Starting phenix.real_space_refine on Fri Mar 15 06:55:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ag8_11776/03_2024/7ag8_11776_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ag8_11776/03_2024/7ag8_11776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ag8_11776/03_2024/7ag8_11776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ag8_11776/03_2024/7ag8_11776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ag8_11776/03_2024/7ag8_11776_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ag8_11776/03_2024/7ag8_11776_updated.pdb" } resolution = 2.68 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= 0.001 sd= 0.086 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 Fe 2 7.16 5 S 38 5.16 5 C 6956 2.51 5 N 1867 2.21 5 O 2059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 94": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 588": "OE1" <-> "OE2" Residue "B ARG 740": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10922 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5364 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5356 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 45, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 702, 5356 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 45, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 5495 Chain: "B" Number of atoms: 5472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 715, 5464 Classifications: {'peptide': 715} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 46, 'TRANS': 668} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 715, 5464 Classifications: {'peptide': 715} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 46, 'TRANS': 668} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 5605 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.47, per 1000 atoms: 0.96 Number of scatterers: 10922 At special positions: 0 Unit cell: (84.66, 97.11, 124.5, 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) Fe 2 26.01 S 38 16.00 O 2059 8.00 N 1867 7.00 C 6956 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 3.8 seconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 4 sheets defined 44.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.709A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.579A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.691A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.921A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 388 through 399 removed outlier: 3.889A pdb=" N ARG A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 417 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.593A pdb=" N ALA A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 503 No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 513 through 530 removed outlier: 3.751A pdb=" N SER A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 559 Processing helix chain 'A' and resid 581 through 587 removed outlier: 4.541A pdb=" N VAL A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 621 through 634 removed outlier: 4.143A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 693 through 700 removed outlier: 4.286A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.686A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.545A pdb=" N HIS B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 64 through 70 removed outlier: 4.351A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 141 through 158 removed outlier: 3.655A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Proline residue: B 150 - end of helix removed outlier: 3.716A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 175 removed outlier: 3.643A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.675A pdb=" N MET B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 401 through 416 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 469 through 480 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 516 through 529 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 581 through 587 removed outlier: 4.466A pdb=" N VAL B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 621 through 633 removed outlier: 3.875A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 693 through 700 removed outlier: 4.542A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 711 removed outlier: 3.529A pdb=" N ALA B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 732 Processing sheet with id= A, first strand: chain 'A' and resid 341 through 345 Processing sheet with id= B, first strand: chain 'A' and resid 667 through 670 Processing sheet with id= C, first