Starting phenix.real_space_refine on Fri Jan 19 20:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/01_2024/6rks_4909_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 46 5.16 5 C 7726 2.51 5 N 2234 2.21 5 O 2502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "D ARG 516": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12572 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4002 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 21, 'TRANS': 486} Chain breaks: 3 Chain: "B" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1595 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 10, 'TRANS': 189} Chain breaks: 2 Chain: "C" Number of atoms: 4002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4002 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 21, 'TRANS': 486} Chain breaks: 3 Chain: "D" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1595 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 10, 'TRANS': 189} Chain breaks: 2 Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 66 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 33 Unusual residues: {'JHN': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 33 Unusual residues: {'JHN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AJHN G 101 " occ=0.50 ... (64 atoms not shown) pdb=" O3 BJHN G 101 " occ=0.50 Time building chain proxies: 7.10, per 1000 atoms: 0.56 Number of scatterers: 12572 At special positions: 0 Unit cell: (102.96, 127.6, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 64 15.00 O 2502 8.00 N 2234 7.00 C 7726 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: 5.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 16 sheets defined 40.4% alpha, 8.2% beta 32 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.87 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.808A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 495 through 512 Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.987A pdb=" N GLY B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 523 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 773 through 776 No H-bonds generated for 'chain 'B' and resid 773 through 776' Processing helix chain 'B' and resid 782 through 785 No H-bonds generated for 'chain 'B' and resid 782 through 785' Processing helix chain 'C' and resid 15 through 28 Processing helix chain 'C' and resid 43 through 54 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 314 through 323 Processing helix chain 'C' and resid 347 through 388 removed outlier: 3.808A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 495 through 512 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.988A pdb=" N GLY D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 519 through 523 Processing helix chain 'D' and resid 549 through 554 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 747 through 753 Processing helix chain 'D' and resid 773 through 776 No H-bonds generated for 'chain 'D' and resid 773 through 776' Processing helix chain 'D' and resid 782 through 785 No H-bonds generated for 'chain 'D' and resid 782 through 785' Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 237 through 243 Processing sheet with id= D, first strand: chain 'A' and resid 303 through 306 removed outlier: 3.604A pdb=" N ILE A 260 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 247 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A 262 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ARG A 245 " --> pdb=" O HIS A 262 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.648A pdb=" N ALA A 336 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 421 through 424 removed outlier: 3.839A pdb=" N VAL B 423 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 493 through 495 Processing sheet with id= H, first strand: chain 'B' and resid 535 through 539 Processing sheet with