Starting phenix.real_space_refine on Wed Mar 4 00:13:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlh_14780/03_2026/7zlh_14780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlh_14780/03_2026/7zlh_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_14780/03_2026/7zlh_14780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlh_14780/03_2026/7zlh_14780.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlh_14780/03_2026/7zlh_14780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlh_14780/03_2026/7zlh_14780.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.03, per 1000 atoms: 0.21 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: 0.62 Conformation dependent library (CDL) restraints added in 349.2 milliseconds 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: 0.34 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: 1.37 Time building geometry restraints manager: 0.84 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: 4.050 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- 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 9723 Z= 0.315 Angle : 0.810 14.300 13215 Z= 0.477 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 : 9.56 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG A 69 TYR 0.018 0.002 TYR A 75 PHE 0.055 0.002 PHE A 56 TRP 0.019 0.002 TRP A 262 HIS 0.015 0.002 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 9715) covalent geometry : angle 0.80828 (13199) SS BOND : bond 0.00688 ( 8) SS BOND : angle 1.81409 ( 16) hydrogen bonds : bond 0.16265 ( 459) hydrogen bonds : angle 6.50875 ( 1305) *********************** 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 : 0.306 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: 0.5621 time to fit residues: 64.4454 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 : 0.290 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 30.0000 chunk 117 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.215813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126671 restraints weight = 10533.294| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.17 r_work: 0.3335 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.005 0.039 9723 Z= 0.195 Angle : 0.684 10.796 13215 Z= 0.362 Chirality : 0.048 0.300 1486 Planarity : 0.005 0.040 1662 Dihedral : 5.211 58.598 1314 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.34 % Favored : 93.58 % Rotamer: Outliers : 1.73 % Allowed : 7.49 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1199 helix: 0.66 (0.25), residues: 446 sheet: 0.44 (0.32), residues: 263 loop : -1.69 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.025 0.002 TYR A 578 PHE 0.033 0.002 PHE A 56 TRP 0.018 0.002 TRP H 109 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9715) covalent geometry : angle 0.68073 (13199) SS BOND : bond 0.00555 ( 8) SS BOND : angle 1.95634 ( 16) hydrogen bonds : bond 0.05674 ( 459) hydrogen bonds : angle 4.92944 ( 1305) *********************** 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 101 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7836 (p0) cc_final: 0.7488 (m-30) REVERT: L 37 TYR cc_start: 0.6198 (m-80) cc_final: 0.5973 (m-80) REVERT: L 46 LYS cc_start: 0.7029 (tmmt) cc_final: 0.6709 (tmtt) REVERT: L 208 LYS cc_start: 0.3126 (mmtp) cc_final: 0.2916 (ttpt) REVERT: A 585 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5910 (pm20) REVERT: A 640 ASP cc_start: 0.8068 (t0) cc_final: 0.7367 (t0) outliers start: 18 outliers final: 7 residues processed: 93 average time/residue: 0.5406 time to fit residues: 54.0375 Evaluate side-chains 89 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 12 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** 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 = 0.4478 r_free = 0.4478 target = 0.214617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126024 restraints weight = 10471.297| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.44 r_work: 0.3293 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9723 Z= 0.217 Angle : 0.691 9.498 13215 Z= 0.366 Chirality : 0.049 0.279 1486 Planarity : 0.005 0.043 1662 Dihedral : 5.271 58.006 1314 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.49 % Rotamer: Outliers : 2.50 % Allowed : 10.75 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1199 helix: 0.65 (0.25), residues: 440 sheet: 0.53 (0.32), residues: 258 loop : -1.69 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.021 0.002 TYR L 50 PHE 0.025 0.002 PHE A 390 TRP 0.021 0.002 TRP H 109 HIS 0.006 0.002 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9715) covalent geometry : angle 0.68885 (13199) SS BOND : bond 0.00501 ( 8) SS BOND : angle 1.83328 ( 16) hydrogen bonds : bond 0.05830 ( 459) hydrogen bonds : angle 4.82728 ( 1305) *********************** 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 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7860 (p0) cc_final: 0.7479 (m-30) REVERT: L 37 TYR cc_start: 0.6259 (m-80) cc_final: 0.5997 (m-80) REVERT: L 46 LYS cc_start: 0.7057 (tmmt) cc_final: 0.6673 (tmtt) REVERT: A 471 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7554 (ttt180) REVERT: A 585 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: A 626 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.3986 (ppt170) REVERT: A 640 ASP cc_start: 0.8107 (t0) cc_final: 0.7409 (t0) outliers start: 26 outliers final: 11 residues processed: 100 average time/residue: 0.5894 time to fit residues: 63.1981 Evaluate side-chains 96 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 50.0000 chunk 16 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 0.0170 chunk 67 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 overall best weight: 1.5422 ------------------------------------------------------------------------------- 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 550 GLN 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 = 0.216026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125772 restraints weight = 10579.938| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.14 r_work: 0.3401 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9723 Z= 0.164 Angle : 0.634 8.647 13215 Z= 0.334 Chirality : 0.047 0.264 1486 Planarity : 0.004 0.044 1662 Dihedral : 5.071 57.506 1314 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.50 % Allowed : 12.67 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1199 helix: 0.93 (0.25), residues: 441 sheet: 0.43 (0.32), residues: 261 loop : -1.66 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.019 0.002 TYR L 50 PHE 0.021 0.002 PHE A 390 TRP 0.013 0.002 TRP A 440 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9715) covalent geometry : angle 0.63173 (13199) SS BOND : bond 0.00487 ( 8) SS BOND : angle 1.75018 ( 16) hydrogen bonds : bond 0.04905 ( 459) hydrogen bonds : angle 4.62788 ( 1305) *********************** 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 to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7755 (p0) cc_final: 0.7472 (m-30) REVERT: H 175 THR cc_start: 0.3648 (OUTLIER) cc_final: 0.3419 (t) REVERT: L 25 ARG cc_start: 0.5478 (mmm-85) cc_final: 0.4777 (mmt180) REVERT: L 37 TYR cc_start: 0.6140 (m-80) cc_final: 0.5909 (m-80) REVERT: L 46 LYS cc_start: 0.7057 (tmmt) cc_final: 0.6785 (ttpt) REVERT: A 297 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.8063 (m-70) REVERT: A 471 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7479 (ttt180) REVERT: A 585 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5799 (pp20) REVERT: A 640 ASP cc_start: 0.8078 (t0) cc_final: 0.7413 (t0) outliers start: 26 outliers final: 10 residues processed: 103 average time/residue: 0.5542 time to fit residues: 61.3721 Evaluate side-chains 96 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 127 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 297 HIS 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 474 LEU 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 39 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 550 GLN 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 = 0.217642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129863 restraints weight = 10565.150| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.26 r_work: 0.3382 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9723 Z= 0.129 Angle : 0.593 9.879 13215 Z= 0.309 Chirality : 0.045 0.270 1486 Planarity : 0.004 0.043 1662 Dihedral : 4.827 57.430 1314 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.21 % Allowed : 14.20 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1199 helix: 1.29 (0.26), residues: 439 sheet: 0.42 (0.32), residues: 263 loop : -1.64 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 25 TYR 0.017 0.001 TYR L 50 PHE 0.016 0.001 PHE A 390 TRP 0.011 0.001 TRP A 27 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9715) covalent geometry : angle 0.59104 (13199) SS BOND : bond 0.00559 ( 8) SS BOND : angle 1.55450 ( 16) hydrogen bonds : bond 0.04183 ( 459) hydrogen bonds : angle 4.42282 ( 1305) *********************** 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 114 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7795 (p0) cc_final: 0.7584 (m-30) REVERT: H 68 LYS cc_start: 0.7697 (tppt) cc_final: 0.7492 (tptm) REVERT: H 175 THR cc_start: 0.3658 (OUTLIER) cc_final: 0.3419 (t) REVERT: L 46 LYS cc_start: 0.7014 (tmmt) cc_final: 0.6707 (ttpt) REVERT: L 136 LEU cc_start: 0.3126 (mm) cc_final: 0.2907 (tp) REVERT: A 297 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.8060 (m-70) REVERT: A 434 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.4850 (mttm) REVERT: A 471 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7368 (ttt180) REVERT: A 585 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5805 (pp20) REVERT: A 640 ASP cc_start: 0.8026 (t0) cc_final: 0.7374 (t0) outliers start: 23 outliers final: 9 residues processed: 108 average time/residue: 0.5028 time to fit residues: 58.7308 Evaluate side-chains 99 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 297 HIS 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 20 optimal weight: 0.0010 chunk 86 optimal weight: 0.0980 chunk 12 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** 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 = 0.4503 r_free = 0.4503 target = 0.217524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128635 restraints weight = 10482.692| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.35 r_work: 0.3360 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9723 