Starting phenix.real_space_refine on Thu Feb 13 22:30:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlh_14780/02_2025/7zlh_14780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlh_14780/02_2025/7zlh_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/cci-nas-00/data/ceres_data/7zlh_14780/02_2025/7zlh_14780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlh_14780/02_2025/7zlh_14780.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlh_14780/02_2025/7zlh_14780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlh_14780/02_2025/7zlh_14780.cif" } 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. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9481 Number of models: 1 Model: "" Number of chains: 5 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: 5278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5278 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 24, 'TRANS': 629} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 6.63, per 1000 atoms: 0.70 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 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: 1.16 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: 3.03 Time building geometry restraints manager: 3.09 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: 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: 0.00 - 2.86: 12993 2.86 - 5.72: 179 5.72 - 8.58: 20 8.58 - 11.44: 6 11.44 - 14.30: 1 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 3.040 nonbonded pdb=" O ALA A 388 " pdb=" OG1 THR A 392 " model vdw 2.200 3.040 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 316 " model vdw 2.206 3.040 nonbonded pdb=" NH1 ARG A 342 " pdb=" O ASN A 437 " model vdw 2.220 3.120 nonbonded pdb=" NE2 GLN H 186 " pdb=" OG SER H 188 " model vdw 2.226 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.790 Find NCS groups from input model: 0.090 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.010 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.049 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: 1.2681 time to fit residues: 145.8538 Evaluate side-chains 82 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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: 4.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.216813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128549 restraints weight = 10354.074| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.37 r_work: 0.3338 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9715 Z= 0.251 Angle : 0.654 10.542 13199 Z= 0.346 Chirality : 0.047 0.268 1486 Planarity : 0.005 0.039 1662 Dihedral : 5.126 59.061 1314 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.63 % Allowed : 7.10 % Favored : 91.27 % 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: -0.37 (0.24), residues: 1199 helix: 0.88 (0.25), residues: 440 sheet: 0.38 (0.32), residues: 266 loop : -1.67 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 440 HIS 0.005 0.001 HIS A 391 PHE 0.032 0.002 PHE A 56 TYR 0.023 0.002 TYR A 578 ARG 0.003 0.000 ARG A 570 *********************** 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 100 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7845 (p0) cc_final: 0.7508 (m-30) REVERT: L 37 TYR cc_start: 0.6179 (m-80) cc_final: 0.5945 (m-80) REVERT: L 46 LYS cc_start: 0.7003 (tmmt) cc_final: 0.6676 (tmtt) REVERT: L 208 LYS cc_start: 0.3124 (mmtp) cc_final: 0.2923 (ttpt) REVERT: A 585 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5939 (pm20) REVERT: A 593 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8495 (mtm) REVERT: A 640 ASP cc_start: 0.8047 (t0) cc_final: 0.7343 (t0) outliers start: 17 outliers final: 6 residues processed: 92 average time/residue: 1.2370 time to fit residues: 122.9781 Evaluate side-chains 88 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 593 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 8 optimal weight: 20.0000 chunk 21 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 chunk 101 optimal weight: 3.9990 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.220264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131850 restraints weight = 10523.732| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.18 r_work: 0.3457 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9715 Z= 0.150 Angle : 0.562 8.105 13199 Z= 0.295 Chirality : 0.043 0.259 1486 Planarity : 0.004 0.040 1662 Dihedral : 4.684 59.573 1314 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.02 % Allowed : 9.88 % Favored : 88.10 % 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: 0.05 (0.25), residues: 1199 helix: 1.46 (0.26), residues: 439 sheet: 0.51 (0.32), residues: 266 loop : -1.60 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 262 HIS 0.004 0.001 HIS A 391 PHE 0.015 0.001 PHE A 387 TYR 0.021 0.001 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 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7769 (p0) cc_final: 0.7553 (m-30) REVERT: L 25 ARG cc_start: 0.5401 (mmm-85) cc_final: 0.4693 (mmt180) REVERT: L 46 LYS cc_start: 0.7011 (tmmt) cc_final: 0.6644 (tmtt) REVERT: A 434 LYS cc_start: 0.5866 (OUTLIER) cc_final: 0.4817 (mttm) REVERT: A 471 