Starting phenix.real_space_refine on Wed Feb 14 15:58:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zli_14781/02_2024/7zli_14781_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zli_14781/02_2024/7zli_14781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zli_14781/02_2024/7zli_14781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zli_14781/02_2024/7zli_14781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zli_14781/02_2024/7zli_14781_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zli_14781/02_2024/7zli_14781_trim.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.064 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 1 5.49 5 S 44 5.16 5 C 6168 2.51 5 N 1580 2.21 5 O 1789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1679 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1598 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5384 Unusual residues: {'IZY': 1} Classifications: {'peptide': 661, 'undetermined': 1, 'water': 13} Link IDs: {'PTRANS': 24, 'TRANS': 636, None: 14} Not linked: pdbres="LEU A 684 " pdbres="IZY A 801 " Not linked: pdbres="IZY A 801 " pdbres="HOH A 901 " Not linked: pdbres="HOH A 901 " pdbres="HOH A 902 " Not linked: pdbres="HOH A 902 " pdbres="HOH A 903 " Not linked: pdbres="HOH A 903 " pdbres="HOH A 904 " ... (remaining 9 not shown) Chain breaks: 1 Time building chain proxies: 5.55, per 1000 atoms: 0.58 Number of scatterers: 9582 At special positions: 0 Unit cell: (100.32, 161.04, 97.02, 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 44 16.00 P 1 15.00 O 1789 8.00 N 1580 7.00 C 6168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 650 " distance=2.03 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: 3.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 40.4% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 207 removed outlier: 4.066A pdb=" N GLN H 207 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.811A pdb=" N GLN K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 184 through 188 Processing helix chain 'A' and resid 25 through 55 Processing helix chain 'A' and resid 56 through 59 removed outlier: 3.580A pdb=" N LEU A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.985A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 removed outlier: 4.119A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 115 through 136 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.642A pdb=" N GLY A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 240 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.770A pdb=" N MET A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 264 through 281 removed outlier: 3.631A pdb=" N THR A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 308 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.661A pdb=" N SER A 337 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 363 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.871A pdb=" N PHE A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.910A pdb=" N THR A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.518A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.606A pdb=" N LEU A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 464 " --> pdb=" O CYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.753A pdb=" N MET A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 499 through 527 removed outlier: 3.522A pdb=" N GLY A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 534 through 548 removed outlier: 4.383A pdb=" N GLU A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.818A pdb=" N ALA A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.544A pdb=" N LYS A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 619 through 622 Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.570A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.838A pdb=" N LEU A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.704A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15 removed outlier: 4.525A pdb=" N TYR H 117 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.242A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.242A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AA7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.437A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE K 98 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP K 109 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.437A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.724A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.056A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 147 through 150 removed outlier: 6.210A pdb=" N HIS L 199 " --> pdb=" O SER L 204 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER L 204 " --> pdb=" O HIS L 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.746A pdb=" N TRP A 143 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 155 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 554 through 556 removed outlier: 4.208A pdb=" N TYR A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 674 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 682 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE A 670 " --> pdb=" O LYS A 682 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1383 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: 3.09 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1500 1.30 - 1.43: 2785 1.43 - 1.56: 5451 1.56 - 1.69: 6 1.69 - 1.82: 66 Bond restraints: 9808 Sorted by residual: bond pdb=" C TRP A 262 " pdb=" O TRP A 262 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.26e-02 6.30e+03 2.49e+01 bond pdb=" C TYR A 75 " pdb=" O TYR A 75 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" C MET A 465 " pdb=" O MET A 465 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.15e-02 7.56e+03 2.02e+01 bond pdb=" C PHE A 264 " pdb=" O PHE A 264 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.26e-02 6.30e+03 1.93e+01 bond pdb=" C PHE A 261 " pdb=" N TRP A 262 " ideal model delta sigma weight residual 1.332 1.271 0.061 1.40e-02 5.10e+03 1.93e+01 ... (remaining 9803 not shown) Histogram of bond angle deviations from ideal: 89.03 - 103.88: 125 103.88 - 118.73: 7704 118.73 - 133.58: 5471 133.58 - 148.44: 20 148.44 - 163.29: 4 Bond angle restraints: 13324 Sorted by residual: angle pdb=" C03 IZY A 801 " pdb=" C02 IZY A 801 " pdb=" C04 IZY A 801 " ideal model delta sigma weight residual 121.02 163.29 -42.27 3.00e+00 1.11e-01 1.99e+02 angle pdb=" N THR A 70 " pdb=" CA THR A 70 " pdb=" C THR A 70 " ideal model delta sigma weight residual 111.07 123.64 -12.57 1.07e+00 8.73e-01 1.38e+02 angle pdb=" C THR A 70 " pdb=" CA THR A 70 " pdb=" CB THR A 70 " ideal model delta sigma weight residual 110.88 93.76 17.12 1.57e+00 4.06e-01 1.19e+02 angle pdb=" C02 IZY A 801 " pdb=" C04 IZY A 801 " pdb=" C05 IZY A 801 " ideal model delta sigma weight residual 128.13 158.83 -30.70 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C07 IZY A 801 " pdb=" C09 IZY A 801 " pdb=" C10 IZY A 801 " ideal model delta sigma weight residual 127.91 154.24 -26.33 3.00e+00 1.11e-01 7.71e+01 ... (remaining 13319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5235 17.28 - 34.55: 474 34.55 - 51.83: 67 51.83 - 69.10: 18 69.10 - 86.38: 8 Dihedral angle restraints: 5802 sinusoidal: 2257 harmonic: 3545 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.06 56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 145.46 -52.46 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual 93.00 47.01 45.99 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 5799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1162 0.054 - 0.109: 284 0.109 - 0.163: 38 0.163 - 0.217: 10 0.217 - 0.272: 5 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA THR A 271 " pdb=" N THR A 271 " pdb=" C THR A 271 " pdb=" CB THR A 271 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA TRP A 262 " pdb=" N TRP A 262 " pdb=" C TRP A 262 " pdb=" CB TRP A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PHE A 261 " pdb=" N PHE A 261 " pdb=" C PHE A 261 " pdb=" CB PHE A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1496 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 261 " -0.019 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE A 261 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE A 261 " -0.022 2.00e-02 2.50e+03 pdb=" N TRP A 262 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 459 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C LEU A 