strand: chain 'B' and resid 342 through 345 Processing sheet with id= D, first strand: chain 'B' and resid 667 through 670 320 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 3705 1.36 - 1.53: 7218 1.53 - 1.71: 233 1.71 - 1.88: 72 1.88 - 2.05: 8 Bond restraints: 11236 Sorted by residual: bond pdb=" C ALA B 130 " pdb=" N PRO B 131 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" C PRO B 89 " pdb=" O PRO B 89 " ideal model delta sigma weight residual 1.238 1.189 0.049 1.33e-02 5.65e+03 1.35e+01 bond pdb=" CA ALA A 93 " pdb=" CB ALA A 93 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.48e-02 4.57e+03 1.32e+01 bond pdb=" C TYR B 98 " pdb=" O TYR B 98 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.19e+01 bond pdb=" N ASN B 133 " pdb=" CA ASN B 133 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.89e+00 ... (remaining 11231 not shown) Histogram of bond angle deviations from ideal: 89.33 - 107.29: 545 107.29 - 125.26: 14435 125.26 - 143.22: 375 143.22 - 161.18: 0 161.18 - 179.14: 4 Bond angle restraints: 15359 Sorted by residual: angle pdb=" C PRO B 89 " pdb=" CA PRO B 89 " pdb=" CB PRO B 89 " ideal model delta sigma weight residual 112.26 104.55 7.71 1.67e+00 3.59e-01 2.13e+01 angle pdb=" N ASN B 133 " pdb=" CA ASN B 133 " pdb=" CB ASN B 133 " ideal model delta sigma weight residual 110.49 117.88 -7.39 1.69e+00 3.50e-01 1.91e+01 angle pdb=" CA TRP A 91 " pdb=" C TRP A 91 " pdb=" N PRO A 92 " ideal model delta sigma weight residual 117.57 121.35 -3.78 8.70e-01 1.32e+00 1.88e+01 angle pdb=" CA TRP B 91 " pdb=" C TRP B 91 " pdb=" O TRP B 91 " ideal model delta sigma weight residual 121.34 117.37 3.97 9.40e-01 1.13e+00 1.78e+01 angle pdb=" N PRO B 89 " pdb=" CA PRO B 89 " pdb=" C PRO B 89 " ideal model delta sigma weight residual 113.81 119.72 -5.91 1.45e+00 4.76e-01 1.66e+01 ... (remaining 15354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5988 17.75 - 35.51: 425 35.51 - 53.26: 58 53.26 - 71.02: 24 71.02 - 88.77: 10 Dihedral angle restraints: 6505 sinusoidal: 2510 harmonic: 3995 Sorted by residual: dihedral pdb=" CA TYR B 28 " pdb=" C TYR B 28 " pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE A 129 " pdb=" C PHE A 129 " pdb=" N ALA A 130 " pdb=" CA ALA A 130 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLY B 451 " pdb=" C GLY B 451 " pdb=" N GLU B 452 " pdb=" CA GLU B 452 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 6502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1243 0.051 - 0.102: 315 0.102 - 0.152: 48 0.152 - 0.203: 2 0.203 - 0.254: 3 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" C PRO A 92 " pdb=" CB PRO A 92 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TYR A 98 " pdb=" N TYR A 98 " pdb=" C TYR A 98 " pdb=" CB TYR A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ASN B 133 " pdb=" N ASN B 133 " pdb=" C ASN B 133 " pdb=" CB ASN B 133 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1608 not shown) Planarity restraints: 2023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 130 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO B 131 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 95 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C TYR A 95 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A 95 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 96 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 133 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C ASN B 133 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 133 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 134 " -0.014 2.00e-02 2.50e+03 ... (remaining 2020 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1836 2.76 - 3.29: 10533 3.29 - 3.83: 18822 3.83 - 4.36: 23387 4.36 - 4.90: 39557 Nonbonded interactions: 94135 Sorted by model distance: nonbonded pdb=" OH TYR B 337 " pdb=" OG1 THR B 394 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR A 337 " pdb=" OG1 THR A 394 " model vdw 2.227 2.440 nonbonded pdb=" NZ LYS B 274 " pdb=" O THR B 275 " model vdw 2.285 2.520 nonbonded pdb=" NH1 ARG A 146 " pdb=" O MET A 296 " model vdw 2.295 2.520 nonbonded pdb=" O MET B 420 " pdb=" NH1 ARG B 425 " model vdw 2.305 2.520 ... (remaining 94130 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' and (resid 26 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 355 or (resid 356 and (name N or n \ ame CA or name C or name O or name CB )) or resid 357 through 417 or resid 419 t \ hrough 512 or (resid 513 and (name N or name CA or name C or name O or name CB ) \ ) or resid 514 through 714 or (resid 715 through 716 and (name N or name CA or n \ ame C or name O or name CB )) or resid 717 through 740 or resid 801)) selection = (chain 'B' and (resid 26 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 202 or (resid 203 and (name N o \ r name CA or name C or name O or name CB )) or resid 204 through 205 or resid 22 \ 1 through 417 or resid 419 through 515 or (resid 516 and (name N or name CA or n \ ame C or name O or name CB )) or resid 517 through 556 or (resid 557 through 559 \ and (name N or name CA or name C or name O or name CB )) or resid 560 through 5 \ 89 or (resid 590 through 591 and (name N or name CA or name C or name O or name \ CB )) or resid 592 through 740 or resid 801)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 5.730 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 37.630 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 59.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.005 0.076 11236 Z= 0.312 Angle : 0.647 8.212 15359 Z= 0.376 Chirality : 0.045 0.254 1611 Planarity : 0.005 0.078 2023 Dihedral : 13.126 88.772 3969 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 0.37 % Allowed : 0.27 % Favored : 99.36 % 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: -0.60 (0.21), residues: 1413 helix: 0.56 (0.22), residues: 584 sheet: -0.45 (1.18), residues: 20 loop : -1.14 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 107 HIS 0.004 0.001 HIS A 49 PHE 0.008 0.001 PHE A 167 TYR 0.015 0.001 TYR B 98 ARG 0.002 0.000 ARG B 736 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.301 Fit side-chains REVERT: A 82 GLU cc_start: 0.7071 (pp20) cc_final: 0.6859 (pp20) REVERT: A 94 ASP cc_start: 0.7954 (m-30) cc_final: 0.7748 (m-30) REVERT: A 225 MET cc_start: 0.4987 (pmm) cc_final: 0.3309 (ptm) REVERT: A 392 ARG cc_start: 0.6911 (ptp-110) cc_final: 0.6698 (mtm110) REVERT: B 304 TYR cc_start: 0.7422 (t80) cc_final: 0.6796 (t80) REVERT: B 663 ASP cc_start: 0.7672 (t0) cc_final: 0.7409 (t0) REVERT: B 703 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6870 (mp0) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 1.2604 time to fit residues: 136.7285 Evaluate side-chains 77 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 97 HIS ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11236 Z= 0.218 Angle : 0.547 9.601 15359 Z= 0.266 Chirality : 0.042 0.155 1611 Planarity : 0.004 0.051 2023 Dihedral : 5.556 74.176 1549 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 0.82 % Allowed : 4.58 % Favored : 94.60 % 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: -0.38 (0.21), residues: 1413 helix: 0.84 (0.22), residues: 575 sheet: -0.67 (0.93), residues: 30 loop : -1.07 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.004 0.001 HIS A 49 PHE 0.008 0.001 PHE B 129 TYR 0.020 0.001 TYR B 155 ARG 0.002 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.242 Fit side-chains REVERT: A 82 GLU cc_start: 0.7169 (pp20) cc_final: 0.6967 (pp20) REVERT: A 225 MET cc_start: 0.4928 (pmm) cc_final: 0.3103 (ptm) REVERT: A 607 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: B 304 TYR cc_start: 0.7452 (t80) cc_final: 0.6775 (t80) REVERT: B 663 ASP cc_start: 0.7682 (t0) cc_final: 0.7425 (t0) REVERT: B 703 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6831 (mp0) outliers start: 6 outliers final: 2 residues processed: 86 average time/residue: 1.1496 time to fit residues: 108.6313 Evaluate side-chains 81 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 128 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11236 Z= 0.299 Angle : 0.569 10.093 15359 Z= 0.277 Chirality : 0.044 0.148 1611 Planarity : 0.004 0.043 2023 Dihedral : 5.539 74.118 1547 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.46 % Rotamer: Outliers : 1.37 % Allowed : 4.67 % Favored : 93.96 % 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: -0.37 (0.21), residues: 1413 helix: 0.86 (0.22), residues: 570 sheet: -0.56 (0.93), residues: 30 loop : -1.07 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 341 HIS 0.005 0.001 HIS B 49 PHE 0.018 0.001 PHE B 129 TYR 0.017 0.002 TYR B 155 ARG 0.004 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.272 Fit side-chains REVERT: A 225 MET cc_start: 0.4918 (pmm) cc_final: 0.3126 (ptm) REVERT: A 392 ARG cc_start: 0.6816 (mtm110) cc_final: 0.6088 (mtt180) REVERT: B 304 TYR cc_start: 0.7438 (t80) cc_final: 0.6787 (t80) outliers start: 12 outliers final: 6 residues processed: 88 average time/residue: 1.1564 time to fit residues: 111.3231 Evaluate side-chains 84 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11236 