Starting phenix.real_space_refine on Sun Mar 10 22:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/03_2024/8e28_27828.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/03_2024/8e28_27828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/03_2024/8e28_27828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/03_2024/8e28_27828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/03_2024/8e28_27828.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/03_2024/8e28_27828.pdb" } resolution = 3.1 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= 0.003 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 15 5.49 5 S 31 5.16 5 C 3638 2.51 5 N 976 2.21 5 O 1129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ASP 620": "OD1" <-> "OD2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 651": "OD1" <-> "OD2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A GLU 826": "OE1" <-> "OE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 847": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5789 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5489 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 41, 'TRANS': 648} Chain breaks: 2 Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 8} Time building chain proxies: 3.53, per 1000 atoms: 0.61 Number of scatterers: 5789 At special positions: 0 Unit cell: (79.86, 86.46, 93.06, 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 31 16.00 P 15 15.00 O 1129 8.00 N 976 7.00 C 3638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 10 sheets defined 32.0% alpha, 23.2% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.438A pdb=" N ASP A 295 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.889A pdb=" N TYR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.765A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.771A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 513 " --> pdb=" O ALA A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.846A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.598A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.674A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.636A pdb=" N GLN A 685 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 764 removed outlier: 3.557A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.253A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 114 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 235 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 252 removed outlier: 6.783A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR A 299 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU A 251 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.424A pdb=" N ARG A 487 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.481A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.430A pdb=" N ALA A 557 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS A 570 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 559 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 796 removed outlier: 3.715A pdb=" N GLY A 776 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 785 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 774 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 802 through 809 removed outlier: 6.713A pdb=" N VAL A 819 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS A 805 " --> pdb=" O THR A 817 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 817 " --> pdb=" O HIS A 805 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 807 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 815 " --> pdb=" O PHE A 807 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1626 1.34 - 1.45: 952 1.45 - 1.57: 3283 1.57 - 1.69: 29 1.69 - 1.81: 47 Bond restraints: 5937 Sorted by residual: bond pdb=" C LEU A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.57e+00 bond pdb=" C GLU A 330 " pdb=" N PRO A 331 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.76e+00 bond pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.87e+00 ... (remaining 5932 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 265 106.72 - 113.54: 3187 113.54 - 120.36: 2283 120.36 - 127.18: 2298 127.18 - 134.00: 64 Bond angle restraints: 8097 Sorted by residual: angle pdb=" CG ARG A 231 " pdb=" CD ARG A 231 " pdb=" NE ARG A 231 " ideal model delta sigma weight residual 112.00 120.35 -8.35 2.20e+00 2.07e-01 1.44e+01 angle pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 112.60 118.96 -6.36 1.70e+00 3.46e-01 1.40e+01 angle pdb=" N ASN A 391 " pdb=" CA ASN A 391 " pdb=" C ASN A 391 " ideal model delta sigma weight residual 113.17 117.74 -4.57 1.26e+00 6.30e-01 1.31e+01 angle pdb=" CA LYS A 283 " pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" N GLY A 482 " pdb=" CA GLY A 482 " pdb=" C GLY A 482 " ideal model delta sigma weight residual 111.37 115.62 -4.25 1.29e+00 6.01e-01 1.09e+01 ... (remaining 8092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 3067 16.13 - 32.25: 428 32.25 - 48.38: 133 48.38 - 64.51: 41 64.51 - 80.63: 12 Dihedral angle restraints: 3681 sinusoidal: 1657 harmonic: 2024 Sorted by residual: dihedral pdb=" CA PHE A 464 " pdb=" C PHE A 464 " pdb=" N SER A 465 " pdb=" CA SER A 465 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 633 0.043 - 0.086: 212 0.086 - 0.129: 65 0.129 - 0.172: 16 0.172 - 0.215: 2 Chirality restraints: 928 Sorted by residual: chirality pdb=" CB ILE A 856 " pdb=" CA ILE A 856 " pdb=" CG1 ILE A 856 " pdb=" CG2 ILE A 856 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL A 99 " pdb=" N VAL A 99 " pdb=" C VAL A 99 " pdb=" CB VAL A 99 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 925 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 444 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 445 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 97 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" CG ASP A 97 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 97 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 728 