id= I, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= K, first strand: chain 'C' and resid 237 through 243 Processing sheet with id= L, first strand: chain 'C' and resid 303 through 306 removed outlier: 3.604A pdb=" N ILE C 260 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 247 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS C 262 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.649A pdb=" N ALA C 336 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 421 through 424 removed outlier: 3.838A pdb=" N VAL D 423 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 493 through 495 Processing sheet with id= P, first strand: chain 'D' and resid 535 through 539 408 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3234 1.33 - 1.45: 2344 1.45 - 1.57: 7122 1.57 - 1.69: 124 1.69 - 1.80: 88 Bond restraints: 12912 Sorted by residual: bond pdb=" C2 BJHN G 101 " pdb=" C3 BJHN G 101 " ideal model delta sigma weight residual 2.160 1.351 0.809 2.00e-02 2.50e+03 1.64e+03 bond pdb=" C2 AJHN G 101 " pdb=" C3 AJHN G 101 " ideal model delta sigma weight residual 2.160 1.351 0.809 2.00e-02 2.50e+03 1.63e+03 bond pdb=" C5 AJHN G 101 " pdb=" C6 AJHN G 101 " ideal model delta sigma weight residual 0.686 1.492 -0.806 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C5 BJHN G 101 " pdb=" C6 BJHN G 101 " ideal model delta sigma weight residual 0.686 1.491 -0.805 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C1 BJHN G 101 " pdb=" C2 BJHN G 101 " ideal model delta sigma weight residual 1.959 1.438 0.521 2.00e-02 2.50e+03 6.79e+02 ... (remaining 12907 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.55: 723 106.55 - 113.40: 7118 113.40 - 120.24: 4860 120.24 - 127.09: 4784 127.09 - 133.94: 235 Bond angle restraints: 17720 Sorted by residual: angle pdb=" C3 BJHN G 101 " pdb=" C4 BJHN G 101 " pdb=" N1 BJHN G 101 " ideal model delta sigma weight residual 17.58 127.06 -109.48 3.00e+00 1.11e-01 1.33e+03 angle pdb=" C3 AJHN G 101 " pdb=" C4 AJHN G 101 " pdb=" N1 AJHN G 101 " ideal model delta sigma weight residual 17.58 126.98 -109.40 3.00e+00 1.11e-01 1.33e+03 angle pdb=" C1 AJHN G 101 " pdb=" N6 AJHN G 101 " pdb=" C23AJHN G 101 " ideal model delta sigma weight residual 29.62 125.57 -95.95 3.00e+00 1.11e-01 1.02e+03 angle pdb=" C1 BJHN G 101 " pdb=" N6 BJHN G 101 " pdb=" C23BJHN G 101 " ideal model delta sigma weight residual 29.62 125.54 -95.92 3.00e+00 1.11e-01 1.02e+03 angle pdb=" C4 AJHN G 101 " pdb=" C24AJHN G 101 " pdb=" N2 AJHN G 101 " ideal model delta sigma weight residual 65.03 129.26 -64.23 3.00e+00 1.11e-01 4.58e+02 ... (remaining 17715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 7495 33.68 - 67.36: 231 67.36 - 101.04: 3 101.04 - 134.73: 15 134.73 - 168.41: 6 Dihedral angle restraints: 7750 sinusoidal: 3648 harmonic: 4102 Sorted by residual: dihedral pdb=" C10AJHN G 101 " pdb=" C11AJHN G 101 " pdb=" N4 AJHN G 101 " pdb=" C14AJHN G 101 " ideal model delta sinusoidal sigma weight residual 113.22 -78.37 -168.41 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C10BJHN G 101 " pdb=" C11BJHN G 101 " pdb=" N4 BJHN G 101 " pdb=" C14BJHN G 101 " ideal model delta sinusoidal sigma weight residual 113.22 -54.17 167.39 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA GLU B 424 " pdb=" C GLU B 424 " pdb=" N GLY B 425 " pdb=" CA GLY B 425 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.986: 1996 0.986 - 1.973: 0 1.973 - 2.959: 0 2.959 - 3.946: 0 3.946 - 4.932: 2 Chirality restraints: 1998 Sorted by residual: chirality pdb=" C11BJHN G 101 " pdb=" C10BJHN G 101 " pdb=" C12BJHN G 101 " pdb=" N4 BJHN G 101 " both_signs ideal model delta sigma weight residual False -2.58 2.35 -4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" C11AJHN G 101 " pdb=" C10AJHN G 101 " pdb=" C12AJHN G 101 " pdb=" N4 AJHN G 101 " both_signs ideal model delta sigma weight residual False -2.58 2.33 -4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" C7 AJHN G 101 " pdb=" C23AJHN G 101 " pdb=" C8 AJHN G 101 " pdb=" N2 AJHN G 101 " both_signs ideal model delta sigma weight residual False -2.39 -2.75 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1995 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 AJHN G 101 " -0.062 2.00e-02 2.50e+03 9.75e-02 3.33e+02 pdb=" C2 AJHN G 101 " 0.001 2.00e-02 2.50e+03 pdb=" C23AJHN G 101 " 0.296 2.00e-02 2.50e+03 pdb=" C24AJHN G 101 " -0.015 2.00e-02 2.50e+03 pdb=" C3 AJHN G 101 " 0.047 2.00e-02 2.50e+03 pdb=" C4 AJHN G 101 " 0.038 2.00e-02 2.50e+03 pdb=" C5 AJHN G 101 " 0.020 2.00e-02 2.50e+03 pdb=" C6 AJHN G 101 " -0.039 2.00e-02 2.50e+03 pdb=" C7 AJHN G 101 " -0.013 2.00e-02 2.50e+03 pdb=" N1 AJHN G 101 " 0.061 2.00e-02 2.50e+03 pdb=" N2 AJHN G 101 " -0.041 2.00e-02 2.50e+03 pdb=" N6 AJHN G 101 " -0.065 2.00e-02 2.50e+03 pdb=" O1 AJHN G 101 " -0.130 2.00e-02 2.50e+03 pdb=" O2 AJHN G 101 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BJHN G 101 " 0.065 2.00e-02 2.50e+03 9.70e-02 3.29e+02 pdb=" C2 BJHN G 101 " 0.001 2.00e-02 2.50e+03 pdb=" C23BJHN G 101 " -0.290 2.00e-02 2.50e+03 pdb=" C24BJHN G 101 " 0.016 2.00e-02 2.50e+03 pdb=" C3 BJHN G 101 " -0.047 2.00e-02 2.50e+03 pdb=" C4 BJHN G 101 " -0.038 2.00e-02 2.50e+03 pdb=" C5 BJHN G 101 " -0.022 2.00e-02 2.50e+03 pdb=" C6 BJHN G 101 " 0.041 2.00e-02 2.50e+03 pdb=" C7 BJHN G 101 " 0.002 2.00e-02 2.50e+03 pdb=" N1 BJHN G 101 " -0.065 2.00e-02 2.50e+03 pdb=" N2 BJHN G 101 " 0.040 2.00e-02 2.50e+03 pdb=" N6 BJHN G 101 " 0.068 2.00e-02 2.50e+03 pdb=" O1 BJHN G 101 " 0.126 2.00e-02 2.50e+03 pdb=" O2 BJHN G 101 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14BJHN G 101 " -0.047 2.00e-02 2.50e+03 2.59e-02 1.50e+01 pdb=" C15BJHN G 101 " 0.013 2.00e-02 2.50e+03 pdb=" C16BJHN G 101 " 0.013 2.00e-02 2.50e+03 pdb=" C17BJHN G 101 " 0.007 2.00e-02 2.50e+03 pdb=" C18BJHN G 101 " 0.010 2.00e-02 2.50e+03 pdb=" C21BJHN G 101 " 0.003 2.00e-02 2.50e+03 pdb=" C22BJHN G 101 " 0.022 2.00e-02 2.50e+03 pdb=" N5 BJHN G 101 " 0.027 2.00e-02 2.50e+03 pdb=" O3 BJHN G 101 " -0.046 2.00e-02 2.50e+03 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2994 2.80 - 3.32: 11146 3.32 - 3.85: 19123 3.85 - 4.37: 20982 4.37 - 4.90: 35562 Nonbonded interactions: 89807 Sorted by model distance: nonbonded pdb=" OE2 GLU B 454 " pdb=" NH1 ARG B 516 " model vdw 2.272 2.520 nonbonded pdb=" OE2 GLU D 454 " pdb=" NH1 ARG D 516 " model vdw 2.272 2.520 nonbonded pdb=" OD2 ASP C 137 " pdb=" NH1 ARG C 365 " model vdw 2.316 2.520 nonbonded pdb=" OD2 ASP A 137 " pdb=" NH1 ARG A 365 " model vdw 2.317 2.520 nonbonded pdb=" O HIS B 491 " pdb=" ND1 HIS B 526 " model vdw 2.380 2.520 ... (remaining 89802 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 15 through 32) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.210 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 38.760 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.020 0.809 12912 Z= 0.985 Angle : 1.939 109.481 17720 Z= 0.705 Chirality : 0.161 4.932 1998 Planarity : 0.006 0.098 2074 Dihedral : 15.709 168.407 5102 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -2.91 (0.20), residues: 1388 helix: -0.31 (0.20), residues: 608 sheet: -2.06 (0.37), residues: 186 loop : -3.72 (0.20), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 415 HIS 0.005 0.001 HIS C 378 PHE 0.014 0.001 PHE B 514 TYR 0.017 0.001 TYR A 266 ARG 0.005 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9052 (t0) cc_final: 0.8753 (t0) REVERT: B 469 THR cc_start: 0.8341 (m) cc_final: 0.7977 (t) REVERT: B 542 GLN cc_start: 0.5600 (mt0) cc_final: 0.5067 (mm-40) REVERT: B 552 MET cc_start: 0.8061 (tpt) cc_final: 0.7588 (tpp) REVERT: B 746 ASN cc_start: 0.8688 (m-40) cc_final: 0.8316 (m-40) REVERT: C 108 ASN cc_start: 0.9013 (t0) cc_final: 0.8684 (t0) REVERT: D 740 LYS cc_start: 