459 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 459 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS A 460 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP H 109 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C TRP H 109 " 0.046 2.00e-02 2.50e+03 pdb=" O TRP H 109 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP H 110 " -0.016 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 47 2.45 - 3.06: 6704 3.06 - 3.67: 13801 3.67 - 4.29: 21063 4.29 - 4.90: 36027 Nonbonded interactions: 77642 Sorted by model distance: nonbonded pdb=" O ALA A 388 " pdb=" OG1 THR A 392 " model vdw 1.834 2.440 nonbonded pdb=" NE2 GLN H 186 " pdb=" OG SER H 188 " model vdw 1.954 2.520 nonbonded pdb=" OD2 ASP K 73 " pdb=" OH TYR K 80 " model vdw 1.956 2.440 nonbonded pdb=" OG1 THR A 70 " pdb=" N GLU A 71 " model vdw 1.971 2.520 nonbonded pdb=" OG SER A 659 " pdb=" OD1 ASP A 661 " model vdw 2.008 2.440 ... (remaining 77637 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: 5.400 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: 13.580 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.840 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.007 0.085 9808 Z= 0.469 Angle : 1.014 42.267 13324 Z= 0.536 Chirality : 0.051 0.272 1499 Planarity : 0.005 0.053 1677 Dihedral : 13.505 86.378 3504 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.54 % Favored : 93.05 % Rotamer: Outliers : 0.96 % Allowed : 0.57 % Favored : 98.47 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.08 % 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: 0.03 (0.25), residues: 1208 helix: 0.55 (0.26), residues: 427 sheet: 0.83 (0.32), residues: 278 loop : -0.86 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 110 HIS 0.011 0.001 HIS A 297 PHE 0.045 0.002 PHE A 56 TYR 0.018 0.002 TYR A 578 ARG 0.004 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: L 82 GLU cc_start: 0.7990 (pm20) cc_final: 0.7599 (pm20) REVERT: A 328 MET cc_start: 0.7180 (tpp) cc_final: 0.6919 (tpt) REVERT: A 549 LYS cc_start: 0.7694 (pttp) cc_final: 0.7483 (pmtt) REVERT: A 584 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7323 (ttp80) outliers start: 10 outliers final: 3 residues processed: 114 average time/residue: 1.4690 time to fit residues: 178.0604 Evaluate side-chains 88 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9808 Z= 0.202 Angle : 0.601 8.106 13324 Z= 0.309 Chirality : 0.044 0.139 1499 Planarity : 0.004 0.038 1677 Dihedral : 6.046 56.226 1378 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.22 % Favored : 94.62 % Rotamer: Outliers : 1.34 % Allowed : 8.41 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1208 helix: 1.09 (0.26), residues: 432 sheet: 0.94 (0.31), residues: 281 loop : -0.67 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 262 HIS 0.004 0.001 HIS A 105 PHE 0.018 0.001 PHE A 56 TYR 0.014 0.001 TYR H 106 ARG 0.003 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.123 Fit side-chains REVERT: H 63 TYR cc_start: 0.8519 (m-80) cc_final: 0.8179 (m-80) REVERT: K 83 MET cc_start: 0.3729 (mmt) cc_final: 0.2677 (mmt) REVERT: L 46 LYS cc_start: 0.8241 (ptmm) cc_final: 0.8037 (ptpp) REVERT: L 106 GLU cc_start: 0.7586 (pm20) cc_final: 0.7356 (mp0) REVERT: A 328 MET cc_start: 0.7112 (tpp) cc_final: 0.6899 (tpt) REVERT: A 584 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7061 (ttp80) outliers start: 14 outliers final: 3 residues processed: 94 average time/residue: 1.4306 time to fit residues: 144.2219 Evaluate side-chains 83 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS A 105 HIS A 577 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9808 Z= 0.162 Angle : 0.558 8.165 13324 Z= 0.286 Chirality : 0.042 0.135 1499 Planarity : 0.004 0.040 1677 Dihedral : 5.286 54.901 1373 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 1.63 % Allowed : 11.57 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.68 (0.25), residues: 1208 helix: 1.43 (0.26), residues: 439 sheet: 1.00 (0.31), residues: 277 loop : -0.75 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 110 HIS 0.004 0.001 HIS A 105 PHE 0.012 0.001 PHE A 123 TYR 0.011 0.001 TYR H 106 ARG 0.003 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.077 Fit side-chains