Starting phenix.real_space_refine on Fri Dec 8 03:55:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/12_2023/6ggs_4399.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/12_2023/6ggs_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_4399/12_2023/6ggs_4399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/12_2023/6ggs_4399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/12_2023/6ggs_4399.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/12_2023/6ggs_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.63, per 1000 atoms: 0.82 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: 2.85 Conformation dependent library (CDL) restraints added in 1.6 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: 1.01 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: 1.81 Time building geometry restraints manager: 3.03 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: 0.040 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: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.450 Find NCS groups from input model: 0.570 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- 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 : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 399 average time/residue: 0.1942 time to fit residues: 100.2384 Evaluate side-chains 326 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1343 ------------------------------------------------------------------------------- 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: 7.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 489 GLN A 437 GLN A 489 GLN B 437 GLN B 438 GLN B 489 GLN ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN 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 458 GLN 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 458 GLN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3336 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= 0.213 Angle : 0.862 9.594 9300 Z= 0.410 Chirality : 0.044 0.230 1100 Planarity : 0.003 0.015 1190 Dihedral : 6.488 20.624 900 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.16 % Allowed : 21.14 % Favored : 75.70 % 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: -5.77 (0.21), residues: 840 helix: -4.31 (0.11), residues: 570 sheet: None (None), residues: 0 loop : -2.05 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 439 PHE 0.008 0.003 PHE A 501 TYR 0.004 0.001 TYR E 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 371 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 346 time to evaluate : 0.904 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 outliers start: 25 outliers final: 4 residues processed: 355 average time/residue: 0.2230 time to fit residues: 101.9060 Evaluate side-chains 326 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0713 time to fit residues: 1.7800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.0470 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- 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** 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 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 512 ASN G 514 GLN ** 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** ** J 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4224 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= 0.193 Angle : 0.839 11.381 9300 Z= 0.388 Chirality : 0.044 0.147 1100 Planarity : 0.003 0.045 1190 Dihedral : 5.672 17.997 900 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.42 % Allowed : 20.00 % Favored : 76.58 % 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: -4.78 (0.23), residues: 840 helix: -3.62 (0.14), residues: 580 sheet: None (None), residues: 0 loop : -1.38 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 439 PHE 0.009 0.003 PHE B 501 TYR 0.016 0.002 TYR E 474 ARG 0.006 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 347 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 320 time to evaluate : 0.866 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 outliers start: 27 outliers final: 17 residues processed: 335 average time/residue: 0.2165 time to fit residues: 93.8182 Evaluate side-chains 312 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 295 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0710 time to fit residues: 3.3905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 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 450 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 450 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6930 Z= 0.208 Angle : 0.870 12.223 9300 Z= 0.390 Chirality : 0.043 0.141 1100 Planarity : 0.003 0.048 1190 Dihedral : 5.439 14.138 900 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.04 % Allowed : 22.78 % Favored : 74.18 % 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: -4.14 (0.24), residues: 840 helix: -3.14 (0.17), residues: 520 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 439 PHE 0.010 0.003 PHE B 501 TYR 0.009 0.001 TYR B 474 ARG 0.006 0.001 ARG A 483 *********************** 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 344 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 320 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 327 average time/residue: 0.2046 time to fit residues: 85.8677 Evaluate side-chains 316 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 302 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0775 time to fit residues: 3.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 overall best weight: 7.2788 ------------------------------------------------------------------------------- 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** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 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** ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 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 450 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 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7732 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6930 Z= 0.343 Angle : 0.950 11.631 9300 Z= 0.438 Chirality : 0.047 0.124 1100 Planarity : 0.004 0.050 1190 Dihedral : 5.902 16.388 900 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.91 % Allowed : 24.56 % Favored : 72.53 % 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: -4.34 (0.23), residues: 840 helix: -3.13 (0.17), residues: 530 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 439 PHE 0.015 0.004 PHE D 501 TYR 0.013 0.002 TYR F 474 ARG 0.008 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 370 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 347 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 354 average time/residue: 0.2054 time to fit residues: 93.2442 Evaluate side-chains 340 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 323 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0681 time to fit residues: 3.1643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 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 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 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 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 450 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 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** ** 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: 0.7585 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6930 Z= 0.196 Angle : 0.943 12.086 9300 Z= 0.417 Chirality : 0.044 0.137 1100 Planarity : 0.003 0.028 1190 Dihedral : 5.299 14.448 900 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.15 % Allowed : 25.82 % Favored : 72.03 % 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: -3.81 (0.24), residues: 840 helix: -2.61 (0.19), residues: 540 sheet: None (None), residues: 0 loop : -2.02 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 439 PHE 0.008 0.002 PHE C 501 TYR 0.010 0.001 TYR D 474 ARG 0.006 0.001 ARG A 466 *********************** 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 348 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 331 time to evaluate : 0.915 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 336 average time/residue: 0.2030 time to fit residues: 88.2474 Evaluate side-chains 322 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 311 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0781 time to fit residues: 2.7486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.5264 ------------------------------------------------------------------------------- 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** A 457 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 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 458 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 457 ASN D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 450 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 457 ASN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 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: 0.7592 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6930 Z= 0.217 Angle : 0.937 11.681 9300 Z= 0.421 Chirality : 0.044 0.151 1100 Planarity : 0.004 0.068 1190 Dihedral : 5.254 14.063 900 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 27.47 % Favored : 70.76 % 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: -2.38 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP E 439 PHE 0.028 0.003 PHE C 501 TYR 0.009 0.001 TYR D 474 ARG 0.013 0.001 ARG F 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 335 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 321 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 327 average time/residue: 0.1954 time to fit residues: 83.0700 Evaluate side-chains 313 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 304 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0642 time to fit residues: 2.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.7844 ------------------------------------------------------------------------------- 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** ** A 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 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 450 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 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** ** J 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6930 Z= 0.257 Angle : 0.961 12.006 9300 Z= 0.435 Chirality : 0.046 0.167 1100 Planarity : 0.003 0.037 1190 Dihedral : 5.328 14.763 900 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.52 % Allowed : 27.22 % Favored : 71.27 % 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: -3.12 (0.26), residues: 840 helix: -2.25 (0.20), residues: 520 sheet: None (None), residues: 0 loop : -1.41 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP E 439 PHE 0.032 0.004 PHE C 501 TYR 0.007 0.002 TYR F 474 ARG 0.007 0.001 ARG F 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 340 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 328 time to evaluate : 0.864 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 330 average time/residue: 0.1875 time to fit residues: 81.1793 Evaluate side-chains 321 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 314 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0681 time to fit residues: 2.0410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.0170 chunk 67 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 0.3980 chunk 46 optimal weight: 7.9990 overall best weight: 3.2824 ------------------------------------------------------------------------------- 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** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 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 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 GLN ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 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 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6930 Z= 0.250 Angle : 0.991 12.185 9300 Z= 0.447 Chirality : 0.046 0.157 1100 Planarity : 0.004 0.033 1190 Dihedral : 5.337 14.680 900 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.14 % Allowed : 28.73 % Favored : 70.13 % 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: -3.05 (0.27), residues: 840 helix: -2.21 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP E 439 PHE 0.029 0.004 PHE C 501 TYR 0.014 0.002 TYR E 474 ARG 0.005 0.001 ARG I 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 332 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 323 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 324 average time/residue: 0.1810 time to fit residues: 77.6878 Evaluate side-chains 317 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 309 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0773 time to fit residues: 2.2628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 489 GLN ** B 457 ASN ** 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 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 457 ASN ** G 458 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 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6930 Z= 0.312 Angle : 1.046 12.048 9300 Z= 0.480 Chirality : 0.048 0.170 1100 Planarity : 0.004 0.036 1190 Dihedral : 5.666 15.769 900 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 27.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.14 % Allowed : 30.51 % Favored : 68.35 % 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: -2.98 (0.27), residues: 840 helix: -2.15 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.34 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP E 439 PHE 0.031 0.005 PHE C 501 TYR 0.015 0.002 TYR E 474 ARG 0.007 0.001 ARG I 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 343 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 334 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 335 average time/residue: 0.1910 time to fit residues: 83.6230 Evaluate side-chains 331 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 322 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0848 time to fit residues: 2.4711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN H 514 GLN ** I 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN ** J 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125536 restraints weight = 12706.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129656 restraints weight = 6789.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132425 restraints weight = 4139.354| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6930 Z= 0.231 Angle : 1.003 13.803 9300 Z= 0.451 Chirality : 0.045 0.158 1100 Planarity : 0.004 0.046 1190 Dihedral : 5.280 17.102 900 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.89 % Allowed : 31.01 % Favored : 68.10 % 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: -3.01 (0.26), residues: 840 helix: -1.97 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.71 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.006 TRP A 439 PHE 0.027 0.003 PHE C 501 TYR 0.015 0.001 TYR E 474 ARG 0.013 0.001 ARG B 466 =============================================================================== Job complete usr+sys time: 1997.73 seconds wall clock time: 37 minutes 2.11 seconds (2222.11 seconds total)