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7367 (ttt180) REVERT: A 585 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5818 (pp20) REVERT: A 626 ARG cc_start: 0.5323 (OUTLIER) cc_final: 0.5042 (ppt170) REVERT: A 640 ASP cc_start: 0.7873 (t0) cc_final: 0.7345 (t0) outliers start: 21 outliers final: 7 residues processed: 103 average time/residue: 1.2143 time to fit residues: 135.0249 Evaluate side-chains 98 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN A 42 ASN A 272 GLN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 550 GLN A 677 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.213004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125271 restraints weight = 10425.802| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.35 r_work: 0.3287 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 9715 Z= 0.481 Angle : 0.769 10.026 13199 Z= 0.407 Chirality : 0.054 0.265 1486 Planarity : 0.005 0.043 1662 Dihedral : 5.118 57.857 1312 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.59 % Favored : 93.16 % Rotamer: Outliers : 2.78 % Allowed : 12.19 % Favored : 85.03 % 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: -0.62 (0.24), residues: 1199 helix: 0.47 (0.24), residues: 440 sheet: 0.41 (0.32), residues: 261 loop : -1.67 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 109 HIS 0.007 0.002 HIS A 546 PHE 0.030 0.003 PHE A 390 TYR 0.021 0.003 TYR A 345 ARG 0.005 0.001 ARG A 570 *********************** 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 114 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7865 (p0) cc_final: 0.7488 (m-30) REVERT: L 46 LYS cc_start: 0.6993 (tmmt) cc_final: 0.6744 (ttpt) REVERT: A 70 THR cc_start: 0.8536 (t) cc_final: 0.8228 (m) REVERT: A 434 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5276 (mttm) REVERT: A 471 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7574 (ttt180) REVERT: A 585 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5949 (pm20) REVERT: A 626 ARG cc_start: 0.5666 (OUTLIER) cc_final: 0.3992 (ppt170) REVERT: A 640 ASP cc_start: 0.8179 (t0) cc_final: 0.7396 (t0) outliers start: 29 outliers final: 12 residues processed: 103 average time/residue: 1.1819 time to fit residues: 131.5100 Evaluate side-chains 97 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 K residue 12 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 249 LEU 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 474 LEU Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 626 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 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 31 ASN A 42 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.217475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128739 restraints weight = 10438.460| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.20 r_work: 0.3379 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9715 Z= 0.183 Angle : 0.588 9.569 13199 Z= 0.308 Chirality : 0.044 0.190 1486 Planarity : 0.004 0.043 1662 Dihedral : 4.668 57.594 1312 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.30 % Allowed : 13.24 % Favored : 84.45 % 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: -0.15 (0.25), residues: 1199 helix: 1.11 (0.25), residues: 445 sheet: 0.48 (0.32), residues: 261 loop : -1.58 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 110 HIS 0.005 0.001 HIS A 391 PHE 0.015 0.001 PHE A 390 TYR 0.017 0.001 TYR L 50 ARG 0.002 0.000 ARG A 570 *********************** 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 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7826 (p0) cc_final: 0.7546 (m-30) REVERT: H 68 LYS cc_start: 0.7746 (tppt) cc_final: 0.7546 (tptm) REVERT: H 175 THR cc_start: 0.3648 (OUTLIER) cc_final: 0.3410 (t) REVERT: L 46 LYS cc_start: 0.6994 (tmmt) cc_final: 0.6703 (ttpt) REVERT: L 71 ASP cc_start: 0.5872 (t0) cc_final: 0.5354 (t70) REVERT: L 136 LEU cc_start: 0.3009 (mm) cc_final: 0.2802 (tp) REVERT: A 71 GLU cc_start: 0.8225 (pt0) cc_final: 0.8018 (pt0) REVERT: A 434 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.4969 (mttm) REVERT: A 471 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7250 (ttt180) REVERT: A 585 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5834 (pp20) REVERT: A 640 ASP cc_start: 0.8001 (t0) cc_final: 0.7369 (t0) outliers start: 24 outliers final: 7 residues processed: 105 average time/residue: 1.1472 time to fit residues: 130.6682 Evaluate side-chains 96 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain K residue 78 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN A 42 ASN A 297 HIS ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.213498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125369 restraints weight = 10457.207| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.25 r_work: 0.3310 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9715 Z= 0.396 Angle : 0.716 10.671 13199 Z= 0.377 Chirality : 0.050 0.242 1486 Planarity : 0.005 0.041 1662 Dihedral : 5.025 56.733 1312 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 2.59 % Allowed : 14.68 % 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: -0.57 (0.24), residues: 1199 helix: 0.55 (0.25), residues: 