Starting phenix.real_space_refine on Wed Feb 14 14:34:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlh_14780/02_2024/7zlh_14780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlh_14780/02_2024/7zlh_14780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlh_14780/02_2024/7zlh_14780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlh_14780/02_2024/7zlh_14780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlh_14780/02_2024/7zlh_14780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlh_14780/02_2024/7zlh_14780.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6106 2.51 5 N 1570 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 627": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9481 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1680 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 5282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5282 Classifications: {'peptide': 654, 'water': 4} Link IDs: {'PTRANS': 24, 'TRANS': 629, None: 4} Not linked: pdbres="LEU A 684 " pdbres="HOH A 801 " Not linked: pdbres="HOH A 801 " pdbres="HOH A 802 " Not linked: pdbres="HOH A 802 " pdbres="HOH A 803 " Not linked: pdbres="HOH A 803 " pdbres="HOH A 804 " Chain breaks: 2 Time building chain proxies: 5.69, per 1000 atoms: 0.60 Number of scatterers: 9481 At special positions: 0 Unit cell: (100.98, 161.04, 99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1761 8.00 N 1570 7.00 C 6106 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=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 630 " distance=2.04 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: 3.61 Conformation dependent library (CDL) restraints added in 1.9 seconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 13 sheets defined 39.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'H' and resid 104 through 108 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 203 through 207 removed outlier: 4.094A pdb=" N GLN H 207 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.788A 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 'A' and resid 24 through 55 Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.972A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.899A 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 115 through 136 Proline residue: A 127 - end of helix removed outlier: 3.614A pdb=" N SER A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 175 through 190 removed outlier: 4.279A pdb=" N SER A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.734A pdb=" N GLY A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.625A pdb=" N THR A 210 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 240 removed outlier: 3.912A pdb=" N PHE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.502A pdb=" N ILE A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.522A 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 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 Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 375 through 385 removed outlier: 3.608A pdb=" N PHE A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 removed outlier: 3.630A pdb=" N TYR A 395 " --> pdb=" O HIS A 391 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.723A pdb=" N THR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.748A pdb=" N LEU A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.607A 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 500 through 517 removed outlier: 3.686A pdb=" N GLY A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 534 through 548 removed outlier: 4.680A pdb=" N GLU A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.673A pdb=" N ALA A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 631 through 636 Processing helix chain 'A' and resid 640 through 644 removed outlier: 3.633A pdb=" N SER A 644 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 removed outlier: 4.185A pdb=" N LEU A 655 " --> pdb=" O ASP A 651 " (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: 6.752A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.660A pdb=" N ALA H 151 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AA5, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.800A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 59 through 60 removed outlier: 5.508A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE K 98 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP K 109 