Z= 0.182 Angle : 0.515 10.130 15359 Z= 0.248 Chirality : 0.041 0.131 1611 Planarity : 0.004 0.041 2023 Dihedral : 5.235 73.026 1547 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 1.10 % Allowed : 5.77 % Favored : 93.13 % 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: -0.14 (0.21), residues: 1413 helix: 1.12 (0.22), residues: 562 sheet: -0.38 (0.94), residues: 30 loop : -0.97 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.003 0.001 HIS A 49 PHE 0.012 0.001 PHE B 129 TYR 0.014 0.001 TYR B 155 ARG 0.002 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.281 Fit side-chains REVERT: A 225 MET cc_start: 0.4965 (pmm) cc_final: 0.3191 (ptm) REVERT: A 392 ARG cc_start: 0.6733 (mtm110) cc_final: 0.6069 (mtt180) REVERT: A 607 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: B 304 TYR cc_start: 0.7404 (t80) cc_final: 0.6663 (t80) REVERT: B 703 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6868 (mp0) outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 1.2079 time to fit residues: 114.0406 Evaluate side-chains 85 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 0.0770 chunk 116 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11236 Z= 0.160 Angle : 0.502 9.924 15359 Z= 0.240 Chirality : 0.040 0.129 1611 Planarity : 0.004 0.041 2023 Dihedral : 5.119 73.008 1547 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 1.10 % Allowed : 6.78 % Favored : 92.12 % 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 (0.22), residues: 1413 helix: 1.16 (0.22), residues: 572 sheet: -0.13 (0.95), residues: 30 loop : -0.88 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.004 0.001 HIS A 108 PHE 0.010 0.001 PHE B 129 TYR 0.013 0.001 TYR B 155 ARG 0.001 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.228 Fit side-chains REVERT: A 225 MET cc_start: 0.4880 (pmm) cc_final: 0.3113 (ptm) REVERT: A 392 ARG cc_start: 0.6713 (mtm110) cc_final: 0.6076 (mtt180) REVERT: A 607 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: B 107 TRP cc_start: 0.6870 (OUTLIER) cc_final: 0.6623 (t60) REVERT: B 304 TYR cc_start: 0.7400 (t80) cc_final: 0.6671 (t80) REVERT: B 703 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6840 (mp0) outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 1.1638 time to fit residues: 107.1438 Evaluate side-chains 83 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11236 Z= 0.193 Angle : 0.512 9.977 15359 Z= 0.245 Chirality : 0.041 0.129 1611 Planarity : 0.004 0.041 2023 Dihedral : 5.134 72.737 1547 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 1.19 % Allowed : 6.87 % Favored : 91.94 % 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 (0.22), residues: 1413 helix: 1.21 (0.22), residues: 566 sheet: 0.07 (0.97), residues: 30 loop : -0.88 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 107 HIS 0.004 0.001 HIS A 108 PHE 0.013 0.001 PHE B 129 TYR 0.015 0.001 TYR B 155 ARG 0.002 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 1.145 Fit side-chains REVERT: A 225 MET cc_start: 0.5024 (pmm) cc_final: 0.4807 (pmm) REVERT: A 392 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6103 (mtt180) REVERT: A 607 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: B 304 TYR cc_start: 0.7373 (t80) cc_final: 0.6655 (t80) REVERT: B 703 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6843 (mp0) outliers start: 10 outliers final: 9 residues processed: 82 average time/residue: 1.1847 time to fit residues: 106.2282 Evaluate side-chains 86 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11236 Z= 0.172 Angle : 0.502 10.021 15359 Z= 0.239 Chirality : 0.041 0.127 1611 Planarity : 0.004 0.040 2023 Dihedral : 5.059 72.289 1547 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 1.37 % Allowed : 6.96 % Favored : 91.67 % 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: 0.11 (0.22), residues: 1413 helix: 1.26 (0.22), residues: 568 sheet: 1.14 (1.13), residues: 20 loop : -0.82 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 107 HIS 0.004 0.001 HIS A 108 PHE 0.011 0.001 PHE B 129 TYR 0.014 0.001 TYR B 155 ARG 0.001 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.219 Fit side-chains REVERT: A 392 ARG cc_start: 0.6710 (mtm110) cc_final: 0.6099 (mtt180) REVERT: A 607 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 304 TYR cc_start: 0.7389 (t80) cc_final: 0.6681 (t80) REVERT: B 693 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7671 (mtp85) REVERT: B 703 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6835 (mp0) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 