REVERT: H 63 TYR cc_start: 0.8493 (m-80) cc_final: 0.8033 (m-80) REVERT: K 83 MET cc_start: 0.3642 (mmt) cc_final: 0.2735 (mmt) REVERT: L 46 LYS cc_start: 0.8247 (ptmm) cc_final: 0.8019 (ptpp) REVERT: L 101 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7122 (pp30) REVERT: A 72 MET cc_start: 0.8517 (mtp) cc_final: 0.7988 (mtp) REVERT: A 328 MET cc_start: 0.7133 (tpp) cc_final: 0.6927 (tpt) REVERT: A 396 THR cc_start: 0.7532 (m) cc_final: 0.7118 (p) REVERT: A 524 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.5853 (mp-120) REVERT: A 584 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7112 (ttp80) outliers start: 17 outliers final: 5 residues processed: 99 average time/residue: 1.4172 time to fit residues: 150.8289 Evaluate side-chains 91 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9808 Z= 0.297 Angle : 0.618 8.441 13324 Z= 0.316 Chirality : 0.045 0.151 1499 Planarity : 0.004 0.044 1677 Dihedral : 5.510 54.123 1373 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 2.68 % Allowed : 13.29 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.47 (0.25), residues: 1208 helix: 1.20 (0.26), residues: 438 sheet: 0.85 (0.31), residues: 281 loop : -0.80 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 110 HIS 0.004 0.001 HIS A 391 PHE 0.015 0.002 PHE A 305 TYR 0.013 0.002 TYR H 112 ARG 0.005 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.879 Fit side-chains REVERT: H 63 TYR cc_start: 0.8569 (m-80) cc_final: 0.8312 (m-80) REVERT: K 83 MET cc_start: 0.3557 (mmt) cc_final: 0.2541 (mmt) REVERT: L 12 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7311 (tt) REVERT: L 46 LYS cc_start: 0.8313 (ptmm) cc_final: 0.8078 (ptpp) REVERT: L 106 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 72 MET cc_start: 0.8573 (mtp) cc_final: 0.8130 (mtp) REVERT: A 328 MET cc_start: 0.7129 (tpp) cc_final: 0.6869 (tpt) REVERT: A 524 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6186 (mp-120) REVERT: A 584 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7046 (tpt90) outliers start: 28 outliers final: 10 residues processed: 106 average time/residue: 1.3865 time to fit residues: 157.7125 Evaluate side-chains 97 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 10.0000 chunk 1 optimal weight: 0.0000 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 0.0980 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 144 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9808 Z= 0.151 Angle : 0.547 8.513 13324 Z= 0.278 Chirality : 0.042 0.135 1499 Planarity : 0.004 0.042 1677 Dihedral : 5.229 50.010 1373 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 2.10 % Allowed : 14.44 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.73 (0.25), residues: 1208 helix: 1.56 (0.26), residues: 438 sheet: 0.85 (0.30), residues: 293 loop : -0.75 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 110 HIS 0.003 0.001 HIS A 105 PHE 0.016 0.001 PHE A 123 TYR 0.010 0.001 TYR H 106 ARG 0.003 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.941 Fit side-chains REVERT: H 63 TYR cc_start: 0.8482 (m-80) cc_final: 0.8006 (m-80) REVERT: K 83 MET cc_start: 0.3625 (mmt) cc_final: 0.2562 (mmt) REVERT: L 46 LYS cc_start: 0.8261 (ptmm) cc_final: 0.8033 (ptpp) REVERT: L 82 GLU cc_start: 0.8352 (pm20) cc_final: 0.7705 (pm20) REVERT: L 101 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7201 (pp30) REVERT: L 106 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: L 164 VAL cc_start: 0.7872 (t) cc_final: 0.7375 (p) REVERT: A 328 MET cc_start: 0.7121 (tpp) cc_final: 0.6872 (tpt) REVERT: A 524 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.5985 (mp-120) REVERT: A 619 MET cc_start: 0.6709 (ptp) cc_final: 0.6506 (pmm) outliers start: 22 outliers final: 6 residues processed: 109 average time/residue: 1.2414 time to fit residues: 145.2055 Evaluate side-chains 97 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 580 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 479 HIS A 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9808 Z= 0.284 Angle : 0.607 8.673 13324 Z= 0.308 Chirality : 0.044 0.148 1499 Planarity : 0.004 0.045 1677 Dihedral : 5.148 51.720 1369 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.58 % Allowed : 14.72 