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 59 through 60 removed outlier: 5.508A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.588A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119 Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 150 Processing sheet with id=AB3, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.981A pdb=" N TRP A 143 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A 155 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.709A pdb=" N ALA A 555 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN A 617 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR A 678 " --> pdb=" O ASN A 673 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 673 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 680 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 669 " --> pdb=" O LYS A 682 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1305 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: 2.82 Time building geometry restraints manager: 3.80 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: 1487 1.30 - 1.43: 2724 1.43 - 1.56: 5438 1.56 - 1.69: 0 1.69 - 1.82: 66 Bond restraints: 9715 Sorted by residual: bond pdb=" C PRO A 216 " pdb=" O PRO A 216 " ideal model delta sigma weight residual 1.240 1.169 0.071 1.12e-02 7.97e+03 4.04e+01 bond pdb=" C THR A 215 " pdb=" O THR A 215 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.17e-02 7.31e+03 3.61e+01 bond pdb=" C PRO A 576 " pdb=" O PRO A 576 " ideal model delta sigma weight residual 1.238 1.168 0.069 1.24e-02 6.50e+03 3.10e+01 bond pdb=" C MET A 470 " pdb=" O MET A 470 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.24e-02 6.50e+03 2.96e+01 bond pdb=" C PRO A 628 " pdb=" O PRO A 628 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.30e-02 5.92e+03 2.55e+01 ... (remaining 9710 not shown) Histogram of bond angle deviations from ideal: 96.42 - 104.12: 133 104.12 - 111.82: 4589 111.82 - 119.52: 3467 119.52 - 127.22: 4896 127.22 - 134.92: 114 Bond angle restraints: 13199 Sorted by residual: angle pdb=" C TYR A 578 " pdb=" CA TYR A 578 " pdb=" CB TYR A 578 " ideal model delta sigma weight residual 110.78 125.08 -14.30 1.60e+00 3.91e-01 7.99e+01 angle pdb=" CA MET A 470 " pdb=" C MET A 470 " pdb=" O MET A 470 " ideal model delta sigma weight residual 121.55 114.18 7.37 1.06e+00 8.90e-01 4.84e+01 angle pdb=" N PHE A 401 " pdb=" CA PHE A 401 " pdb=" C PHE A 401 " ideal model delta sigma weight residual 111.87 102.25 9.62 1.41e+00 5.03e-01 4.65e+01 angle pdb=" N PRO A 216 " pdb=" CA PRO A 216 " pdb=" C PRO A 216 " ideal model delta sigma weight residual 110.70 118.73 -8.03 1.22e+00 6.72e-01 4.33e+01 angle pdb=" CA PRO A 216 " pdb=" C PRO A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 117.93 124.64 -6.71 1.20e+00 6.94e-01 3.13e+01 ... (remaining 13194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5218 17.95 - 35.89: 412 35.89 - 53.84: 65 53.84 - 71.78: 11 71.78 - 89.73: 15 Dihedral angle restraints: 5721 sinusoidal: 2194 harmonic: 3527 Sorted by residual: 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 93.00 169.90 -76.90 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" C THR A 70 " pdb=" N THR A 70 " pdb=" CA THR A 70 " pdb=" CB THR A 70 " ideal model delta harmonic sigma weight residual -122.00 -143.17 21.17 0 2.50e+00 1.60e-01 7.17e+01 dihedral pdb=" C GLU A 579 " pdb=" N GLU A 579 " pdb=" CA GLU A 579 " pdb=" CB GLU A 579 " ideal model delta harmonic sigma weight residual -122.60 -104.25 -18.35 0 2.50e+00 1.60e-01 5.39e+01 ... (remaining 5718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1467 0.151 - 0.302: 14 0.302 - 0.454: 3 0.454 - 0.605: 1 0.605 - 0.756: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA THR A 70 " pdb=" N THR A 70 " pdb=" C THR A 70 " pdb=" CB THR A 70 " both_signs ideal model delta sigma weight residual False 2.53 1.77 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA GLU A 579 " pdb=" N GLU A 579 " pdb=" C GLU A 579 " pdb=" CB GLU A 579 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CA PRO A 216 " pdb=" N PRO A 216 " pdb=" C PRO A 216 " pdb=" CB PRO A 216 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 1483 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 261 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A 261 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A 261 " -0.029 2.00e-02 2.50e+03 pdb=" N TRP A 262 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 262 