 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6838 (pp-130) outliers start: 38 outliers final: 6 residues processed: 350 average time/residue: 0.2151 time to fit residues: 95.5029 Evaluate side-chains 324 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 306 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 515 MET Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 509 LEU Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN C 489 GLN D 437 GLN D 489 GLN ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6930 Z= 0.195 Angle : 0.783 10.030 9300 Z= 0.370 Chirality : 0.043 0.122 1100 Planarity : 0.004 0.055 1190 Dihedral : 5.671 15.565 900 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.94 % Allowed : 16.58 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.15 (0.22), residues: 840 helix: -3.74 (0.14), residues: 590 sheet: None (None), residues: 0 loop : -1.88 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 439 PHE 0.008 0.003 PHE G 501 TYR 0.004 0.001 TYR D 474 ARG 0.007 0.001 ARG C 483 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 326 time to evaluate : 0.859 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: F 450 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8160 (tm-30) REVERT: F 451 MET cc_start: 0.8129 (tpp) cc_final: 0.7906 (tpp) REVERT: F 458 GLN cc_start: 0.8490 (pt0) cc_final: 0.7939 (pt0) REVERT: F 461 ASP cc_start: 0.8574 (t70) cc_final: 0.8098 (t0) REVERT: F 474 TYR cc_start: 0.6800 (t80) cc_final: 0.6593 (t80) REVERT: A 437 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6382 (mt0) REVERT: A 441 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: A 450 GLN cc_start: 0.8651 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 461 ASP cc_start: 0.8903 (t70) cc_final: 0.8329 (t70) REVERT: A 469 ILE cc_start: 0.8883 (tp) cc_final: 0.8678 (tt) REVERT: A 473 ASP cc_start: 0.8530 (p0) cc_final: 0.8240 (p0) REVERT: A 500 GLU cc_start: 0.6357 (mp0) cc_final: 0.6096 (mp0) REVERT: B 437 GLN cc_start: 0.7202 (mt0) cc_final: 0.6961 (tt0) REVERT: B 450 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 457 ASN cc_start: 0.9098 (m110) cc_final: 0.8862 (m-40) REVERT: B 458 GLN cc_start: 0.8365 (pt0) cc_final: 0.8053 (pt0) REVERT: B 469 ILE cc_start: 0.8873 (tp) cc_final: 0.8506 (tt) REVERT: B 482 THR cc_start: 0.7970 (t) cc_final: 0.7619 (t) REVERT: C 443 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8408 (mtpp) REVERT: C 450 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 466 ARG cc_start: 0.8441 (mpp-170) cc_final: 0.8048 (mtm-85) REVERT: C 469 ILE cc_start: 0.8700 (tp) cc_final: 0.8369 (tt) REVERT: D 444 ARG cc_start: 0.8757 (ttt180) cc_final: 0.8496 (ttt180) REVERT: D 469 ILE cc_start: 0.8820 (tp) cc_final: 0.8540 (tt) REVERT: D 473 ASP cc_start: 0.8510 (p0) cc_final: 0.8200 (p0) REVERT: E 450 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8463 (tm-30) REVERT: E 451 MET cc_start: 0.8108 (tpt) cc_final: 0.7817 (tpt) REVERT: E 458 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: E 470 MET cc_start: 0.7749 (mtp) cc_final: 0.7219 (mtp) REVERT: E 500 GLU cc_start: 0.7040 (mp0) cc_final: 0.6692 (mp0) REVERT: G 458 GLN cc_start: 0.8623 (pt0) cc_final: 0.8053 (pt0) REVERT: G 500 GLU cc_start: 0.6253 (mp0) cc_final: 0.6039 (mp0) REVERT: G 515 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6370 (pp-130) REVERT: H 450 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8285 (tm-30) REVERT: H 451 MET cc_start: 0.8111 (tpt) cc_final: 0.7441 (tpt) REVERT: H 515 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6409 (pp-130) REVERT: I 451 MET cc_start: 0.8557 (tpp) cc_final: 0.8315 (tpt) REVERT: I 457 ASN cc_start: 0.8821 (m-40) cc_final: 0.8530 (m-40) REVERT: J 443 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8528 (mtpp) REVERT: J 470 MET cc_start: 0.7461 (mtp) cc_final: 0.6952 (mtp) REVERT: J 473 ASP cc_start: 0.8443 (p0) cc_final: 0.8159 (p0) REVERT: J 500 GLU cc_start: 0.5980 (mp0) cc_final: 0.5758 (mp0) outliers start: 39 outliers final: 23 residues processed: 342 average time/residue: 0.2026 time to fit residues: 88.6097 Evaluate side-chains 338 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 310 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 515 MET Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 20 optimal weight: 0.0970 chunk 64 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 457 ASN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6930 Z= 0.198 Angle : 0.803 12.547 9300 Z= 0.361 Chirality : 0.043 0.121 1100 Planarity : 0.003 0.036 1190 Dihedral : 5.450 14.289 