0.7898 (mttp) cc_final: 0.7631 (tmtt) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2879 time to fit residues: 134.9235 Evaluate side-chains 161 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 84 optimal weight: 0.0070 chunk 130 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 338 HIS A 357 HIS A 378 HIS C 224 ASN C 357 HIS C 378 HIS D 505 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 12912 Z= 0.278 Angle : 1.519 85.497 17720 Z= 0.560 Chirality : 0.041 0.170 1998 Planarity : 0.005 0.049 2074 Dihedral : 18.957 148.810 2292 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.93 % Allowed : 10.99 % Favored : 87.08 % 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: -1.54 (0.22), residues: 1388 helix: 1.11 (0.22), residues: 604 sheet: -1.58 (0.42), residues: 154 loop : -3.18 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 415 HIS 0.003 0.001 HIS C 471 PHE 0.022 0.001 PHE B 513 TYR 0.012 0.001 TYR C 266 ARG 0.006 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8977 (t0) cc_final: 0.8691 (t0) REVERT: A 231 GLU cc_start: 0.7875 (tp30) cc_final: 0.7476 (tp30) REVERT: B 746 ASN cc_start: 0.8837 (m-40) cc_final: 0.8463 (m110) REVERT: C 108 ASN cc_start: 0.8967 (t0) cc_final: 0.8605 (t0) REVERT: C 231 GLU cc_start: 0.7676 (tp30) cc_final: 0.7340 (tp30) REVERT: C 263 GLU cc_start: 0.7421 (pt0) cc_final: 0.7214 (pt0) REVERT: D 518 MET cc_start: 0.8174 (mtp) cc_final: 0.7749 (mpp) outliers start: 23 outliers final: 15 residues processed: 188 average time/residue: 0.2434 time to fit residues: 66.3567 Evaluate side-chains 155 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 542 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.0030 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN C 165 ASN C 169 ASN C 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 12912 Z= 0.274 Angle : 1.499 82.071 17720 Z= 0.546 Chirality : 0.040 0.160 1998 Planarity : 0.005 0.050 2074 Dihedral : 18.842 149.142 2292 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.52 % Allowed : 12.25 % Favored : 85.23 % 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: -0.95 (0.23), residues: 1388 helix: 1.61 (0.22), residues: 606 sheet: -1.33 (0.42), residues: 158 loop : -2.89 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 415 HIS 0.002 0.001 HIS A 471 PHE 0.014 0.001 PHE B 513 TYR 0.013 0.001 TYR D 535 ARG 0.002 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8613 (mmm) cc_final: 0.8379 (mmt) REVERT: A 108 ASN cc_start: 0.8984 (t0) cc_final: 0.8700 (t0) REVERT: A 231 GLU cc_start: 0.7784 (tp30) cc_final: 0.7582 (tp30) REVERT: A 263 GLU cc_start: 0.7507 (pt0) cc_final: 0.7286 (pt0) REVERT: B 535 TYR cc_start: 0.8418 (m-80) cc_final: 0.6049 (m-80) REVERT: B 745 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7320 (ptt) REVERT: B 746 ASN cc_start: 0.8868 (m-40) cc_final: 0.8493 (m-40) REVERT: C 108 ASN cc_start: 0.8987 (t0) cc_final: 0.8573 (t0) REVERT: C 231 GLU cc_start: 0.7699 (tp30) cc_final: 0.7343 (tp30) REVERT: D 518 MET cc_start: 0.8253 (mtp) cc_final: 0.7875 (mpp) outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 0.2211 time to fit residues: 56.4606 Evaluate side-chains 149 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 409 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 139 optimal weight: 0.0030 chunk 68 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 12912 Z= 0.259 Angle : 1.500 82.486 17720 Z= 0.543 Chirality : 0.039 0.149 1998 Planarity : 0.004 0.050 2074 Dihedral : 18.801 151.353 2292 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.52 % Allowed : 13.26 % Favored : 84.23 % 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: -0.55 (0.23), residues: 1388 helix: 1.97 (0.22), residues: 604 sheet: -0.96 (0.40), residues: 170 loop : -2.78 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.003 0.001 HIS C 338 PHE 