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C TRP A 262 " 0.058 2.00e-02 2.50e+03 pdb=" O TRP A 262 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 263 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 56 " 0.024 2.00e-02 2.50e+03 2.38e-02 9.93e+00 pdb=" CG PHE A 56 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 56 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 56 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 56 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 56 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 56 " 0.004 2.00e-02 2.50e+03 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 382 2.72 - 3.26: 9411 3.26 - 3.81: 15221 3.81 - 4.35: 18868 4.35 - 4.90: 31957 Nonbonded interactions: 75839 Sorted by model distance: nonbonded pdb=" OH TYR A 116 " pdb=" O LEU A 307 " model vdw 2.169 2.440 nonbonded pdb=" O ALA A 388 " pdb=" OG1 THR A 392 " model vdw 2.200 2.440 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 316 " model vdw 2.206 2.440 nonbonded pdb=" NH1 ARG A 342 " pdb=" O ASN A 437 " model vdw 2.220 2.520 nonbonded pdb=" NE2 GLN H 186 " pdb=" OG SER H 188 " model vdw 2.226 2.520 ... (remaining 75834 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: 3.600 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: 14.030 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.800 Find NCS groups from input model: 0.260 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9715 Z= 0.340 Angle : 0.808 14.300 13199 Z= 0.476 Chirality : 0.057 0.756 1486 Planarity : 0.005 0.046 1662 Dihedral : 13.853 89.729 3433 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.42 % Favored : 94.16 % Rotamer: Outliers : 0.48 % Allowed : 0.86 % Favored : 98.66 % Cbeta Deviations : 0.27 % 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 (0.24), residues: 1199 helix: 0.36 (0.25), residues: 436 sheet: 0.49 (0.33), residues: 265 loop : -1.72 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 262 HIS 0.015 0.002 HIS A 580 PHE 0.055 0.002 PHE A 56 TYR 0.018 0.002 TYR A 75 ARG 0.004 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7586 (p0) cc_final: 0.7284 (m-30) REVERT: L 6 THR cc_start: 0.6669 (t) cc_final: 0.6356 (p) REVERT: L 37 TYR cc_start: 0.5852 (m-80) cc_final: 0.5627 (m-80) REVERT: L 46 LYS cc_start: 0.6902 (tmmt) cc_final: 0.6535 (tmtt) REVERT: L 208 LYS cc_start: 0.3030 (mmtp) cc_final: 0.2803 (ttpt) REVERT: A 640 ASP cc_start: 0.7591 (t0) cc_final: 0.7314 (t0) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 1.2324 time to fit residues: 142.1285 Evaluate side-chains 82 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 578 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 545 GLN A 550 GLN A 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9715 Z= 0.180 Angle : 0.596 9.729 13199 Z= 0.311 Chirality : 0.044 0.276 1486 Planarity : 0.004 0.039 1662 Dihedral : 4.910 59.030 1314 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 1.54 % Allowed : 6.91 % Favored : 91.55 % 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: -0.11 (0.25), residues: 1199 helix: 1.20 (0.26), residues: 439 sheet: 0.46 (0.32), residues: 268 loop : -1.59 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 262 HIS 0.006 0.001 HIS A 391 PHE 0.026 0.002 PHE A 56 TYR 0.020 0.001 TYR L 50 ARG 0.002 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7473 (tppt) cc_final: 0.7262 (tppp) REVERT: L 46 LYS cc_start: 0.6926 (tmmt) cc_final: 0.6541 (tmtt) REVERT: L 208 LYS cc_start: 0.3020 (mmtp) cc_final: 0.2811 (ttpt) REVERT: A 70 THR cc_start: 0.8064 (t) cc_final: 0.7732 (m) REVERT: A 585 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5547 (pm20) REVERT: A 640 ASP cc_start: 0.7627 (t0) cc_final: 0.7325 (t0) outliers start: 16 outliers final: 6 residues processed: 98 average time/residue: 1.1688 time to fit residues: 123.6840 Evaluate side-chains 89 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 585 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 109 optimal weight: 0.0570 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- 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** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9715 Z= 0.202 Angle : 0.586 7.959 13199 Z= 0.308 Chirality : 0.045 0.231 1486 Planarity : 0.004 0.039 1662 Dihedral : 4.774 57.473 1314 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 1.73 % Allowed : 9.88 % Favored : 88.39 % 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: -0.07 (0.25), residues: 1199 helix: 1.29 (0.25), residues: 439 sheet: 0.41 (0.32), residues: 270 loop : -1.58 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 110 HIS 0.005 0.001 HIS A 391 PHE 0.023 0.002 PHE A 390 TYR 0.020 0.002 TYR L 50 ARG 0.003 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7531 (p0) cc_final: 0.7260 (m-30) REVERT: H 185 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5400 (tm) REVERT: L 25 ARG cc_start: 0.5208 (mmm-85) cc_final: 0.4584 (mmt180) REVERT: L 46 LYS cc_start: 0.6984 (tmmt) cc_final: 0.6615 (tmtt) REVERT: L 208 LYS cc_start: 0.2969 (mmtp) cc_final: 0.2760 (ttpt) REVERT: A 434 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.5448 (mttm) REVERT: A 471 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6837 (ttt180) REVERT: A 578 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.6772 (t80) REVERT: A 640 ASP cc_start: 0.7625 (t0) cc_final: 0.7288 (t0) outliers start: 18 outliers final: 6 residues processed: 97 average time/residue: 1.1869 time to fit residues: 124.2912 Evaluate side-chains 92 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9715 Z= 0.272 Angle : 0.624 8.385 13199 Z= 0.329 Chirality : 0.047 0.260 1486 Planarity : 0.004 0.040 1662 Dihedral : 4.747 57.647 1312 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 2.40 % Allowed : 11.32 % Favored : 86.28 % 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: -0.26 (0.24), residues: 1199 helix: 1.03 (0.25), residues: 440 sheet: 0.46 (0.33), residues: 253 loop : -1.62 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 109 HIS 0.005 0.001 HIS A 479 PHE 0.026 0.002 PHE A 390 TYR 0.020 0.002 TYR L 50 ARG 0.003 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7530 (p0) cc_final: 0.7235 (m-30) REVERT: H 175 THR cc_start: 0.3133 (OUTLIER) cc_final: 0.2817 (t) REVERT: H 185 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5471 (tm) REVERT: L 25 ARG cc_start: 0.5205 (mmm-85) cc_final: 0.4594 (mmt180) REVERT: L 46 LYS cc_start: 0.6959 (tmmt) cc_final: 0.6709 (ttpt) REVERT: A 434 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.5569 (mttm) REVERT: A 471 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6929 (ttt180) REVERT: A 578 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 585 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5570 (pm20) REVERT: A 640 ASP cc_start: 0.7740 (t0) cc_final: 0.7297 (t0) outliers start: 25 outliers final: 5 residues processed: 101 average time/residue: 1.1246 time to fit residues: 123.0698 Evaluate side-chains 95 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 585 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 29 optimal weight: 20.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9715 Z= 0.188 Angle : 0.578 10.019 13199 Z= 0.301 Chirality : 0.044 0.242 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.567 57.335 1312 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 2.11 % Allowed : 12.96 % Favored : 84.93 % 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: -0.06 (0.25), residues: 1199 helix: 1.32 (0.26), residues: 439 sheet: 0.53 (0.33), residues: 251 loop : -1.59 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 110 HIS 0.005 0.001 HIS A 391 PHE 0.018 0.001 PHE A 390 TYR 0.019 0.001 TYR L 50 ARG 0.002 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 175 THR cc_start: 0.3136 (OUTLIER) cc_final: 0.2831 (t) REVERT: H 185 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5470 (tm) REVERT: L 46 LYS cc_start: 0.6994 (tmmt) cc_final: 0.6778 (ttpt) REVERT: L 136 LEU cc_start: 0.3382 (mm) cc_final: 0.3159 (tp) REVERT: A 434 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.5449 (mttm) REVERT: A 471 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6900 (ttt180) REVERT: A 578 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6777 (t80) REVERT: A 585 GLU cc_start: 0.6185 (pm20) cc_final: 0.5850 (pp20) REVERT: A 640 ASP cc_start: 0.7649 (t0) cc_final: 0.7305 (t0) outliers start: 22 outliers final: 10 residues processed: 104 average time/residue: 1.1219 time to fit residues: 126.2221 Evaluate side-chains 98 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 593 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** L 101 GLN A 272 GLN A 297 HIS ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9715 Z= 0.264 Angle : 0.624 9.367 13199 Z= 0.327 Chirality : 0.046 0.207 1486 Planarity : 0.004 0.041 1662 Dihedral : 4.734 57.609 1312 