443 sheet: 0.42 (0.32), residues: 257 loop : -1.68 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 109 HIS 0.007 0.002 HIS A 546 PHE 0.027 0.002 PHE A 390 TYR 0.019 0.002 TYR A 345 ARG 0.004 0.000 ARG A 570 *********************** 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 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7791 (p0) cc_final: 0.7478 (m-30) REVERT: H 175 THR cc_start: 0.3659 (OUTLIER) cc_final: 0.3415 (t) REVERT: L 37 TYR cc_start: 0.5913 (m-80) cc_final: 0.5647 (m-80) REVERT: L 46 LYS cc_start: 0.6965 (tmmt) cc_final: 0.6700 (ttpt) REVERT: L 136 LEU cc_start: 0.3075 (mm) cc_final: 0.2844 (tp) REVERT: A 434 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5219 (mttm) REVERT: A 471 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7365 (ttt180) REVERT: A 585 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5822 (pp20) REVERT: A 640 ASP cc_start: 0.8138 (t0) cc_final: 0.7369 (t0) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 1.1719 time to fit residues: 130.4629 Evaluate side-chains 105 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 105 VAL 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 173 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 396 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 30.0000 chunk 85 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 30.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.216255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126390 restraints weight = 10518.770| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.31 r_work: 0.3340 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9715 Z= 0.235 Angle : 0.620 9.731 13199 Z= 0.325 Chirality : 0.045 0.201 1486 Planarity : 0.004 0.043 1662 Dihedral : 4.801 56.038 1312 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.59 % Allowed : 15.55 % Favored : 81.86 % 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: -0.37 (0.24), residues: 1199 helix: 0.82 (0.25), residues: 447 sheet: 0.40 (0.32), residues: 261 loop : -1.62 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 110 HIS 0.006 0.001 HIS A 391 PHE 0.020 0.002 PHE A 390 TYR 0.017 0.002 TYR L 50 ARG 0.002 0.000 ARG A 570 *********************** 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 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7777 (p0) cc_final: 0.7503 (m-30) REVERT: H 68 LYS cc_start: 0.7738 (tppt) cc_final: 0.7536 (tptm) REVERT: H 175 THR cc_start: 0.3692 (OUTLIER) cc_final: 0.3444 (t) REVERT: L 37 TYR cc_start: 0.5925 (m-80) cc_final: 0.5637 (m-80) REVERT: L 46 LYS cc_start: 0.6990 (tmmt) cc_final: 0.6701 (ttpt) REVERT: L 136 LEU cc_start: 0.3048 (mm) cc_final: 0.2838 (tp) REVERT: A 434 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5079 (mttm) REVERT: A 471 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7403 (ttt180) REVERT: A 585 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5785 (pp20) REVERT: A 640 ASP cc_start: 0.8079 (t0) cc_final: 0.7373 (t0) outliers start: 27 outliers final: 14 residues processed: 105 average time/residue: 1.1316 time to fit residues: 129.1165 Evaluate side-chains 100 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 24 SER 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 585 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.215974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127935 restraints weight = 10589.560| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.22 r_work: 0.3315 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1809 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= 0.257 Angle : 0.632 10.021 13199 Z= 0.331 Chirality : 0.046 0.203 1486 Planarity : 0.004 0.043 1662 Dihedral : 4.794 55.260 1312 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.59 % Allowed : 16.03 % Favored : 81.38 % 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: -0.38 (0.24), residues: 1199 helix: 0.82 (0.25), residues: 447 sheet: 0.42 (0.32), residues: 261 loop : -1.66 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 440 HIS 0.006 0.001 HIS A 391 PHE 0.022 0.002 PHE A 390 TYR 0.016 0.002 TYR L 50 ARG 0.002 0.000 ARG A 570 *********************** 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 to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7759 (p0) cc_final: 0.7553 (m-30) REVERT: H 68 LYS cc_start: 0.7779 (tppt) cc_final: 0.7567 (tptm) REVERT: H 175 THR cc_start: 0.3615 (OUTLIER) cc_final: 0.3352 (t) REVERT: L 37 TYR cc_start: 0.5941 (m-80) cc_final: 0.5648 (m-80) REVERT: L 46 LYS cc_start: 0.6985 (tmmt) cc_final: 0.6692 (ttpt) REVERT: L 136 LEU cc_start: 0.3108 (mm) cc_final: 0.2900 (tp) REVERT: A 434 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5207 (mttm) REVERT: A 471 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7414 (ttt180) REVERT: A 585 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5826 (pp20) REVERT: A 640 ASP cc_start: 0.8096 (t0) cc_final: 0.7422 (t0) outliers start: 27 outliers final: 16 residues processed: 104 average time/residue: 1.1468 time to fit residues: 129.0608 Evaluate side-chains 103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 105 VAL 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 