900 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.32 % Allowed : 20.38 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.50 (0.23), residues: 840 helix: -3.30 (0.16), residues: 530 sheet: None (None), residues: 0 loop : -2.01 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 439 PHE 0.009 0.003 PHE B 501 TYR 0.004 0.001 TYR F 474 ARG 0.006 0.001 ARG I 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 333 time to evaluate : 0.775 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: F 458 GLN cc_start: 0.8577 (pt0) cc_final: 0.8001 (pt0) REVERT: F 461 ASP cc_start: 0.8738 (t70) cc_final: 0.7917 (t70) REVERT: F 474 TYR cc_start: 0.6901 (t80) cc_final: 0.6485 (t80) REVERT: F 500 GLU cc_start: 0.6168 (mp0) cc_final: 0.5938 (mp0) REVERT: A 437 GLN cc_start: 0.7415 (mt0) cc_final: 0.6410 (mt0) REVERT: A 441 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: A 450 GLN cc_start: 0.8698 (tm-30) cc_final: 0.7899 (tm-30) REVERT: A 458 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: A 461 ASP cc_start: 0.8954 (t70) cc_final: 0.7975 (t70) REVERT: A 466 ARG cc_start: 0.8443 (mpp-170) cc_final: 0.8197 (mtm-85) REVERT: A 469 ILE cc_start: 0.8904 (tp) cc_final: 0.8683 (tt) REVERT: A 473 ASP cc_start: 0.8406 (p0) cc_final: 0.8177 (p0) REVERT: A 474 TYR cc_start: 0.7647 (t80) cc_final: 0.7212 (t80) REVERT: A 500 GLU cc_start: 0.6402 (mp0) cc_final: 0.6149 (mp0) REVERT: B 441 GLN cc_start: 0.7572 (mp10) cc_final: 0.6941 (mp10) REVERT: B 450 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 458 GLN cc_start: 0.8244 (pt0) cc_final: 0.7865 (pt0) REVERT: B 469 ILE cc_start: 0.8968 (tp) cc_final: 0.8614 (tt) REVERT: B 482 THR cc_start: 0.8021 (t) cc_final: 0.7669 (t) REVERT: B 515 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6761 (pp-130) REVERT: C 443 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8325 (mtpp) REVERT: C 450 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 458 GLN cc_start: 0.8200 (pt0) cc_final: 0.7432 (pt0) REVERT: C 469 ILE cc_start: 0.8844 (tp) cc_final: 0.8543 (tt) REVERT: D 444 ARG cc_start: 0.8852 (ttt180) cc_final: 0.8511 (ttt180) REVERT: D 445 GLU cc_start: 0.8398 (tp30) cc_final: 0.7926 (tp30) REVERT: D 450 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 469 ILE cc_start: 0.8814 (tp) cc_final: 0.8521 (tt) REVERT: D 473 ASP cc_start: 0.8503 (p0) cc_final: 0.8269 (p0) REVERT: E 450 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8496 (tm-30) REVERT: E 458 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: E 500 GLU cc_start: 0.7116 (mp0) cc_final: 0.6813 (mp0) REVERT: G 450 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8293 (tm-30) REVERT: G 451 MET cc_start: 0.8133 (tpt) cc_final: 0.7814 (tpt) REVERT: G 458 GLN cc_start: 0.8703 (pt0) cc_final: 0.8290 (pt0) REVERT: G 515 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6441 (pp-130) REVERT: H 450 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8238 (tm-30) REVERT: H 451 MET cc_start: 0.8237 (tpt) cc_final: 0.7448 (tpt) REVERT: H 458 GLN cc_start: 0.8838 (pt0) cc_final: 0.8234 (pt0) REVERT: H 515 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6384 (pp-130) REVERT: I 451 MET cc_start: 0.8633 (tpp) cc_final: 0.8419 (tpt) REVERT: I 457 ASN cc_start: 0.8766 (m-40) cc_final: 0.8493 (m-40) REVERT: I 482 THR cc_start: 0.8110 (t) cc_final: 0.7840 (t) REVERT: I 500 GLU cc_start: 0.5886 (mp0) cc_final: 0.5551 (mp0) REVERT: J 443 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8573 (mtpp) REVERT: J 470 MET cc_start: 0.7733 (mtp) cc_final: 0.6994 (mtp) REVERT: J 500 GLU cc_start: 0.6000 (mp0) cc_final: 0.5768 (mp0) outliers start: 42 outliers final: 27 residues processed: 344 average time/residue: 0.1913 time to fit residues: 85.0091 Evaluate side-chains 359 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 326 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 515 MET Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 460 LEU Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.0060 chunk 1 optimal weight: 0.0170 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 overall best weight: 4.