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 2.40 % Allowed : 14.20 % Favored : 83.40 % 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: -0.29 (0.24), residues: 1199 helix: 1.07 (0.25), residues: 440 sheet: 0.42 (0.32), residues: 259 loop : -1.72 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 109 HIS 0.005 0.001 HIS A 479 PHE 0.025 0.002 PHE A 390 TYR 0.017 0.002 TYR L 50 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 175 THR cc_start: 0.3140 (OUTLIER) cc_final: 0.2848 (t) REVERT: H 185 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5508 (tm) REVERT: L 46 LYS cc_start: 0.7011 (tmmt) cc_final: 0.6707 (ttpt) REVERT: L 136 LEU cc_start: 0.3475 (mm) cc_final: 0.3228 (tp) REVERT: A 434 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.5553 (mttm) REVERT: A 471 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6899 (ttt180) REVERT: A 578 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6872 (t80) REVERT: A 585 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5883 (pp20) REVERT: A 640 ASP cc_start: 0.7750 (t0) cc_final: 0.7315 (t0) outliers start: 25 outliers final: 10 residues processed: 101 average time/residue: 1.1626 time to fit residues: 126.9359 Evaluate side-chains 99 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 593 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9715 Z= 0.230 Angle : 0.596 9.057 13199 Z= 0.312 Chirality : 0.045 0.198 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.664 57.432 1312 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 93.99 % Rotamer: Outliers : 2.69 % Allowed : 14.59 % Favored : 82.73 % 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: -0.23 (0.24), residues: 1199 helix: 1.16 (0.25), residues: 438 sheet: 0.43 (0.32), residues: 259 loop : -1.71 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 110 HIS 0.005 0.001 HIS A 391 PHE 0.021 0.002 PHE A 390 TYR 0.016 0.002 TYR L 50 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 175 THR cc_start: 0.3128 (OUTLIER) cc_final: 0.2840 (t) REVERT: H 185 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5463 (tm) REVERT: L 46 LYS cc_start: 0.7009 (tmmt) cc_final: 0.6747 (ttpt) REVERT: L 136 LEU cc_start: 0.3466 (mm) cc_final: 0.3233 (tp) REVERT: A 434 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5481 (mttm) REVERT: A 471 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6885 (ttt180) REVERT: A 578 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6865 (t80) REVERT: A 585 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5878 (pp20) REVERT: A 626 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.3874 (pmt170) REVERT: A 640 ASP cc_start: 0.7714 (t0) cc_final: 0.7336 (t0) outliers start: 28 outliers final: 14 residues processed: 103 average time/residue: 1.1504 time to fit residues: 128.1679 Evaluate side-chains 102 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 626 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9715 Z= 0.242 Angle : 0.606 9.496 13199 Z= 0.317 Chirality : 0.045 0.200 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.683 57.421 1312 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 2.78 % Allowed : 14.59 % Favored : 82.63 % 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: -0.26 (0.24), residues: 1199 helix: 1.11 (0.25), residues: 438 sheet: 0.43 (0.32), residues: 257 loop : -1.68 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 109 HIS 0.005 0.001 HIS A 479 PHE 0.023 0.002 PHE A 390 TYR 0.015 0.002 TYR L 50 ARG 0.004 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7451 (tppt) cc_final: 0.7237 (tptm) REVERT: H 175 THR cc_start: 0.3092 (OUTLIER) cc_final: 0.2803 (t) REVERT: H 185 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5474 (tm) REVERT: L 46 LYS cc_start: 0.7014 (tmmt) cc_final: 0.6753 (ttpt) REVERT: L 136 LEU cc_start: 0.3459 (mm) cc_final: 0.3229 (tp) REVERT: A 434 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.5512 (mttm) REVERT: A 471 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6897 (ttt180) REVERT: A 578 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6888 (t80) REVERT: A 585 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5832 (pp20) REVERT: A 640 ASP cc_start: 0.7750 (t0) cc_final: 0.7355 (t0) outliers start: 29 outliers final: 17 residues processed: 103 average time/residue: 1.1912 time to fit residues: 133.2606 Evaluate side-chains 107 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 593 