Starting phenix.real_space_refine on Sat Dec 9 22:43:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_4909_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_4909.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_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_4909/12_2023/6rks_4909_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_4909_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_4909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_4909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_4909_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rks_4909/12_2023/6rks_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.18, per 1000 atoms: 0.57 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: 5.50 Conformation dependent library (CDL) restraints added in 2.1 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: 5.64 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: 4.22 Time building geometry restraints manager: 5.89 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: 2.150 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: 9.720 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.780 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.770 ------------------------------------------------------------------------------- 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 : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2920 time to fit residues: 137.2763 Evaluate side-chains 158 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9413 ------------------------------------------------------------------------------- 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: 0.1980 chunk 130 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 319 ASN C 357 HIS C 378 HIS D 505 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 12912 Z= 0.274 Angle : 1.532 86.716 17720 Z= 0.565 Chirality : 0.041 0.170 1998 Planarity : 0.005 0.047 2074 Dihedral : 18.952 148.704 2292 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.01 % Allowed : 10.99 % Favored : 87.00 % 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: -1.59 (0.22), residues: 1388 helix: 1.03 (0.22), residues: 606 sheet: -1.58 (0.42), residues: 154 loop : -3.19 (0.20), residues: 628 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 0.030 0.001 TYR B 535 ARG 0.005 0.000 ARG D 413 *********************** 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 192 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 183 average time/residue: 0.2402 time to fit residues: 63.8415 Evaluate side-chains 144 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1141 time to fit residues: 4.9391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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 A 319 ASN B 746 ASN ** 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: 0.8342 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 12912 Z= 0.274 Angle : 1.499 82.314 17720 Z= 0.546 Chirality : 0.040 0.146 1998 Planarity : 0.005 0.050 2074 Dihedral : 18.836 149.219 2292 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.93 % Allowed : 12.50 % Favored : 85.57 % 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: -0.85 (0.23), residues: 1388 helix: 1.67 (0.22), residues: 610 sheet: -1.20 (0.40), residues: 170 loop : -2.88 (0.22), residues: 608 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 0.012 0.001 TYR C 266 ARG 0.003 0.000 ARG B 788 *********************** 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 171 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.416 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: 23 outliers final: 13 residues processed: 166 average time/residue: 0.2319 time to fit residues: 57.7004 Evaluate side-chains 141 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1148 time to fit residues: 4.6524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 139 optimal weight: 0.0050 chunk 68 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3019 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= 0.271 Angle : 1.506 82.386 17720 Z= 0.548 Chirality : 0.039 0.165 1998 Planarity : 0.005 0.050 2074 Dihedral : 18.779 151.163 2292 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.01 % Allowed : 13.42 % Favored : 85.57 % 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: -0.54 (0.23), residues: 1388 helix: 1.93 (0.22), residues: 606 sheet: -0.94 (0.40), residues: 170 loop : -2.72 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.005 0.001 HIS A 45 PHE 0.022 0.001 PHE D 777 TYR 0.011 0.001 TYR A 266 ARG 0.007 0.000 ARG B 788 *********************** 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 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 159 average time/residue: 0.2374 time to fit residues: 56.6871 Evaluate side-chains 148 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1239 time to fit residues: 3.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 169 ASN C 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3228 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= 0.274 Angle : 1.496 82.227 17720 Z= 0.543 Chirality : 0.039 0.147 1998 Planarity : 0.004 0.050 2074 Dihedral : 18.709 152.413 2292 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.76 % Allowed : 14.18 % Favored : 85.07 % 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: -0.28 (0.23), residues: 1388 helix: 2.14 (0.22), residues: 604 sheet: -0.76 (0.40), residues: 170 loop : -2.57 (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 C 338 PHE 0.018 0.001 PHE D 777 TYR 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG A 309 *********************** 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 159 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 157 average time/residue: 0.2298 time to fit residues: 54.9158 Evaluate side-chains 144 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1156 time to fit residues: 3.1857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 