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1208 helix: 1.27 (0.26), residues: 439 sheet: 0.80 (0.30), residues: 293 loop : -0.76 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 PHE 0.017 0.002 PHE A 123 TYR 0.019 0.002 TYR H 83 ARG 0.006 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.211 Fit side-chains REVERT: H 63 TYR cc_start: 0.8544 (m-80) cc_final: 0.8239 (m-80) REVERT: K 83 MET cc_start: 0.3577 (mmt) cc_final: 0.2522 (mmt) REVERT: L 12 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7263 (tt) REVERT: L 46 LYS cc_start: 0.8318 (ptmm) cc_final: 0.8102 (ptpp) REVERT: L 82 GLU cc_start: 0.8297 (pm20) cc_final: 0.7633 (pm20) REVERT: L 106 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: A 72 MET cc_start: 0.8562 (mtp) cc_final: 0.8136 (mtp) REVERT: A 328 MET cc_start: 0.7113 (tpp) cc_final: 0.6866 (tpt) REVERT: A 524 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.5967 (mp-120) REVERT: A 584 ARG cc_start: 0.7904 (ttt90) cc_final: 0.7455 (ttm110) outliers start: 27 outliers final: 18 residues processed: 105 average time/residue: 1.2757 time to fit residues: 144.1905 Evaluate side-chains 107 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9808 Z= 0.167 Angle : 0.555 9.030 13324 Z= 0.281 Chirality : 0.042 0.138 1499 Planarity : 0.004 0.042 1677 Dihedral : 4.974 48.604 1369 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 2.10 % Allowed : 15.77 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.74 (0.25), residues: 1208 helix: 1.57 (0.26), residues: 438 sheet: 0.87 (0.31), residues: 293 loop : -0.76 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 110 HIS 0.003 0.001 HIS A 105 PHE 0.021 0.001 PHE A 123 TYR 0.018 0.001 TYR H 83 ARG 0.004 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.138 Fit side-chains REVERT: H 63 TYR cc_start: 0.8477 (m-80) cc_final: 0.8002 (m-80) REVERT: K 83 MET cc_start: 0.3546 (mmt) cc_final: 0.2564 (mmt) REVERT: L 46 LYS cc_start: 0.8253 (ptmm) cc_final: 0.8047 (ptpp) REVERT: L 82 GLU cc_start: 0.8270 (pm20) cc_final: 0.7607 (pm20) REVERT: L 101 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7074 (pp30) REVERT: L 106 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: L 164 VAL cc_start: 0.7904 (t) cc_final: 0.7403 (p) REVERT: A 328 MET cc_start: 0.7093 (tpp) cc_final: 0.6856 (tpt) REVERT: A 524 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6021 (mp-120) REVERT: A 584 ARG cc_start: 0.7837 (ttt90) cc_final: 0.7410 (ttm110) outliers start: 22 outliers final: 9 residues processed: 108 average time/residue: 1.2585 time to fit residues: 146.0809 Evaluate side-chains 101 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 580 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 40.0000 chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 527 ASN A 617 GLN A 673 ASN A 675 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9808 Z= 0.180 Angle : 0.562 8.908 13324 Z= 0.286 Chirality : 0.042 0.139 1499 Planarity : 0.004 0.043 1677 Dihedral : 4.964 48.630 1369 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 2.49 % Allowed : 15.49 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.74 (0.25), residues: 1208 helix: 1.55 (0.26), residues: 445 sheet: 0.93 (0.31), residues: 291 loop : -0.82 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 110 HIS 0.003 0.001 HIS A 105 PHE 0.022 0.001 PHE A 123 TYR 0.021 0.001 TYR H 83 ARG 0.006 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.096 Fit side-chains REVERT: H 63 TYR cc_start: 0.8460 (m-80) cc_final: 0.7977 (m-80) REVERT: K 83 MET cc_start: 0.3570 (mmt) cc_final: 0.2542 (mmt) REVERT: L 46 LYS cc_start: 0.8261 (ptmm) cc_final: 0.8056 (ptpp) REVERT: L 82 GLU cc_start: 0.8242 (pm20) cc_final: 0.7531 (pm20) REVERT: L 101 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7066 (pp30) REVERT: L 106 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: L 164 VAL cc_start: 0.7896 (t) cc_final: 0.7417 (p) REVERT: A 328 MET cc_start: 0.7100 (tpp) cc_final: 0.6859 (tpt) REVERT: A 524 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6007 (mp-120) REVERT: A 584 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7440 (ttm110) outliers start: 26 outliers final: 15 residues processed: 108 average