Starting phenix.real_space_refine on Sun Aug 4 03:04:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/08_2024/8u53_41911.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/08_2024/8u53_41911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/08_2024/8u53_41911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/08_2024/8u53_41911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/08_2024/8u53_41911.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/08_2024/8u53_41911.cif" } resolution = 2.6 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= 0.004 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 4 5.49 5 S 34 5.16 5 C 6476 2.51 5 N 1442 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9562 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "B" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 6.00, per 1000 atoms: 0.63 Number of scatterers: 9562 At special positions: 0 Unit cell: (130.81, 118.45, 90.64, 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 34 16.00 P 4 15.00 O 1606 8.00 N 1442 7.00 C 6476 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: 4.48 Conformation dependent library (CDL) restraints added in 1.3 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 84.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY A 32 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 184 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 281 through 303 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 355 through 377 Processing helix chain 'A' and resid 377 through 388 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 428 through 439 removed outlier: 3.503A pdb=" N LEU A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 464 through 474 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 501 through 523 removed outlier: 3.841A pdb=" N TYR A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 537 Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.591A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 573 Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 578 through 601 Processing helix chain 'A' and resid 612 through 638 Processing helix chain 'A' and resid 642 through 645 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY B 32 " --> pdb=" O ARG B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU B 101 " --> pdb=" O CYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 184 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 281 through 303 Processing helix chain 'B' and resid 317 through 325 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 355 through 377 Processing helix chain 'B' and resid 377 through 388 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.504A pdb=" N LEU B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 463 Processing helix chain 'B' and resid 464 through 474 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 501 through 523 removed outlier: 3.841A pdb=" N TYR B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.591A pdb=" N TRP B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 573 Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 578 through 601 Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 642 through 645 Processing helix chain 'B' and resid 646 through 665 Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 685 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 229 removed outlier: 3.530A pdb=" N ARG A 226 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 226 through 229 removed outlier: 3.531A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1911 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: 2.80 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1587 1.31 - 1.44: 3076 1.44 - 1.58: 4940 1.58 - 1.71: 121 1.71 - 1.84: 60 Bond restraints: 9784 Sorted by residual: bond pdb=" O4P CPL A 801 " pdb=" P CPL A 801 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O4P CPL B 802 " pdb=" P CPL B 802 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C10 82T B 803 " pdb=" C9 82T B 803 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C10 82T A 802 " pdb=" C9 82T A 802 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CB LEU B 566 " pdb=" CG LEU B 566 " ideal model delta sigma weight residual 1.530 1.397 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.21: 313 106.21 - 113.21: 4919 113.21 - 120.20: 4393 120.20 - 127.19: 3430 127.19 - 134.18: 101 Bond angle restraints: 13156 Sorted by residual: angle pdb=" N VAL B 601 " pdb=" CA VAL B 601 " pdb=" C VAL B 601 " ideal model delta sigma weight residual 111.62 118.85 -7.23 7.90e-01 1.60e+00 8.38e+01 angle pdb=" N VAL A 601 " pdb=" CA VAL A 601 " pdb=" C VAL A 601 " ideal model delta sigma weight residual 111.62 118.82 -7.20 7.90e-01 1.60e+00 8.31e+01 angle pdb=" C ALA A 576 " pdb=" N PRO A 577 " pdb=" CA PRO A 577 " ideal model delta sigma weight residual 119.56 128.78 -9.22 1.02e+00 9.61e-01 8.17e+01 angle pdb=" C ALA B 576 " pdb=" N PRO B 577 " pdb=" CA PRO B 577 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" CA PHE A 513 " pdb=" CB PHE A 513 " pdb=" CG PHE A 513 " ideal model delta sigma weight residual 113.80 122.41 -8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 13151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 5670 34.85 - 69.70: 120 69.70 - 104.56: 16 104.56 - 139.41: 4 139.41 - 174.26: 6 Dihedral angle restraints: 5816 sinusoidal: 2434 harmonic: 3382 Sorted by residual: dihedral pdb=" C3 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C2 CPL B 802 " pdb=" O3P CPL B 802 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 309.18 135.88 173.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1076 0.106 - 0.212: 319 0.212 - 0.318: 61 0.318 - 0.424: 6 0.424 - 0.530: 6 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C3 CPL A 801 " pdb=" O2 CPL A 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C2 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C3 CPL B 802 " pdb=" O2 CPL B 802 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CG LEU A 102 " pdb=" CB LEU A 102 " pdb=" CD1 LEU A 102 " pdb=" CD2 LEU A 102 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 1465 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " -0.068 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR A 171 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 171 " 0.068 2.00e-02 2.50e+03 3.44e-02 2.37e+01 pdb=" CG TYR B 171 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 171 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 171 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 171 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 171 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 171 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 171 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " 0.045 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR B 215 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " 0.048 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4899 2.98 - 3.46: 9897 3.46 - 3.94: 15885 3.94 - 4.42: 20207 4.42 - 4.90: 29622 Nonbonded interactions: 80510 Sorted by model distance: nonbonded pdb=" NH1 ARG A 178 " pdb=" O GLY A 667 " model vdw 2.498 3.120 nonbonded pdb=" NH1 ARG B 178 " pdb=" O GLY B 667 " model vdw 2.499 3.120 nonbonded pdb=" C SER A 501 " pdb=" OG SER A 501 " model vdw 2.534 2.616 nonbonded pdb=" C SER B 501 " pdb=" OG SER B 501 " model vdw 2.534 2.616 nonbonded pdb=" CB PLM A 809 " pdb=" CE PLM A 809 " model vdw 2.553 3.072 ... (remaining 80505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 231 or resid 234 through 697 or resid 804 throug \ h 812)) selection = (chain 'B' and (resid 2 through 231 or resid 234 through 697 or resid 804 throug \ h 812)) } 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: 0.420 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.970 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.024 0.150 9784 Z= 1.527 Angle : 1.715 16.408 13156 Z= 1.115 Chirality : 0.104 0.530 1468 Planarity : 0.009 0.036 1572 Dihedral : 15.246 174.260 3624 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.71 (0.24), residues: 1054 helix: 0.53 (0.17), residues: 742 sheet: None (None), residues: 0 loop : 0.70 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP A 336 HIS 0.006 0.002 HIS A 696 PHE 0.037 0.007 PHE A 513 TYR 0.068 0.009 TYR A 171 ARG 0.008 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7298 (tt0) cc_final: 0.7037 (tt0) REVERT: B 343 GLU cc_start: 0.7362 (tt0) cc_final: 0.7078 (tt0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.0947 time to fit residues: 212.3388 Evaluate side-chains 121 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9784 Z= 0.225 Angle : 0.605 9.013 13156 Z= 0.327 Chirality : 0.043 0.164 1468 Planarity : 0.005 0.042 1572 Dihedral : 17.474 177.878 1666 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 6.45 % Favored : 90.65 % 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: 1.65 (0.25), residues: 1054 helix: 1.42 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.45 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 613 HIS 0.005 0.002 HIS A 696 PHE 0.037 0.003 PHE B 513 TYR 0.019 0.002 TYR B 536 ARG 0.004 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.982 Fit side-chains REVERT: A 428 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4028 (tmt) REVERT: B 428 MET cc_start: 0.5183 (OUTLIER) cc_final: 0.4031 (tmt) outliers start: 27 outliers final: 8 residues processed: 166 average time/residue: 0.9477 time to fit residues: 171.3276 Evaluate side-chains 121 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9784 Z= 0.214 Angle : 0.572 7.365 13156 