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 729 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 729 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 729 " -0.033 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1725 2.83 - 3.35: 4525 3.35 - 3.87: 8908 3.87 - 4.38: 10327 4.38 - 4.90: 18495 Nonbonded interactions: 43980 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR A 696 " pdb=" OP1 U C 13 " model vdw 2.334 2.440 nonbonded pdb=" OD1 ASP A 288 " pdb=" OH TYR A 296 " model vdw 2.348 2.440 nonbonded pdb=" NH2 ARG A 543 " pdb=" OE2 GLU A 584 " model vdw 2.374 2.520 nonbonded pdb=" NE2 GLN A 827 " pdb=" O GLU A 828 " model vdw 2.379 2.520 ... (remaining 43975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.320 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: 6.060 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.004 0.048 5937 Z= 0.257 Angle : 0.832 10.320 8097 Z= 0.443 Chirality : 0.049 0.215 928 Planarity : 0.007 0.062 997 Dihedral : 17.293 80.633 2363 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.72 (0.30), residues: 684 helix: -1.10 (0.32), residues: 210 sheet: -0.21 (0.42), residues: 163 loop : -1.62 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 468 HIS 0.010 0.002 HIS A 610 PHE 0.039 0.003 PHE A 80 TYR 0.037 0.002 TYR A 689 ARG 0.017 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.635 Fit side-chains REVERT: A 51 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7058 (pt0) REVERT: A 495 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 586 MET cc_start: 0.8192 (mmt) cc_final: 0.7863 (mmt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1702 time to fit residues: 14.0845 Evaluate side-chains 49 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.0570 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5937 Z= 0.216 Angle : 0.524 5.691 8097 Z= 0.271 Chirality : 0.042 0.147 928 Planarity : 0.005 0.055 997 Dihedral : 11.651 73.591 984 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.49 % Allowed : 7.25 % Favored : 92.26 % 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: -1.09 (0.31), residues: 684 helix: -0.01 (0.36), residues: 210 sheet: -0.16 (0.42), residues: 157 loop : -1.48 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 468 HIS 0.003 0.001 HIS A 571 PHE 0.014 0.002 PHE A 464 TYR 0.012 0.001 TYR A 674 ARG 0.006 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.595 Fit side-chains REVERT: A 51 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7098 (pt0) REVERT: A 334 GLU cc_start: 0.7435 (tt0) cc_final: 0.7186 (tt0) REVERT: A 511 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7604 (tttm) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.2336 time to fit residues: 16.6862 Evaluate side-chains 52 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5937 Z= 0.128 Angle : 0.465 5.205 8097 Z= 0.238 Chirality : 0.040 0.147 928 Planarity : 0.004 0.038 997 Dihedral : 11.354 73.606 984 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.99 % Allowed : 11.20 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.32), residues: 684 helix: 0.53 (0.37), residues: 210 sheet: 0.07 (0.43), residues: 162 loop : -1.20 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 PHE 0.011 0.001 PHE A 648 TYR 0.008 0.001 TYR A 653 ARG 0.010 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.600 Fit side-chains REVERT: A 51 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7053 (pt0) REVERT: A 334 GLU cc_start: 0.7368 (tt0) cc_final: 0.7028 (tt0) outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 0.2251 time to fit residues: 18.3523 Evaluate side-chains 56 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5937 Z= 0.158 Angle : 0.465 5.126 8097 Z= 0.238 Chirality : 0.041 0.137 928 Planarity : 0.004 0.033 997 Dihedral : 11.263 73.593 984 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.32 % Allowed : 13.34 % Favored : 85.34 % 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: -0.33 (0.32), residues: 684 helix: 0.77 (0.37), residues: 210 sheet: 0.16 (0.43), residues: 162 loop : -1.09 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.002 0.001 HIS A 610 PHE 0.012 0.001 PHE A 648 TYR 0.008 0.001 TYR A 674 ARG 0.006 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.665 Fit side-chains REVERT: A 51 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7050 (pt0) REVERT: A 334 GLU cc_start: 0.7425 (tt0) cc_final: 0.7040 (tt0) REVERT: A 737 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: A 764 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5350 (mp0) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.1980 time to fit residues: 15.2582 Evaluate side-chains 60 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5937 Z= 0.264 Angle : 0.522 5.526 8097 Z= 0.266 Chirality : 0.043 0.141 928 Planarity : 0.004 0.036 997 Dihedral : 11.339 73.599 984 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.31 % Allowed : 14.17 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.32), residues: 684 helix: 0.80 (0.37), residues: 204 sheet: 0.45 (0.44), residues: 158 loop : -1.21 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 468 HIS 0.003 0.001 HIS A 610 PHE 0.015 0.002 PHE A 481 TYR 0.010 0.002 TYR A 653 ARG 0.004 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.706 Fit side-chains REVERT: A 51 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7106 (pt0) REVERT: A 334 GLU cc_start: 0.7521 (tt0) cc_final: 0.7078 (tt0) REVERT: A 737 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: A 764 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5588 (mp0) outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.1815 time to fit residues: 14.9665 Evaluate side-chains 64 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5937 Z= 0.137 Angle : 0.454 5.165 8097 Z= 0.232 Chirality : 0.040 0.136 928 Planarity : 0.004 0.031 997 Dihedral : 11.234 73.598 984 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 15.98 % 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: 0.02 (0.32), residues: 