1.1541 time to fit residues: 108.4321 Evaluate side-chains 88 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11236 Z= 0.216 Angle : 0.521 10.067 15359 Z= 0.250 Chirality : 0.042 0.134 1611 Planarity : 0.004 0.041 2023 Dihedral : 5.165 72.353 1547 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 1.37 % Allowed : 7.05 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1413 helix: 1.19 (0.22), residues: 568 sheet: 1.00 (1.15), residues: 20 loop : -0.83 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 107 HIS 0.004 0.001 HIS B 49 PHE 0.015 0.001 PHE B 129 TYR 0.016 0.001 TYR B 155 ARG 0.002 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.026 Fit side-chains REVERT: A 607 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: B 304 TYR cc_start: 0.7389 (t80) cc_final: 0.6668 (t80) REVERT: B 675 ASP cc_start: 0.7307 (m-30) cc_final: 0.7061 (t0) REVERT: B 703 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6847 (mp0) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 1.1223 time to fit residues: 105.6359 Evaluate side-chains 86 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 97 HIS ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11236 Z= 0.281 Angle : 0.546 10.169 15359 Z= 0.264 Chirality : 0.043 0.144 1611 Planarity : 0.004 0.042 2023 Dihedral : 5.353 72.121 1547 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 1.28 % Allowed : 7.23 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1413 helix: 1.04 (0.22), residues: 569 sheet: 0.89 (1.14), residues: 20 loop : -0.87 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 107 HIS 0.005 0.001 HIS B 49 PHE 0.018 0.001 PHE B 129 TYR 0.018 0.001 TYR B 155 ARG 0.004 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.206 Fit side-chains REVERT: A 392 ARG cc_start: 0.6720 (mtm110) cc_final: 0.6151 (mtt180) REVERT: B 304 TYR cc_start: 0.7373 (t80) cc_final: 0.6625 (t80) REVERT: B 663 ASP cc_start: 0.7500 (t0) cc_final: 0.7300 (t0) REVERT: B 703 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6871 (mp0) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 1.1917 time to fit residues: 110.6415 Evaluate side-chains 86 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 129 optimal weight: 0.0170 chunk 111 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11236 Z= 0.140 Angle : 0.496 9.766 15359 Z= 0.237 Chirality : 0.040 0.129 1611 Planarity : 0.004 0.040 2023 Dihedral : 4.964 71.433 1547 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 1.19 % Allowed : 7.60 % Favored : 91.21 % 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: 0.23 (0.22), residues: 1413 helix: 1.36 (0.22), residues: 561 sheet: 1.32 (1.14), residues: 20 loop : -0.74 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 107 HIS 0.004 0.001 HIS A 108 PHE 0.006 0.001 PHE A 528 TYR 0.011 0.001 TYR B 155 ARG 0.005 0.000 ARG A 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.242 Fit side-chains REVERT: A 392 ARG cc_start: 0.6665 (mtm110) cc_final: 0.6088 (mtt180) REVERT: B 107 TRP cc_start: 0.6863 (OUTLIER) cc_final: 0.6607 (t60) REVERT: B 304 TYR cc_start: 0.7346 (t80) cc_final: 0.6715 (t80) REVERT: B 675 ASP cc_start: 0.7278 (m-30) cc_final: 0.7044 (t0) REVERT: B 693 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7669 (mtp85) REVERT: B 703 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6810 (mp0) outliers start: 10 outliers final: 5 residues processed: 86 average time/residue: 1.1601 time to fit residues: 109.1698 Evaluate side-chains 84 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.0570 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 0.0270 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 98 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100888 restraints weight = 19628.727| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.78 r_work: 0.3290 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11236 Z= 0.132 Angle : 0.489 9.306 15359 Z= 0.233 Chirality : 0.040 0.130 1611 Planarity : 0.004 0.039 2023 Dihedral : 4.843 71.889 1547 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 0.82 % Allowed : 8.24 % Favored : 90.93 % 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 (0.22), residues: 1413 helix: 1.50 (0.22), residues: 565 sheet: 1.46 (1.11), residues: 20 loop : -0.65 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 107 HIS 0.006 0.001 HIS A 108 PHE 0.006 0.001 PHE A 657 TYR 0.012 0.001 TYR B 155 ARG 0.005 0.000 ARG A 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3224.47 seconds wall clock time: 57 minutes 52.63 seconds (3472.63 seconds total)