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6930 Z= 0.233 Angle : 0.822 11.002 9300 Z= 0.369 Chirality : 0.044 0.149 1100 Planarity : 0.003 0.044 1190 Dihedral : 5.434 14.446 900 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 6.58 % Allowed : 22.03 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.07 (0.24), residues: 840 helix: -2.93 (0.18), residues: 530 sheet: None (None), residues: 0 loop : -1.90 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 439 PHE 0.011 0.003 PHE F 501 TYR 0.007 0.001 TYR E 474 ARG 0.007 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 343 time to evaluate : 0.850 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: F 450 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8151 (tm-30) REVERT: F 458 GLN cc_start: 0.8514 (pt0) cc_final: 0.8135 (pt0) REVERT: F 461 ASP cc_start: 0.8809 (t70) cc_final: 0.8051 (t70) REVERT: F 474 TYR cc_start: 0.7068 (t80) cc_final: 0.6815 (t80) REVERT: F 500 GLU cc_start: 0.6244 (mp0) cc_final: 0.5978 (mp0) REVERT: A 437 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6529 (mt0) REVERT: A 441 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: A 445 GLU cc_start: 0.8209 (tp30) cc_final: 0.7778 (pm20) REVERT: A 450 GLN cc_start: 0.8712 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 458 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: A 461 ASP cc_start: 0.9000 (t70) cc_final: 0.7812 (t70) REVERT: A 469 ILE cc_start: 0.8952 (tp) cc_final: 0.8717 (tt) REVERT: A 474 TYR cc_start: 0.7795 (t80) cc_final: 0.7220 (t80) REVERT: A 500 GLU cc_start: 0.6416 (mp0) cc_final: 0.6210 (mp0) REVERT: B 450 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 469 ILE cc_start: 0.9020 (tp) cc_final: 0.8671 (tt) REVERT: B 482 THR cc_start: 0.7728 (t) cc_final: 0.7369 (t) REVERT: C 443 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8389 (mtpp) REVERT: C 450 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8164 (tm-30) REVERT: C 458 GLN cc_start: 0.8111 (pt0) cc_final: 0.7378 (pt0) REVERT: C 469 ILE cc_start: 0.8879 (tp) cc_final: 0.8599 (tt) REVERT: D 444 ARG cc_start: 0.8806 (ttt180) cc_final: 0.8308 (ttt180) REVERT: D 445 GLU cc_start: 0.8470 (tp30) cc_final: 0.7973 (tp30) REVERT: D 450 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 469 ILE cc_start: 0.8894 (tp) cc_final: 0.8593 (tt) REVERT: E 441 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: E 450 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8396 (tm-30) REVERT: E 451 MET cc_start: 0.8281 (tpt) cc_final: 0.7827 (tpt) REVERT: E 458 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: E 470 MET cc_start: 0.7575 (mtp) cc_final: 0.6495 (mtp) REVERT: E 500 GLU cc_start: 0.7148 (mp0) cc_final: 0.6833 (mp0) REVERT: G 450 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8525 (tm-30) REVERT: G 451 MET cc_start: 0.8181 (tpt) cc_final: 0.7747 (tpt) REVERT: G 458 GLN cc_start: 0.8604 (pt0) cc_final: 0.8282 (pt0) REVERT: G 515 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6612 (pp-130) REVERT: H 450 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8323 (tm-30) REVERT: H 451 MET cc_start: 0.8219 (tpt) cc_final: 0.7454 (tpt) REVERT: H 458 GLN cc_start: 0.8878 (pt0) cc_final: 0.8353 (pt0) REVERT: H 515 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6248 (pp-130) REVERT: I 451 MET cc_start: 0.8603 (tpp) cc_final: 0.8361 (tpt) REVERT: I 457 ASN cc_start: 0.8738 (m-40) cc_final: 0.8453 (m-40) REVERT: I 482 THR cc_start: 0.8203 (t) cc_final: 0.7872 (t) REVERT: I 500 GLU cc_start: 0.6247 (mp0) cc_final: 0.5931 (mp0) REVERT: J 443 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8514 (mtpp) REVERT: J 450 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8306 (tm-30) REVERT: J 500 GLU cc_start: 0.6211 (mp0) cc_final: 0.5998 (mp0) outliers start: 52 outliers final: 38 residues processed: 351 average time/residue: 0.1977 time to fit residues: 89.5122 Evaluate side-chains 381 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 336 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 515 MET Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 0.0470 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.0170 chunk 74 optimal weight: 6.9990 overall best weight: 1.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN E 438 GLN ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6930 Z= 0.173 Angle : 0.817 11.605 9300 Z= 0.358 Chirality : 0.043 0.136 1100 Planarity : 0.003 0.035 1190 Dihedral : 5.152 13.427 900 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 7.34 % Allowed : 21.77 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.94 (0.25), residues: 840 helix: -2.53 (0.19), residues: 610 sheet: None (None), residues: 0 loop : -2.19 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 439 PHE 0.008 0.002 PHE F 501 TYR 0.006 0.001 TYR D 474 ARG 0.006 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 336 time to evaluate : 0.849 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: F 450 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8228 (tm-30) REVERT: F 458 GLN cc_start: 0.8486 (pt0) cc_final: 0.8270 (pt0) REVERT: A 437 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6698 (mt0) REVERT: A 441 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: A 443 LYS cc_start: 0.8346 (mtpp) cc_final: 0.8114 (ptpp) REVERT: A 450 GLN cc_start: 0.8721 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 458 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7190 (pt0) REVERT: A 461 ASP cc_start: 0.9008 (t70) cc_final: 0.8758 (t70) REVERT: A 469 ILE cc_start: 0.8899 (tp) cc_final: 0.8657 (tt) REVERT: A 500 GLU cc_start: 0.6325 (mp0) cc_final: 0.6085 (mp0) REVERT: B 441 GLN cc_start: 0.7642 (mp10) cc_final: 0.6935 (tp-100) REVERT: B 450 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 458 GLN cc_start: 0.8385 (pt0) cc_final: 0.8056 (pt0) REVERT: B 469 ILE cc_start: 0.8971 (tp) cc_final: 0.8644 (tt) REVERT: B 482 THR cc_start: 0.7774 (t) cc_final: 0.7433 (t) REVERT: C 443 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8385 (mtpp) REVERT: C 450 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 458 GLN cc_start: 0.8059 (pt0) cc_final: 0.7055 (pt0) REVERT: C 469 ILE cc_start: 0.8791 (tp) cc_final: 0.8546 (tt) REVERT: C 482 THR cc_start: 0.8246 (t) cc_final: 0.7907 (t) REVERT: C 500 GLU cc_start: 0.6566 (mp0) cc_final: 0.6329 (mp0) REVERT: D 450 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 469 ILE cc_start: 0.8917 (tp) cc_final: 0.8595 (tt) REVERT: E 441 GLN cc_start: 0.8195 (mp10) cc_final: 0.7792 (mp10) REVERT: E 443 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8357 (ptpp) REVERT: E 450 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8394 (tm-30) REVERT: E 451 MET cc_start: 0.8300 (tpt) cc_final: 0.7774 (tpt) REVERT: E 458 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: E 470 MET cc_start: 0.7575 (mtp) cc_final: 0.6556 (mtp) REVERT: E 474 TYR cc_start: 0.6493 (t80) cc_final: 0.6278 (t80) REVERT: E 500 GLU cc_start: 0.7008 (mp0) cc_final: 0.6746 (mp0) REVERT: G 450 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8377 (tm-30) REVERT: G 458 GLN cc_start: 0.8566 (pt0) cc_final: 0.8272 (pt0) REVERT: G 470 MET cc_start: 0.7398 (mtp) cc_final: 0.7145 (mtp) REVERT: G 515 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6558 (pp-130) REVERT: H 450 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8293 (tm-30) REVERT: H 451 MET cc_start: 0.8286 (tpt) cc_final: 0.7373 (tpt) REVERT: H 457 ASN cc_start: 0.8558 (m-40) cc_final: 0.7870 (t0) REVERT: H 458 GLN cc_start: 0.8847 (pt0) cc_final: 0.8315 (pt0) REVERT: I 451 MET cc_start: 0.8632 (tpp) cc_final: 0.7522 (ttm) REVERT: I 457 ASN cc_start: 0.8660 (m-40) cc_final: 0.8380 (m-40) REVERT: I 482 THR cc_start: 0.8208 (t) cc_final: 0.7884 (t) REVERT: I 500 GLU cc_start: 0.6452 (mp0) cc_final: 0.6140 (mp0) REVERT: J 443 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8490 (mtpp) REVERT: J 457 ASN cc_start: 0.8518 (m-40) cc_final: 0.8125 (t0) REVERT: J 470 MET cc_start: 0.7089 (mtp) cc_final: 0.6572 (mtp) REVERT: J 472 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5974 (pp20) REVERT: J 515 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6533 (pp-130) outliers start: 58 outliers final: 44 residues processed: 346 average time/residue: 0.2005 time to fit residues: 89.8231 Evaluate side-chains 376 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 325 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 515 MET Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 460 LEU Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 40.0000 chunk 65 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6930 Z= 0.308 Angle : 0.917 11.413 9300 Z= 0.415 Chirality : 0.048 0.168 1100 Planarity : 0.004 0.044 1190 Dihedral : 5.751 15.484 900 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 7.34 % Allowed : 23.04 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.63 (0.25), residues: 840 helix: -2.65 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 439 PHE 0.015 0.004 PHE G 501 TYR 0.009 0.002 TYR E 474 ARG 0.006 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 350 time to evaluate : 0.875 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: F 450 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8130 (tm-30) REVERT: F 453 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: F 461 ASP cc_start: 0.8923 (t70) cc_final: 0.8148 (t70) REVERT: F 474 TYR cc_start: 0.7370 (t80) cc_final: 0.6925 (t80) REVERT: A 437 GLN cc_start: 0.7933 (mt0) cc_final: 0.6607 (mt0) REVERT: A 441 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: A 