Z= 0.306 Chirality : 0.041 0.161 1468 Planarity : 0.005 0.034 1572 Dihedral : 16.487 175.802 1666 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.47 % Allowed : 10.54 % Favored : 86.99 % 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: 1.66 (0.25), residues: 1054 helix: 1.53 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.14 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 613 HIS 0.004 0.001 HIS A 447 PHE 0.029 0.002 PHE B 513 TYR 0.015 0.002 TYR B 157 ARG 0.008 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.034 Fit side-chains REVERT: A 332 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: B 332 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8086 (mtp) outliers start: 23 outliers final: 12 residues processed: 144 average time/residue: 0.8436 time to fit residues: 133.9257 Evaluate side-chains 128 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0570 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.157 Angle : 0.509 6.605 13156 Z= 0.272 Chirality : 0.039 0.148 1468 Planarity : 0.004 0.031 1572 Dihedral : 15.861 174.004 1666 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.26 % Allowed : 11.40 % Favored : 86.34 % 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: 1.98 (0.26), residues: 1054 helix: 1.73 (0.18), residues: 752 sheet: None (None), residues: 0 loop : 0.41 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 613 HIS 0.002 0.001 HIS A 615 PHE 0.026 0.002 PHE B 513 TYR 0.014 0.001 TYR B 157 ARG 0.006 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.048 Fit side-chains REVERT: A 161 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 638 LYS cc_start: 0.4862 (OUTLIER) cc_final: 0.3642 (tmtt) outliers start: 21 outliers final: 6 residues processed: 134 average time/residue: 0.8625 time to fit residues: 127.4761 Evaluate side-chains 123 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 overall best weight: 0.2886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9784 Z= 0.137 Angle : 0.486 6.794 13156 Z= 0.257 Chirality : 0.039 0.141 1468 Planarity : 0.004 0.029 1572 Dihedral : 15.307 172.799 1666 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.15 % Allowed : 12.37 % Favored : 85.48 % 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: 1.99 (0.26), residues: 1054 helix: 1.78 (0.19), residues: 766 sheet: None (None), residues: 0 loop : 0.18 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 548 HIS 0.002 0.001 HIS A 696 PHE 0.024 0.001 PHE B 513 TYR 0.010 0.001 TYR A 157 ARG 0.007 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.117 Fit side-chains REVERT: A 428 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.4097 (tmt) REVERT: A 638 LYS cc_start: 0.4731 (OUTLIER) cc_final: 0.4520 (tttt) REVERT: B 428 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.4085 (tmt) outliers start: 20 outliers final: 4 residues processed: 137 average time/residue: 0.9632 time to fit residues: 143.8044 Evaluate side-chains 123 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.0000 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.245 Angle : 0.567 7.940 13156 Z= 0.301 Chirality : 0.042 0.162 1468 Planarity : 0.005 0.033 1572 Dihedral : 15.622 171.840 1666 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.61 % Allowed : 14.41 % Favored : 83.98 % 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: 1.77 (0.25), residues: 1054 helix: 1.66 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.08 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 613 HIS 0.006 0.002 HIS B 447 PHE 0.029 0.002 PHE A 513 TYR 0.010 0.002 TYR B 157 ARG 0.004 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.885 Fit side-chains REVERT: A 222 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5711 (tt0) REVERT: A 428 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.4126 (tmt) REVERT: B 222 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5620 (tt0) REVERT: B 332 MET cc_start: 0.8383 (mtp) cc_final: 0.8165 (mtm) REVERT: B 428 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4177 (tmt) outliers start: 15 outliers final: 5 residues processed: 136 average time/residue: 0.9880 time to fit residues: 146.0289 Evaluate side-chains 127 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9784 Z= 0.164 Angle : 0.510 7.871 13156 Z= 0.270 Chirality : 0.040 0.146 1468 Planarity : 0.004 0.031 1572 Dihedral : 15.334 171.610 1666 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.83 % Allowed : 14.62 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.26), residues: 1054 helix: 1.79 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.17 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 548 HIS 0.004 0.001 HIS B 696 PHE 0.026 0.002 PHE B 513 TYR 0.018 0.001 TYR A 225 ARG 0.003 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.980 Fit