436 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN A 42 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.217840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127085 restraints weight = 10496.822| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.24 r_work: 0.3427 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9715 Z= 0.195 Angle : 0.592 10.471 13199 Z= 0.309 Chirality : 0.044 0.176 1486 Planarity : 0.004 0.044 1662 Dihedral : 4.600 54.596 1312 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.11 % Allowed : 16.60 % Favored : 81.29 % 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: -0.18 (0.24), residues: 1199 helix: 1.12 (0.25), residues: 445 sheet: 0.48 (0.32), residues: 261 loop : -1.64 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 143 HIS 0.006 0.001 HIS A 391 PHE 0.017 0.001 PHE A 390 TYR 0.016 0.001 TYR L 50 ARG 0.002 0.000 ARG A 570 *********************** 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 110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7724 (tppt) cc_final: 0.7516 (tptm) REVERT: H 175 THR cc_start: 0.3683 (OUTLIER) cc_final: 0.3437 (t) REVERT: L 37 TYR cc_start: 0.5941 (m-80) cc_final: 0.5686 (m-80) REVERT: L 46 LYS cc_start: 0.7023 (tmmt) cc_final: 0.6781 (ttpt) REVERT: A 313 MET cc_start: 0.7279 (tmm) cc_final: 0.6985 (tpp) REVERT: A 434 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5145 (mttm) REVERT: A 471 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7377 (ttt180) REVERT: A 585 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5816 (pp20) REVERT: A 619 MET cc_start: 0.7740 (ptm) cc_final: 0.7326 (ptm) REVERT: A 640 ASP cc_start: 0.7999 (t0) cc_final: 0.7424 (t0) outliers start: 22 outliers final: 15 residues processed: 107 average time/residue: 1.1264 time to fit residues: 130.9119 Evaluate side-chains 103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 23 THR 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 145 VAL Chi-restraints excluded: chain A residue 173 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN K 65 GLN A 42 ASN A 97 HIS ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.214671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129015 restraints weight = 10594.033| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.50 r_work: 0.3292 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9715 Z= 0.358 Angle : 0.701 10.039 13199 Z= 0.368 Chirality : 0.049 0.224 1486 Planarity : 0.005 0.042 1662 Dihedral : 4.934 53.838 1312 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.58 % Rotamer: Outliers : 2.59 % Allowed : 16.03 % Favored : 81.38 % 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: -0.52 (0.24), residues: 1199 helix: 0.63 (0.25), residues: 443 sheet: 0.41 (0.32), residues: 261 loop : -1.68 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 109 HIS 0.007 0.002 HIS A 546 PHE 0.026 0.002 PHE A 390 TYR 0.018 0.002 TYR A 345 ARG 0.003 0.000 ARG A 393 ********************** 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 to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7763 (tppt) cc_final: 0.7532 (tptm) REVERT: H 175 THR cc_start: 0.3715 (OUTLIER) cc_final: 0.3455 (t) REVERT: L 37 TYR cc_start: 0.5922 (m-80) cc_final: 0.5673 (m-80) REVERT: L 46 LYS cc_start: 0.7005 (tmmt) cc_final: 0.6765 (ttpt) REVERT: A 434 LYS cc_start: 0.6209 (OUTLIER) cc_final: 0.5205 (mttm) REVERT: A 471 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: A 585 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5829 (pp20) REVERT: A 619 MET cc_start: 0.7873 (ptm) cc_final: 0.7482 (ptm) REVERT: A 640 ASP cc_start: 0.8142 (t0) cc_final: 0.7387 (t0) outliers start: 27 outliers final: 20 residues processed: 105 average time/residue: 1.1380 time to fit residues: 129.6746 Evaluate side-chains 106 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 K residue 12 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 ILE 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 173 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 436 THR Chi-restraints excluded: chain A residue 448 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 0.0070 chunk 46 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN A 42 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.218095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130410 restraints weight = 10512.119| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.19 r_work: 0.3387 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9715 Z= 0.189 Angle : 0.597 10.559 13199 Z= 0.312 Chirality : 0.044 0.182 1486 Planarity : 0.004 0.044 1662 Dihedral : 4.648 53.139 1312 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.11 % Allowed : 16.41 % Favored : 81.48 % 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: -0.22 (0.24), residues: 1199 helix: 1.07 (0.25), residues: 446 sheet: 0.49 (0.32), residues: 269 loop : -1.71 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 653 HIS 0.006 0.001 HIS A 391 PHE 0.016 0.001 PHE A 390 TYR 0.015 0.001 TYR L 50 ARG 0.002 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9629.18 seconds wall clock time: 170 minutes 57.34 seconds (10257.34 seconds total)