450 GLN cc_start: 0.8685 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 451 MET cc_start: 0.8194 (tpt) cc_final: 0.7645 (tpt) REVERT: A 458 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: A 469 ILE cc_start: 0.9008 (tp) cc_final: 0.8695 (tt) REVERT: A 500 GLU cc_start: 0.6774 (mp0) cc_final: 0.6569 (mp0) REVERT: B 441 GLN cc_start: 0.7944 (mp10) cc_final: 0.7500 (tp-100) REVERT: B 450 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 451 MET cc_start: 0.7780 (tpt) cc_final: 0.7458 (tpt) REVERT: B 458 GLN cc_start: 0.8583 (pt0) cc_final: 0.8380 (pt0) REVERT: B 466 ARG cc_start: 0.8641 (mpp-170) cc_final: 0.8121 (mtm-85) REVERT: B 469 ILE cc_start: 0.9106 (tp) cc_final: 0.8817 (tt) REVERT: B 482 THR cc_start: 0.7837 (t) cc_final: 0.7366 (t) REVERT: C 443 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8328 (mtpp) REVERT: C 450 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 458 GLN cc_start: 0.8154 (pt0) cc_final: 0.7040 (pt0) REVERT: C 469 ILE cc_start: 0.8997 (tp) cc_final: 0.8743 (tt) REVERT: C 515 MET cc_start: 0.6994 (pp-130) cc_final: 0.6684 (pp-130) REVERT: D 450 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8156 (tm-30) REVERT: D 469 ILE cc_start: 0.9052 (tp) cc_final: 0.8830 (tt) REVERT: E 441 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: E 445 GLU cc_start: 0.8452 (tp30) cc_final: 0.8157 (tp30) REVERT: E 450 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8446 (tm-30) REVERT: E 451 MET cc_start: 0.8157 (tpt) cc_final: 0.7658 (tpt) REVERT: E 453 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: E 470 MET cc_start: 0.7675 (mtp) cc_final: 0.6577 (mtp) REVERT: E 474 TYR cc_start: 0.7156 (t80) cc_final: 0.6599 (t80) REVERT: E 500 GLU cc_start: 0.7231 (mp0) cc_final: 0.6979 (mp0) REVERT: G 450 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8296 (tm-30) REVERT: G 451 MET cc_start: 0.8230 (tpt) cc_final: 0.7813 (tpt) REVERT: G 458 GLN cc_start: 0.8741 (pt0) cc_final: 0.8450 (pt0) REVERT: G 515 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7031 (pp-130) REVERT: H 444 ARG cc_start: 0.8681 (ttt180) cc_final: 0.8295 (ttt180) REVERT: H 450 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8411 (tm-30) REVERT: H 451 MET cc_start: 0.8313 (tpt) cc_final: 0.7692 (tpt) REVERT: H 457 ASN cc_start: 0.8757 (m-40) cc_final: 0.7999 (t0) REVERT: H 458 GLN cc_start: 0.8967 (pt0) cc_final: 0.8491 (pt0) REVERT: H 470 MET cc_start: 0.7945 (mtm) cc_final: 0.7667 (mtm) REVERT: I 450 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8065 (tm-30) REVERT: I 451 MET cc_start: 0.8540 (tpp) cc_final: 0.8173 (tpt) REVERT: I 457 ASN cc_start: 0.8831 (m-40) cc_final: 0.8554 (m-40) REVERT: I 469 ILE cc_start: 0.8828 (tp) cc_final: 0.8549 (tt) REVERT: I 470 MET cc_start: 0.7818 (mtp) cc_final: 0.7536 (mtp) REVERT: I 500 GLU cc_start: 0.6633 (mp0) cc_final: 0.6291 (mp0) REVERT: J 443 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8656 (mtpp) REVERT: J 450 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8116 (tm-30) REVERT: J 500 GLU cc_start: 0.6131 (mp0) cc_final: 0.5917 (mp0) outliers start: 58 outliers final: 44 residues processed: 366 average time/residue: 0.1906 time to fit residues: 91.8140 Evaluate side-chains 386 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 336 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 515 MET Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain I residue 443 LYS Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN A 437 GLN A 438 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 438 GLN ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6930 Z= 0.209 Angle : 0.895 11.887 9300 Z= 0.396 Chirality : 0.045 0.156 1100 Planarity : 0.003 0.037 1190 Dihedral : 5.344 15.548 900 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 7.34 % Allowed : 24.43 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.25 (0.27), residues: 840 helix: -2.29 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.47 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 439 PHE 0.010 0.003 PHE A 501 TYR 0.008 0.001 TYR D 474 ARG 0.006 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 347 time to evaluate : 0.852 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: F 450 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8238 (tm-30) REVERT: F 457 ASN cc_start: 0.8962 (m-40) cc_final: 0.8669 (m110) REVERT: F 458 GLN cc_start: 0.8682 (pt0) cc_final: 0.7710 (pt0) REVERT: A 437 GLN cc_start: 0.7838 (mt0) cc_final: 0.6851 (mt0) REVERT: A 441 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: A 450 GLN