684 helix: 1.16 (0.37), residues: 204 sheet: 0.68 (0.44), residues: 154 loop : -1.07 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 PHE 0.012 0.001 PHE A 648 TYR 0.008 0.001 TYR A 653 ARG 0.005 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.608 Fit side-chains REVERT: A 51 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7056 (pt0) REVERT: A 334 GLU cc_start: 0.7441 (tt0) cc_final: 0.7011 (tt0) REVERT: A 352 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8338 (mp) REVERT: A 764 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.5454 (mp0) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.1865 time to fit residues: 14.6870 Evaluate side-chains 62 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 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 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5937 Z= 0.134 Angle : 0.446 5.258 8097 Z= 0.227 Chirality : 0.040 0.159 928 Planarity : 0.004 0.031 997 Dihedral : 11.152 73.570 984 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.98 % Allowed : 16.80 % Favored : 81.22 % 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: 0.06 (0.33), residues: 684 helix: 1.16 (0.37), residues: 210 sheet: 0.66 (0.43), residues: 153 loop : -1.04 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 PHE 0.012 0.001 PHE A 648 TYR 0.008 0.001 TYR A 653 ARG 0.008 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.686 Fit side-chains REVERT: A 51 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7043 (pt0) REVERT: A 334 GLU cc_start: 0.7467 (tt0) cc_final: 0.7019 (tt0) REVERT: A 352 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 764 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5345 (mp0) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.1782 time to fit residues: 14.3821 Evaluate side-chains 61 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5937 Z= 0.155 Angle : 0.453 5.226 8097 Z= 0.231 Chirality : 0.040 0.135 928 Planarity : 0.004 0.030 997 Dihedral : 11.132 73.584 984 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.81 % Allowed : 17.46 % Favored : 80.72 % 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: 0.06 (0.33), residues: 684 helix: 1.14 (0.37), residues: 211 sheet: 0.64 (0.43), residues: 153 loop : -1.02 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.003 0.000 HIS A 610 PHE 0.013 0.001 PHE A 648 TYR 0.008 0.001 TYR A 653 ARG 0.006 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.685 Fit side-chains REVERT: A 51 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7045 (pt0) REVERT: A 334 GLU cc_start: 0.7469 (tt0) cc_final: 0.7093 (tt0) REVERT: A 352 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 764 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5409 (mp0) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.2062 time to fit residues: 15.9093 Evaluate side-chains 62 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.0040 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.0270 overall best weight: 0.4450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5937 Z= 0.113 Angle : 0.426 5.276 8097 Z= 0.217 Chirality : 0.039 0.131 928 Planarity : 0.003 0.030 997 Dihedral : 11.073 73.605 984 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.65 % Allowed : 17.46 % Favored : 80.89 % 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: 0.17 (0.33), residues: 684 helix: 1.33 (0.38), residues: 211 sheet: 0.51 (0.43), residues: 153 loop : -0.91 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 PHE 0.013 0.001 PHE A 648 TYR 0.008 0.001 TYR A 653 ARG 0.005 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.654 Fit side-chains REVERT: A 51 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7020 (pt0) REVERT: A 334 GLU cc_start: 0.7425 (tt0) cc_final: 0.6975 (tt0) REVERT: A 352 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 764 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5180 (mp0) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.2130 time to fit residues: 17.7455 Evaluate side-chains 63 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5937 Z= 0.194 Angle : 0.471 5.250 8097 Z= 0.240 Chirality : 0.041 0.139 928 Planarity : 0.004 0.031 997 Dihedral : 11.103 73.557 984 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.81 % Allowed : 17.79 % Favored : 80.40 % 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: 0.04 (0.33), residues: 684 helix: 1.12 (0.37), residues: 211 sheet: 0.59 (0.43), residues: 155 loop : -1.01 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 468 HIS 0.002 0.001 HIS A 610 PHE 0.014 0.001 PHE A 481 TYR 0.009 0.001 TYR A 653 ARG 0.005 0.000 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.660 Fit side-chains REVERT: A 51 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7050 (pt0) REVERT: A 334 GLU cc_start: 0.7488 (tt0) cc_final: 0.7104 (tt0) REVERT: A 352 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 764 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5489 (mp0) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.1960 time to fit residues: 15.4402 Evaluate side-chains 64 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 48 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107423 restraints weight = 7066.562| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.84 r_work: 0.3033 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5937 Z= 0.124 Angle : 0.438 5.232 8097 Z= 0.223 Chirality : 0.040 0.136 928 Planarity : 0.003 0.031 997 Dihedral : 11.082 73.591 984 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.98 % Allowed : 17.46 % Favored : 80.56 % 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: 0.21 (0.33), residues: 684 helix: 1.30 (0.37), residues: 211 sheet: 0.66 (0.43), residues: 151 loop : -0.89 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 610 PHE 0.013 0.001 PHE A 648 TYR 0.008 0.001 TYR A 653 ARG 0.006 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1610.18 seconds wall clock time: 29 minutes 37.79 seconds (1777.79 seconds total)