12912 Z= 0.359 Angle : 1.534 82.072 17720 Z= 0.569 Chirality : 0.041 0.173 1998 Planarity : 0.005 0.051 2074 Dihedral : 18.623 153.281 2292 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.01 % Allowed : 14.68 % Favored : 83.31 % 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: -0.51 (0.23), residues: 1388 helix: 1.89 (0.22), residues: 604 sheet: -0.76 (0.41), residues: 156 loop : -2.65 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 415 HIS 0.004 0.001 HIS C 132 PHE 0.026 0.002 PHE B 777 TYR 0.017 0.002 TYR A 266 ARG 0.006 0.001 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 169 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 159 average time/residue: 0.2257 time to fit residues: 54.4412 Evaluate side-chains 154 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1210 time to fit residues: 5.7350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8356 moved from start: 0.3551 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= 0.268 Angle : 1.511 82.130 17720 Z= 0.550 Chirality : 0.039 0.173 1998 Planarity : 0.004 0.049 2074 Dihedral : 18.541 153.789 2292 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.25 % Allowed : 15.86 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1388 helix: 2.30 (0.22), residues: 594 sheet: -0.67 (0.41), residues: 160 loop : -2.36 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.004 0.001 HIS C 338 PHE 0.020 0.001 PHE B 777 TYR 0.009 0.001 TYR A 266 ARG 0.004 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 157 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 155 average time/residue: 0.2233 time to fit residues: 52.9173 Evaluate side-chains 145 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1373 time to fit residues: 2.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.193 12912 Z= 0.324 Angle : 1.524 81.986 17720 Z= 0.559 Chirality : 0.040 0.155 1998 Planarity : 0.005 0.051 2074 Dihedral : 18.453 154.452 2292 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.59 % Allowed : 16.86 % Favored : 82.55 % 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: -0.20 (0.23), residues: 1388 helix: 2.13 (0.22), residues: 604 sheet: -0.56 (0.41), residues: 156 loop : -2.46 (0.22), residues: 628 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 0.021 0.001 PHE B 777 TYR 0.014 0.001 TYR A 266 ARG 0.005 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 143 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 140 average time/residue: 0.2215 time to fit residues: 47.6415 Evaluate side-chains 139 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1207 time to fit residues: 2.6790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.0170 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 0.0670 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** 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: 0.8340 moved from start: 0.3796 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= 0.266 Angle : 1.514 81.985 17720 Z= 0.550 Chirality : 0.039 0.165 1998 Planarity : 0.004 0.049 2074 Dihedral : 18.327 155.178 2292 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.42 % Allowed : 17.28 % 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: 0.12 (0.23), residues: 1388 helix: 2.42 (0.22), residues: 594 sheet: -0.33 (0.41), residues: 156 loop : -2.27 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.002 0.001 HIS C 262 PHE 0.019 0.001 PHE B 777 TYR 0.008 0.001 TYR C 266 ARG 0.005 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 153 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 152 average time/residue: 0.2273 time to fit residues: 52.5768 Evaluate side-chains 142 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1286 time to fit residues: 2.2314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 132 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** 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: 0.8357 moved from start: 0.3848 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= 0.275 Angle : 1.518 82.054 17720 Z= 0.552 Chirality : 0.039 0.156 1998 Planarity : 0.004 0.049 2074 Dihedral : 18.261 155.982 2292 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.17 % Allowed : 17.62 % 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: 0.18 (0.23), residues: 1388 helix: 2.38 (0.22), residues: 606 sheet: -0.26 (0.42), residues: 156 loop : -2.24 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.002 0.001 HIS C 262 PHE 0.030 0.001 PHE D 777 TYR 0.010 0.001 TYR A 266 ARG 0.005 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 143 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 142 average time/residue: 0.2351 time to fit residues: 50.1149 Evaluate side-chains 140 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1345 time to fit residues: 2.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.0050 chunk 100 optimal weight: 0.0010 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 169 ASN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096576 restraints weight = 29851.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098802 restraints weight = 17373.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100390 restraints weight = 11942.190| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4002 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= 0.263 Angle : 1.514 82.043 17720 Z= 0.549 Chirality : 0.039 0.176 1998 Planarity : 0.004 0.049 2074 Dihedral : 18.192 156.680 2292 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.08 % Allowed : 17.87 % Favored : 82.05 % 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: 0.40 (0.23), residues: 1388 helix: 2.57 (0.22), residues: 596 sheet: -0.12 (0.41), residues: 156 loop : -2.05 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.003 0.001 HIS A 339 PHE 0.028 0.001 PHE D 777 TYR 0.009 0.001 TYR C 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: 2372.35 seconds wall clock time: 45 minutes 56.17 seconds (2756.17 seconds total)