cc_start: 0.8679 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 469 ILE cc_start: 0.8958 (tp) cc_final: 0.8659 (tt) REVERT: B 441 GLN cc_start: 0.7875 (mp10) cc_final: 0.7404 (tp-100) REVERT: B 450 GLN cc_start: 0.8556 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 451 MET cc_start: 0.7834 (tpt) cc_final: 0.7497 (tpt) REVERT: B 469 ILE cc_start: 0.9044 (tp) cc_final: 0.8808 (tt) REVERT: B 482 THR cc_start: 0.7755 (t) cc_final: 0.7362 (t) REVERT: B 515 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7184 (pp-130) REVERT: C 441 GLN cc_start: 0.7909 (mp10) cc_final: 0.7593 (tp-100) REVERT: C 443 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8336 (mtpp) REVERT: C 450 GLN cc_start: 0.8770 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 458 GLN cc_start: 0.8137 (pt0) cc_final: 0.7342 (pt0) REVERT: C 469 ILE cc_start: 0.8912 (tp) cc_final: 0.8599 (tt) REVERT: C 488 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8257 (mtm180) REVERT: C 515 MET cc_start: 0.6948 (pp-130) cc_final: 0.6653 (pp-130) REVERT: D 450 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8096 (tm-30) REVERT: D 469 ILE cc_start: 0.9002 (tp) cc_final: 0.8729 (tt) REVERT: E 441 GLN cc_start: 0.8527 (mp10) cc_final: 0.8058 (mp10) REVERT: E 445 GLU cc_start: 0.8380 (tp30) cc_final: 0.8114 (tp30) REVERT: E 450 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8405 (tm-30) REVERT: E 451 MET cc_start: 0.8348 (tpt) cc_final: 0.7956 (tpt) REVERT: E 472 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6002 (pp20) REVERT: E 474 TYR cc_start: 0.6654 (t80) cc_final: 0.6202 (t80) REVERT: E 500 GLU cc_start: 0.7135 (mp0) cc_final: 0.6910 (mp0) REVERT: E 515 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6427 (pp-130) REVERT: G 450 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8476 (tm-30) REVERT: G 451 MET cc_start: 0.8306 (tpt) cc_final: 0.7917 (tpt) REVERT: G 458 GLN cc_start: 0.8634 (pt0) cc_final: 0.8313 (pt0) REVERT: G 470 MET cc_start: 0.7683 (mtp) cc_final: 0.7316 (mtt) REVERT: H 444 ARG cc_start: 0.8598 (ttt180) cc_final: 0.8229 (ttt180) REVERT: H 450 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8408 (tm-30) REVERT: H 451 MET cc_start: 0.8437 (tpt) cc_final: 0.7542 (tpt) REVERT: H 457 ASN cc_start: 0.8592 (m-40) cc_final: 0.7962 (t0) REVERT: H 458 GLN cc_start: 0.8895 (pt0) cc_final: 0.8410 (pt0) REVERT: I 450 GLN cc_start: 0.8747 (tm-30) cc_final: 0.7957 (tm-30) REVERT: I 451 MET cc_start: 0.8561 (tpp) cc_final: 0.7495 (ttm) REVERT: I 457 ASN cc_start: 0.8755 (m-40) cc_final: 0.8502 (m-40) REVERT: I 500 GLU cc_start: 0.6652 (mp0) cc_final: 0.6354 (mp0) REVERT: J 443 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8689 (mtpp) REVERT: J 444 ARG cc_start: 0.8856 (ttt180) cc_final: 0.8461 (ttt180) REVERT: J 450 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8255 (tm-30) REVERT: J 457 ASN cc_start: 0.8587 (m-40) cc_final: 0.7869 (t0) REVERT: J 515 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6773 (pp-130) outliers start: 58 outliers final: 39 residues processed: 363 average time/residue: 0.1915 time to fit residues: 90.1418 Evaluate side-chains 381 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 337 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 438 GLN Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 438 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 64 optimal weight: 0.0870 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6930 Z= 0.210 Angle : 0.923 12.270 9300 Z= 0.407 Chirality : 0.045 0.156 1100 Planarity : 0.003 0.032 1190 Dihedral : 5.247 15.418 900 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 6.08 % Allowed : 25.32 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.09 (0.27), residues: 840 helix: -2.05 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -1.72 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 439 PHE 0.018 0.003 PHE H 501 TYR 0.008 0.001 TYR D 474 ARG 0.009 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 336 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8212 (tm-30) REVERT: F 451 MET cc_start: 0.8033 (tpt) cc_final: 0.7787 (tpt) REVERT: F 458 GLN cc_start: 0.8578 (pt0) cc_final: 0.8059 (pt0) REVERT: A 437 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: A 441 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 450 GLN cc_start: 0.8754 (tm-30) cc_final: 0.7795 (tm-30) REVERT: A 469 ILE cc_start: 0.8948 (tp) cc_final: 0.8652 (tt) REVERT: B 441 GLN cc_start: 0.7802 (mp10) cc_final: 0.7341 (tp-100) REVERT: B 450 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 