side-chains REVERT: A 222 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5749 (tt0) REVERT: A 428 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.4087 (tmt) REVERT: B 222 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5632 (tt0) REVERT: B 428 MET cc_start: 0.5462 (OUTLIER) cc_final: 0.4392 (tmt) outliers start: 17 outliers final: 5 residues processed: 122 average time/residue: 1.0052 time to fit residues: 133.2613 Evaluate side-chains 117 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9784 Z= 0.181 Angle : 0.529 8.854 13156 Z= 0.279 Chirality : 0.040 0.151 1468 Planarity : 0.004 0.030 1572 Dihedral : 15.363 170.470 1666 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.04 % Allowed : 14.62 % Favored : 83.33 % 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: 1.92 (0.26), residues: 1054 helix: 1.77 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.13 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 613 HIS 0.004 0.001 HIS B 696 PHE 0.026 0.002 PHE A 513 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.967 Fit side-chains REVERT: A 222 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5720 (tt0) REVERT: A 428 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.4104 (tmt) REVERT: B 222 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5660 (tt0) REVERT: B 428 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.4411 (tmt) outliers start: 19 outliers final: 7 residues processed: 128 average time/residue: 1.0080 time to fit residues: 141.1209 Evaluate side-chains 124 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9784 Z= 0.162 Angle : 0.515 9.067 13156 Z= 0.272 Chirality : 0.039 0.147 1468 Planarity : 0.004 0.030 1572 Dihedral : 15.159 170.057 1666 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.83 % Allowed : 14.84 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.26), residues: 1054 helix: 1.87 (0.19), residues: 752 sheet: None (None), residues: 0 loop : 0.18 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 548 HIS 0.004 0.001 HIS B 696 PHE 0.026 0.001 PHE A 513 TYR 0.010 0.001 TYR B 157 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.133 Fit side-chains REVERT: A 222 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5735 (tt0) REVERT: A 428 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4271 (tmt) REVERT: B 222 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5692 (tt0) REVERT: B 428 MET cc_start: 0.5482 (OUTLIER) cc_final: 0.4414 (tmt) outliers start: 17 outliers final: 8 residues processed: 124 average time/residue: 0.9791 time to fit residues: 132.8986 Evaluate side-chains 124 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 73 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9784 Z= 0.172 Angle : 0.531 9.357 13156 Z= 0.280 Chirality : 0.040 0.149 1468 Planarity : 0.004 0.030 1572 Dihedral : 15.094 169.427 1666 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.29 % Allowed : 15.81 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.26), residues: 1054 helix: 1.83 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.16 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 613 HIS 0.004 0.001 HIS B 696 PHE 0.026 0.002 PHE A 513 TYR 0.010 0.001 TYR A 215 ARG 0.003 0.000 ARG A 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.948 Fit side-chains REVERT: A 183 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7057 (mmm) REVERT: A 222 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5732 (tt0) REVERT: A 428 MET cc_start: 0.5416 (OUTLIER) cc_final: 0.4282 (tmt) REVERT: B 222 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5668 (tt0) REVERT: B 428 MET cc_start: 0.5415 (OUTLIER) cc_final: 0.4315 (tmt) outliers start: 12 outliers final: 7 residues processed: 118 average time/residue: 0.9756 time to fit residues: 125.4524 Evaluate side-chains 122 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.0170 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.135978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114783 restraints weight = 14343.629| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.83 r_work: 0.3498 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.170 Angle : 0.531 9.374 13156 Z= 0.279 Chirality : 0.040 0.148 1468 Planarity : 0.004 0.030 1572 Dihedral : 15.142 169.170 1666 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.40 % Allowed : 15.59 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.26), residues: 1054 helix: 1.92 (0.19), residues: 744 sheet: None (None), residues: 0 loop : 0.04 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 613 HIS 0.004 0.001 HIS B 696 PHE 0.026 0.001 PHE A 513 TYR 0.010 0.001 TYR B 215 ARG 0.003 0.000 ARG B 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.48 seconds wall clock time: 57 minutes 40.55 seconds (3460.55 seconds total)