time/residue: 1.2143 time to fit residues: 141.2131 Evaluate side-chains 108 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 527 ASN A 675 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9808 Z= 0.218 Angle : 0.586 9.102 13324 Z= 0.298 Chirality : 0.043 0.143 1499 Planarity : 0.004 0.044 1677 Dihedral : 5.068 48.741 1369 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 2.58 % Allowed : 15.58 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.66 (0.25), residues: 1208 helix: 1.48 (0.26), residues: 439 sheet: 0.90 (0.31), residues: 293 loop : -0.83 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 PHE 0.023 0.001 PHE A 123 TYR 0.016 0.001 TYR H 83 ARG 0.005 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.047 Fit side-chains REVERT: H 63 TYR cc_start: 0.8495 (m-80) cc_final: 0.8060 (m-80) REVERT: K 83 MET cc_start: 0.3534 (mmt) cc_final: 0.2567 (mmt) REVERT: L 12 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7356 (tt) REVERT: L 46 LYS cc_start: 0.8281 (ptmm) cc_final: 0.8073 (ptpp) REVERT: L 82 GLU cc_start: 0.8251 (pm20) cc_final: 0.7533 (pm20) REVERT: L 101 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7099 (pp30) REVERT: L 106 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: L 164 VAL cc_start: 0.7968 (t) cc_final: 0.7481 (p) REVERT: A 328 MET cc_start: 0.7107 (tpp) cc_final: 0.6849 (tpt) REVERT: A 524 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6042 (mp-120) REVERT: A 584 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7465 (ttm110) REVERT: A 585 GLU cc_start: 0.7192 (tp30) cc_final: 0.6982 (tp30) outliers start: 27 outliers final: 14 residues processed: 108 average time/residue: 1.2568 time to fit residues: 145.8245 Evaluate side-chains 108 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 527 ASN A 675 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9808 Z= 0.172 Angle : 0.568 9.351 13324 Z= 0.289 Chirality : 0.042 0.138 1499 Planarity : 0.004 0.043 1677 Dihedral : 4.984 47.627 1369 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 2.10 % Allowed : 16.25 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.76 (0.25), residues: 1208 helix: 1.60 (0.26), residues: 445 sheet: 0.98 (0.31), residues: 291 loop : -0.85 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 PHE 0.026 0.001 PHE A 123 TYR 0.020 0.001 TYR H 83 ARG 0.009 0.000 ARG A 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.510 Fit side-chains REVERT: H 63 TYR cc_start: 0.8454 (m-80) cc_final: 0.7957 (m-80) REVERT: K 83 MET cc_start: 0.3519 (mmt) cc_final: 0.2561 (mmt) REVERT: L 12 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7351 (tt) REVERT: L 82 GLU cc_start: 0.8250 (pm20) cc_final: 0.7534 (pm20) REVERT: L 101 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7062 (pp30) REVERT: L 106 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: L 164 VAL cc_start: 0.7880 (t) cc_final: 0.7396 (p) REVERT: A 328 MET cc_start: 0.7102 (tpp) cc_final: 0.6851 (tpt) REVERT: A 524 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6044 (mp-120) REVERT: A 584 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7345 (ttm110) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 1.2691 time to fit residues: 147.8554 Evaluate side-chains 106 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 527 ASN A 675 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.209962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123408 restraints weight = 9640.825| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.19 r_work: 0.3255 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9808 Z= 0.306 Angle : 0.642 10.702 13324 Z= 0.326 Chirality : 0.045 0.155 1499 Planarity : 0.004 0.045 1677 Dihedral : 5.310 48.993 1369 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 2.20 % Allowed : 16.54 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1208 helix: 1.27 (0.26), residues: 440 sheet: 0.92 (0.31), residues: 292 loop : -0.92 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 110 HIS 0.003 0.001 HIS A 55 PHE 0.015 0.002 PHE A 305 TYR 0.020 0.002 TYR H 83 ARG 0.008 0.000 ARG A 676 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3555.09 seconds wall clock time: 64 minutes 54.31 seconds (3894.31 seconds total)