469 ILE cc_start: 0.9044 (tp) cc_final: 0.8715 (tt) REVERT: B 482 THR cc_start: 0.7698 (t) cc_final: 0.7298 (t) REVERT: C 441 GLN cc_start: 0.8083 (mp10) cc_final: 0.7601 (tp-100) REVERT: C 443 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8359 (mtpp) REVERT: C 450 GLN cc_start: 0.8819 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 458 GLN cc_start: 0.8135 (pt0) cc_final: 0.7425 (pt0) REVERT: C 469 ILE cc_start: 0.8864 (tp) cc_final: 0.8578 (tt) REVERT: C 488 ARG cc_start: 0.8357 (mtm180) cc_final: 0.8059 (mtm180) REVERT: C 515 MET cc_start: 0.6918 (pp-130) cc_final: 0.6624 (pp-130) REVERT: D 450 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7412 (tm-30) REVERT: D 469 ILE cc_start: 0.9001 (tp) cc_final: 0.8727 (tt) REVERT: D 515 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6632 (pp-130) REVERT: E 441 GLN cc_start: 0.8527 (mp10) cc_final: 0.8047 (mp10) REVERT: E 443 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8087 (ptpt) REVERT: E 445 GLU cc_start: 0.8330 (tp30) cc_final: 0.8003 (tp30) REVERT: E 450 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8376 (tm-30) REVERT: E 451 MET cc_start: 0.8310 (tpt) cc_final: 0.7953 (tpt) REVERT: E 470 MET cc_start: 0.7833 (mtp) cc_final: 0.7536 (mtp) REVERT: E 472 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5984 (pp20) REVERT: E 474 TYR cc_start: 0.6491 (t80) cc_final: 0.6234 (t80) REVERT: E 500 GLU cc_start: 0.7101 (mp0) cc_final: 0.6839 (mp0) REVERT: E 515 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6569 (pp-130) REVERT: G 450 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8177 (tm-30) REVERT: G 451 MET cc_start: 0.8265 (tpt) cc_final: 0.7906 (tpt) REVERT: G 458 GLN cc_start: 0.8622 (pt0) cc_final: 0.8318 (pt0) REVERT: G 470 MET cc_start: 0.7568 (mtp) cc_final: 0.7218 (mtt) REVERT: H 450 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8218 (tm-30) REVERT: H 451 MET cc_start: 0.8395 (tpt) cc_final: 0.8090 (tpt) REVERT: H 457 ASN cc_start: 0.8680 (m-40) cc_final: 0.7974 (t0) REVERT: H 458 GLN cc_start: 0.8891 (pt0) cc_final: 0.8404 (pt0) REVERT: H 470 MET cc_start: 0.7542 (mtm) cc_final: 0.7241 (mtm) REVERT: I 450 GLN cc_start: 0.8734 (tm-30) cc_final: 0.7906 (tm-30) REVERT: I 451 MET cc_start: 0.8554 (tpp) cc_final: 0.7480 (ttm) REVERT: I 457 ASN cc_start: 0.8751 (m-40) cc_final: 0.8284 (t0) REVERT: I 500 GLU cc_start: 0.6758 (mp0) cc_final: 0.6475 (mp0) REVERT: I 515 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6748 (pp-130) REVERT: J 443 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8634 (mtpp) REVERT: J 444 ARG cc_start: 0.8853 (ttt180) cc_final: 0.8373 (ttt180) REVERT: J 450 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8335 (tm-30) REVERT: J 457 ASN cc_start: 0.8558 (m-40) cc_final: 0.7829 (t0) REVERT: J 470 MET cc_start: 0.6964 (mtt) cc_final: 0.6720 (mtt) REVERT: J 472 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5712 (pp20) REVERT: J 515 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6824 (pp-130) outliers start: 48 outliers final: 35 residues processed: 347 average time/residue: 0.1820 time to fit residues: 82.9037 Evaluate side-chains 373 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 330 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain J residue 438 GLN Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 457 ASN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 489 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6930 Z= 0.201 Angle : 0.933 12.656 9300 Z= 0.409 Chirality : 0.045 0.168 1100 Planarity : 0.003 0.033 1190 Dihedral : 5.162 13.953 900 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.08 % Allowed : 25.95 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.17 (0.28), residues: 840 helix: -2.13 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 439 PHE 0.017 0.003 PHE H 501 TYR 0.008 0.001 TYR D 474 ARG 0.009 0.001 ARG B 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 328 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8260 (tm-30) REVERT: F 451 MET cc_start: 0.8039 (tpt) cc_final: 0.7817 (tpt) REVERT: A 437 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: A 441 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: A 450 GLN cc_start: 0.8609 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 469 ILE cc_start: 0.8923 (tp) cc_final: 0.8603 (tt) REVERT: A 515 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6725 (pp-130) REVERT: B 441 GLN cc_start: 0.7819 (mp10) cc_final: 0.7356 (tp-100) REVERT: B 450 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 458 GLN cc_start: 