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9715 Z= 0.176 Angle : 0.564 10.171 13199 Z= 0.294 Chirality : 0.043 0.175 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.505 57.130 1312 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.11 % Allowed : 15.64 % Favored : 82.25 % 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: -0.04 (0.25), residues: 1199 helix: 1.38 (0.26), residues: 439 sheet: 0.51 (0.33), residues: 257 loop : -1.63 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.006 0.001 HIS A 391 PHE 0.017 0.001 PHE A 390 TYR 0.015 0.001 TYR L 50 ARG 0.004 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7424 (tppt) cc_final: 0.7221 (tptm) REVERT: H 175 THR cc_start: 0.3096 (OUTLIER) cc_final: 0.2812 (t) REVERT: H 185 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5467 (tm) REVERT: L 46 LYS cc_start: 0.7031 (tmmt) cc_final: 0.6775 (ttpt) REVERT: L 136 LEU cc_start: 0.3477 (mm) cc_final: 0.3261 (tp) REVERT: A 434 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.5410 (mttm) REVERT: A 471 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6852 (ttt180) REVERT: A 578 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6865 (t80) REVERT: A 585 GLU cc_start: 0.6205 (pm20) cc_final: 0.5802 (pp20) REVERT: A 640 ASP cc_start: 0.7667 (t0) cc_final: 0.7365 (t0) outliers start: 22 outliers final: 15 residues processed: 101 average time/residue: 1.0434 time to fit residues: 114.6691 Evaluate side-chains 102 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 593 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0970 chunk 79 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 0.0170 chunk 95 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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** A 42 ASN A 97 HIS ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9715 Z= 0.139 Angle : 0.525 7.915 13199 Z= 0.273 Chirality : 0.042 0.164 1486 Planarity : 0.004 0.041 1662 Dihedral : 4.302 56.514 1312 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.92 % Allowed : 16.31 % Favored : 81.77 % 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: 0.21 (0.25), residues: 1199 helix: 1.68 (0.26), residues: 440 sheet: 0.63 (0.33), residues: 266 loop : -1.63 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 143 HIS 0.005 0.001 HIS A 391 PHE 0.013 0.001 PHE A 390 TYR 0.014 0.001 TYR L 50 ARG 0.004 0.000 ARG A 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: H 175 THR cc_start: 0.2965 (OUTLIER) cc_final: 0.2709 (t) REVERT: H 185 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5461 (tm) REVERT: L 38 GLN cc_start: 0.5411 (tt0) cc_final: 0.5172 (tt0) REVERT: L 46 LYS cc_start: 0.7077 (tmmt) cc_final: 0.6794 (ttpt) REVERT: L 136 LEU cc_start: 0.3499 (mm) cc_final: 0.3271 (tp) REVERT: A 313 MET cc_start: 0.6681 (tpp) cc_final: 0.6344 (tmm) REVERT: A 471 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6735 (ttt180) REVERT: A 578 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6771 (t80) REVERT: A 585 GLU cc_start: 0.6205 (pm20) cc_final: 0.5819 (pp20) REVERT: A 626 ARG cc_start: 0.5271 (OUTLIER) cc_final: 0.1409 (mtp85) outliers start: 20 outliers final: 10 residues processed: 105 average time/residue: 1.0948 time to fit residues: 125.3030 Evaluate side-chains 97 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 626 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 40.0000 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.0000 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.217542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127641 restraints weight = 10487.420| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.14 r_work: 0.3384 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9715 Z= 0.224 Angle : 0.591 8.426 13199 Z= 0.310 Chirality : 0.045 0.178 1486 Planarity : 0.004 0.041 1662 Dihedral : 4.475 56.982 1312 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.50 % Rotamer: Outliers : 1.54 % Allowed : 16.79 % Favored : 81.67 % 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: 0.01 (0.25), residues: 1199 helix: 1.33 (0.26), residues: 440 sheet: 0.60 (0.33), residues: 271 loop : -1.62 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 110 HIS 0.006 0.001 HIS A 391 PHE 0.025 0.002 PHE A 390 TYR 0.015 0.002 TYR L 50 ARG 0.004 0.000 ARG A 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.79 seconds wall clock time: 63 minutes 1.20 seconds (3781.20 seconds total)