0.021 0.001 PHE D 777 TYR 0.010 0.001 TYR A 266 ARG 0.007 0.000 ARG B 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8628 (mmm) cc_final: 0.8373 (mmt) REVERT: A 108 ASN cc_start: 0.8986 (t0) cc_final: 0.8658 (t0) REVERT: B 746 ASN cc_start: 0.8816 (m-40) cc_final: 0.8522 (m110) REVERT: C 108 ASN cc_start: 0.9013 (t0) cc_final: 0.8587 (t0) REVERT: C 231 GLU cc_start: 0.7674 (tp30) cc_final: 0.7246 (tp30) REVERT: D 518 MET cc_start: 0.8035 (mtp) cc_final: 0.7796 (mpp) outliers start: 30 outliers final: 21 residues processed: 177 average time/residue: 0.2236 time to fit residues: 59.2745 Evaluate side-chains 160 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 ASP Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN C 45 HIS ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 12912 Z= 0.324 Angle : 1.513 82.236 17720 Z= 0.556 Chirality : 0.040 0.146 1998 Planarity : 0.005 0.051 2074 Dihedral : 18.699 152.395 2292 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.85 % Allowed : 13.67 % Favored : 83.47 % 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: -0.50 (0.23), residues: 1388 helix: 1.91 (0.22), residues: 608 sheet: -0.87 (0.40), residues: 166 loop : -2.66 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.003 0.001 HIS C 132 PHE 0.027 0.002 PHE B 777 TYR 0.016 0.001 TYR D 535 ARG 0.014 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8714 (mmm) cc_final: 0.8507 (mmt) REVERT: A 108 ASN cc_start: 0.9043 (t0) cc_final: 0.8689 (t0) REVERT: A 231 GLU cc_start: 0.7771 (tp30) cc_final: 0.7393 (tp30) REVERT: B 746 ASN cc_start: 0.8873 (m-40) cc_final: 0.8542 (m110) REVERT: C 108 ASN cc_start: 0.9033 (t0) cc_final: 0.8597 (t0) REVERT: C 231 GLU cc_start: 0.7754 (tp30) cc_final: 0.7406 (tp30) REVERT: D 493 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8598 (mt) REVERT: D 518 MET cc_start: 0.8190 (mtp) cc_final: 0.7903 (mpp) REVERT: D 745 MET cc_start: 0.7867 (ptt) cc_final: 0.7648 (ptt) outliers start: 34 outliers final: 26 residues processed: 161 average time/residue: 0.2196 time to fit residues: 53.6226 Evaluate side-chains 166 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 409 ASP Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 12912 Z= 0.275 Angle : 1.507 82.169 17720 Z= 0.548 Chirality : 0.039 0.141 1998 Planarity : 0.005 0.050 2074 Dihedral : 18.653 153.073 2292 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.52 % Allowed : 14.85 % Favored : 82.63 % 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: -0.26 (0.23), residues: 1388 helix: 2.15 (0.22), residues: 602 sheet: -0.59 (0.44), residues: 146 loop : -2.53 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.003 0.001 HIS A 471 PHE 0.019 0.001 PHE B 777 TYR 0.011 0.001 TYR A 266 ARG 0.007 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8704 (mmm) cc_final: 0.8500 (mmt) REVERT: A 108 ASN cc_start: 0.9017 (t0) cc_final: 0.8670 (t0) REVERT: A 231 GLU cc_start: 0.7768 (tp30) cc_final: 0.7354 (tp30) REVERT: B 493 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8596 (mt) REVERT: B 746 ASN cc_start: 0.8861 (m-40) cc_final: 0.8492 (m110) REVERT: C 108 ASN cc_start: 0.9040 (t0) cc_final: 0.8596 (t0) REVERT: C 231 GLU cc_start: 0.7742 (tp30) cc_final: 0.7356 (tp30) REVERT: D 493 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8617 (mt) REVERT: D 518 MET cc_start: 0.8150 (mtp) cc_final: 0.7849 (mpp) outliers start: 30 outliers final: 22 residues processed: 169 average time/residue: 0.2183 time to fit residues: 55.6544 Evaluate side-chains 165 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 409 ASP Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 12912 Z= 0.276 Angle : 1.507 82.136 17720 Z= 0.547 Chirality : 0.039 0.156 1998 Planarity : 0.004 0.050 2074 Dihedral : 18.564 153.942 2292 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.60 % Allowed : 15.18 % Favored : 82.21 % 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: -0.13 (0.23), residues: 1388 helix: 2.25 (0.22), residues: 602 sheet: -0.66 (0.43), residues: 150 loop : -2.43 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.002 0.001 HIS A 471 PHE 0.019 0.001 PHE B 777 TYR 0.010 0.001 TYR A 266 ARG 0.006 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9025 (t0) cc_final: 0.8680 (t0) REVERT: A 231 GLU cc_start: 0.7768 (tp30) cc_final: 0.7355 (tp30) REVERT: B 493 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8603 (mt) REVERT: B 746 ASN cc_start: 0.8831 (m-40) cc_final: 0.8538 (m110) REVERT: C 108 ASN cc_start: 0.9055 (t0) cc_final: 0.8620 (t0) REVERT: C 135 MET cc_start: 0.8775 (mtm) cc_final: 0.8574 (mtm) REVERT: C 209 MET cc_start: 0.8259 (tpt) cc_final: 0.7939 (tpp) REVERT: C 231 GLU cc_start: 0.7749 (tp30) cc_final: 0.7335 (tp30) REVERT: C 263 GLU cc_start: 0.7457 (pt0) cc_final: 0.7214 (pt0) REVERT: D 493 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8614 (mt) REVERT: D 518 MET cc_start: 0.8184 (mtp) cc_final: 0.7877 (mpp) outliers start: 31 outliers final: 24 residues processed: 163 average time/residue: 0.2111 time to fit residues: 52.2104 Evaluate side-chains 172 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain D residue 409 ASP Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 759 SER Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 0.0970 chunk 41 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 12912 Z= 0.266 Angle : 1.502 82.096 17720 Z= 0.544 Chirality : 0.039 0.152 1998 Planarity : 0.004 0.049 2074 Dihedral : 18.393 155.150 2292 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.77 % Allowed : 14.93 % Favored : 82.30 % 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: -0.01 (0.23), residues: 1388 helix: 2.31 (0.22), residues: 604 sheet: -0.79 (0.39), residues: 170 loop : -2.33 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.002 0.001 HIS A 471 PHE 0.018 0.001 PHE B 777 TYR 0.009 0.001 TYR A 266 ARG 0.006 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9039 (t0) cc_final: 0.8695 (t0) REVERT: A 231 GLU cc_start: 0.7752 (tp30) cc_final: 0.7491 (tp30) REVERT: B 493 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8567 (mt) REVERT: B 746 ASN cc_start: 0.8815 (m-40) cc_final: 0.8461 (m110) REVERT: C 108 ASN cc_start: 0.9072 (t0) cc_final: 0.8627 (t0) REVERT: C 209 MET cc_start: 0.8234 (tpt) cc_final: 0.7899 (tpp) REVERT: C 231 GLU cc_start: 0.7732 (tp30) cc_final: 0.7309 (tp30) REVERT: C 263 GLU cc_start: 0.7442 (pt0) cc_final: 0.7219 (pt0) REVERT: D 493 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8572 (mt) REVERT: D 518 MET cc_start: 0.8169 (mtp) cc_final: 0.7886 (mpp) REVERT: D 523 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8778 (tp30) outliers start: 33 outliers final: 24 residues processed: 177 average time/residue: 0.2139 time to fit residues: 57.2400 Evaluate side-chains 167 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 409 ASP Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 759 SER Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.0000 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 77 optimal weight: 0.0470 chunk 56 optimal weight: 0.0370 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 12912 Z= 0.258 Angle : 1.510 82.124 17720 Z= 0.546 Chirality : 0.039 0.154 1998 Planarity : 0.004 0.048 2074 Dihedral : 18.268 156.651 2292 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.01 % Allowed : 16.02 % Favored : 81.96 % 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: 0.24 (0.23), residues: 1388 helix: 2.46 (0.22), residues: 596 sheet: -0.36 (0.41), residues: 160 loop : -2.13 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.002 0.000 HIS D 491 PHE 0.027 0.001 PHE D 777 TYR 0.006 0.001 TYR A 266 ARG 0.006 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9018 (t0) cc_final: 0.8661 (t0) REVERT: A 231 GLU cc_start: 0.7723 (tp30) cc_final: 0.7461 (tp30) REVERT: A 250 VAL cc_start: 0.8697 (t) cc_final: 0.8465 (p) REVERT: B 490 TYR cc_start: 0.7519 (m-80) cc_final: 0.7280 (m-80) REVERT: B 756 ASP cc_start: 0.8556 (t0) cc_final: 0.8183 (t0) REVERT: C 108 ASN cc_start: 0.9100 (t0) cc_final: 0.8691 (t0) REVERT: C 209 MET cc_start: 0.8169 (tpt) cc_final: 0.7890 (tpp) REVERT: C 231 GLU cc_start: 0.7699 (tp30) cc_final: 0.7241 (tp30) REVERT: C 250 VAL cc_start: 0.8658 (t) cc_final: 0.8423 (p) REVERT: C 263 GLU cc_start: 0.7370 (pt0) cc_final: 0.7163 (pt0) REVERT: D 518 MET cc_start: 0.8110 (mtp) cc_final: 0.7810 (mpp) outliers start: 24 outliers final: 19 residues processed: 192 average time/residue: 0.2236 time to fit residues: 64.0568 Evaluate side-chains 169 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 483 TYR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 759 SER Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 0.0670 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 0.0050 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 12912 Z= 0.264 Angle : 1.505 82.108 17720 Z= 0.545 Chirality : 0.039 0.155 1998 Planarity : 0.004 0.049 2074 Dihedral : 18.251 157.216 2292 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.43 % Allowed : 16.44 % Favored : 82.13 % 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: 0.35 (0.23), residues: 1388 helix: 2.60 (0.23), residues: 584 sheet: -0.16 (0.41), residues: 156 loop : -2.06 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 415 HIS 0.002 0.001 HIS C 338 PHE 0.027 0.001 PHE D 777 TYR 0.008 0.001 TYR A 266 ARG 0.006 0.000 ARG D 738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9034 (t0) cc_final: 0.8675 (t0) REVERT: A 209 MET cc_start: 0.8237 (tpt) cc_final: 0.7915 (tpp) REVERT: A 231 GLU cc_start: 0.7762 (tp30) cc_final: 0.7461 (tp30) REVERT: A 250 VAL cc_start: 0.8693 (t) cc_final: 0.8442 (p) REVERT: B 490 TYR cc_start: 0.7586 (m-80) cc_final: 0.7327 (m-80) REVERT: B 746 ASN cc_start: 0.8744 (m-40) cc_final: 0.8407 (m110) REVERT: C 108 ASN cc_start: 0.9092 (t0) cc_final: 0.8677 (t0) REVERT: C 209 MET cc_start: 0.8187 (tpt) cc_final: 0.7916 (tpp) REVERT: C 231 GLU cc_start: 0.7712 (tp30) cc_final: 0.7262 (tp30) REVERT: C 250 VAL cc_start: 0.8644 (t) cc_final: 0.8420 (p) REVERT: C 263 GLU cc_start: 0.7375 (pt0) cc_final: 0.7169 (pt0) REVERT: D 518 MET cc_start: 0.8182 (mtp) cc_final: 0.7847 (mpp) outliers start: 17 outliers final: 16 residues processed: 166 average time/residue: 0.2147 time to fit residues: 54.0716 Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 542 GLN Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 117 optimal weight: 0.0670 chunk 14 optimal weight: 0.0040 chunk 21 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 overall best weight: 0.2330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099702 restraints weight = 29996.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101987 restraints weight = 17472.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103556 restraints weight = 11981.220| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 12912 Z= 0.261 Angle : 1.510 82.064 17720 Z= 0.545 Chirality : 0.039 0.159 1998 Planarity : 0.004 0.048 2074 Dihedral : 18.194 157.718 2292 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.59 % Allowed : 16.78 % Favored : 81.63 % 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: 0.44 (0.23), residues: 1388 helix: 2.53 (0.22), residues: 594 sheet: 0.18 (0.42), residues: 152 loop : -2.01 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 415 HIS 0.002 0.000 HIS C 338 PHE 0.025 0.001 PHE D 777 TYR 0.008 0.001 TYR A 266 ARG 0.006 0.000 ARG D 738 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.62 seconds wall clock time: 46 minutes 29.07 seconds (2789.07 seconds total)