0.7838 (pt0) cc_final: 0.7351 (pt0) REVERT: B 469 ILE cc_start: 0.8981 (tp) cc_final: 0.8655 (tt) REVERT: B 482 THR cc_start: 0.7662 (t) cc_final: 0.7268 (t) REVERT: B 489 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8718 (mm-40) REVERT: C 441 GLN cc_start: 0.8039 (mp10) cc_final: 0.7495 (tp-100) REVERT: C 443 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8355 (mtpp) REVERT: C 450 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 458 GLN cc_start: 0.8114 (pt0) cc_final: 0.7369 (pt0) REVERT: C 469 ILE cc_start: 0.8726 (tp) cc_final: 0.8434 (tt) REVERT: C 488 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8025 (mtm180) REVERT: C 501 PHE cc_start: 0.8634 (t80) cc_final: 0.8297 (t80) REVERT: C 515 MET cc_start: 0.6881 (pp-130) cc_final: 0.6609 (pp-130) REVERT: D 450 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7431 (tm-30) REVERT: D 469 ILE cc_start: 0.9032 (tp) cc_final: 0.8753 (tt) REVERT: D 515 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6615 (pp-130) REVERT: E 441 GLN cc_start: 0.8475 (mp10) cc_final: 0.7993 (mp10) REVERT: E 443 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7979 (ptpt) REVERT: E 445 GLU cc_start: 0.8320 (tp30) cc_final: 0.7985 (tp30) REVERT: E 450 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8267 (tm-30) REVERT: E 451 MET cc_start: 0.8378 (tpt) cc_final: 0.7967 (tpt) REVERT: E 470 MET cc_start: 0.7725 (mtp) cc_final: 0.7447 (mtp) REVERT: E 472 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: E 500 GLU cc_start: 0.6950 (mp0) cc_final: 0.6743 (mp0) REVERT: E 515 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6588 (pp-130) REVERT: G 450 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8181 (tm-30) REVERT: G 451 MET cc_start: 0.8270 (tpt) cc_final: 0.7891 (tpt) REVERT: G 458 GLN cc_start: 0.8571 (pt0) cc_final: 0.8227 (pt0) REVERT: G 470 MET cc_start: 0.7565 (mtp) cc_final: 0.7200 (mtt) REVERT: H 450 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8190 (tm-30) REVERT: H 451 MET cc_start: 0.8414 (tpt) cc_final: 0.8135 (tpt) REVERT: H 457 ASN cc_start: 0.8595 (m-40) cc_final: 0.7953 (t0) REVERT: H 458 GLN cc_start: 0.8887 (pt0) cc_final: 0.8378 (pt0) REVERT: H 470 MET cc_start: 0.7490 (mtm) cc_final: 0.7182 (mtm) REVERT: I 450 GLN cc_start: 0.8702 (tm-30) cc_final: 0.7822 (tm-30) REVERT: I 451 MET cc_start: 0.8551 (tpp) cc_final: 0.7356 (ttm) REVERT: I 457 ASN cc_start: 0.8621 (m-40) cc_final: 0.8202 (t0) REVERT: I 500 GLU cc_start: 0.6691 (mp0) cc_final: 0.6436 (mp0) REVERT: I 515 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6793 (pp-130) REVERT: J 443 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8722 (mtpp) REVERT: J 450 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8295 (tm-30) REVERT: J 457 ASN cc_start: 0.8584 (m-40) cc_final: 0.8117 (t0) REVERT: J 472 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5648 (pp20) REVERT: J 515 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6659 (pp-130) outliers start: 48 outliers final: 35 residues processed: 340 average time/residue: 0.1775 time to fit residues: 80.6357 Evaluate side-chains 360 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 316 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 495 ASP Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 517 LEU Chi-restraints excluded: chain J residue 438 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 515 MET Chi-restraints excluded: chain J residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 overall best weight: 1.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 ASN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN E 438 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123339 restraints weight = 13249.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127148 restraints weight = 7252.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129821 restraints weight = 4525.800| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6930 Z= 0.193 Angle : 0.925 12.183 9300 Z= 0.403 Chirality : 0.044 0.178 1100 Planarity : 0.003 0.037 1190 Dihedral : 5.057 14.429 900 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.57 % Allowed : 26.96 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.34 (0.26), residues: 840 helix: -2.13 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 439 PHE 0.016 0.003 PHE H 501 TYR 0.008 0.001 TYR D 474 ARG 0.008 0.001 ARG E 466 =============================================================================== Job complete usr+sys time: 1980.98 seconds wall clock time: 36 minutes 43.25 seconds (2203.25 seconds total)