Z= 0.139 Angle : 0.594 9.650 13215 Z= 0.310 Chirality : 0.045 0.204 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.593 57.065 1312 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.50 % Allowed : 15.45 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1199 helix: 1.20 (0.25), residues: 445 sheet: 0.52 (0.33), residues: 247 loop : -1.68 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 570 TYR 0.018 0.001 TYR L 50 PHE 0.019 0.001 PHE A 390 TRP 0.012 0.001 TRP A 440 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9715) covalent geometry : angle 0.59270 (13199) SS BOND : bond 0.00487 ( 8) SS BOND : angle 1.44683 ( 16) hydrogen bonds : bond 0.04415 ( 459) hydrogen bonds : angle 4.36815 ( 1305) *********************** 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 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7792 (p0) cc_final: 0.7566 (m-30) REVERT: H 68 LYS cc_start: 0.7694 (tppt) cc_final: 0.7492 (tptm) REVERT: H 175 THR cc_start: 0.3713 (OUTLIER) cc_final: 0.3490 (t) REVERT: L 46 LYS cc_start: 0.6986 (tmmt) cc_final: 0.6682 (ttpt) REVERT: L 136 LEU cc_start: 0.3107 (mm) cc_final: 0.2903 (tp) REVERT: A 71 GLU cc_start: 0.8186 (pt0) cc_final: 0.7985 (pt0) REVERT: A 434 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.4905 (mttm) REVERT: A 471 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7306 (ttt180) REVERT: A 585 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5769 (pp20) REVERT: A 626 ARG cc_start: 0.5617 (OUTLIER) cc_final: 0.4026 (ppt170) REVERT: A 640 ASP cc_start: 0.8027 (t0) cc_final: 0.7346 (t0) outliers start: 26 outliers final: 16 residues processed: 107 average time/residue: 0.5324 time to fit residues: 61.6070 Evaluate side-chains 104 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 34 VAL 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 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 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 Chi-restraints excluded: chain A residue 626 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 40.0000 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** 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 = 0.4501 r_free = 0.4501 target = 0.217338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127442 restraints weight = 10525.640| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.32 r_work: 0.3360 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9723 Z= 0.144 Angle : 0.599 9.677 13215 Z= 0.312 Chirality : 0.044 0.187 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.631 56.408 1312 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.78 % Allowed : 15.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1199 helix: 1.17 (0.25), residues: 445 sheet: 0.52 (0.33), residues: 247 loop : -1.69 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.017 0.001 TYR L 50 PHE 0.020 0.002 PHE A 390 TRP 0.012 0.001 TRP A 440 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9715) covalent geometry : angle 0.59690 (13199) SS BOND : bond 0.00705 ( 8) SS BOND : angle 1.52368 ( 16) hydrogen bonds : bond 0.04456 ( 459) hydrogen bonds : angle 4.40513 ( 1305) *********************** 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 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7705 (tppt) cc_final: 0.7500 (tptm) REVERT: H 175 THR cc_start: 0.3671 (OUTLIER) cc_final: 0.3420 (t) REVERT: H 185 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5692 (tm) REVERT: L 37 TYR cc_start: 0.5814 (m-80) cc_final: 0.5610 (m-80) REVERT: L 46 LYS cc_start: 0.6982 (tmmt) cc_final: 0.6683 (ttpt) REVERT: L 136 LEU cc_start: 0.3085 (mm) cc_final: 0.2883 (tp) REVERT: A 434 LYS cc_start: 0.6059 (OUTLIER) cc_final: 0.4965 (mttm) REVERT: A 471 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7378 (ttt180) REVERT: A 585 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5790 (pp20) REVERT: A 640 ASP cc_start: 0.8007 (t0) cc_final: 0.7372 (t0) outliers start: 29 outliers final: 19 residues processed: 108 average time/residue: 0.5384 time to fit residues: 62.7797 Evaluate side-chains 110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 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 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 15 optimal weight: 8.9990 chunk 53 optimal weight: 40.0000 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.218621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128640 restraints weight = 10560.039| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.31 r_work: 0.3391 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9723 Z= 0.125 Angle : 0.582 10.158 13215 Z= 0.302 Chirality : 0.043 0.162 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.513 55.978 1312 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.07 % Allowed : 15.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1199 helix: 1.34 (0.26), residues: 445 sheet: 0.57 (0.33), residues: 253 loop : -1.71 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.016 0.001 TYR L 50 PHE 0.016 0.001 PHE A 390 TRP 0.013 0.001 TRP A 143 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9715) covalent geometry : angle 0.58075 (13199) SS BOND : bond 0.00614 ( 8) SS BOND : angle 1.32108 ( 16) hydrogen bonds : bond 0.04009 ( 459) hydrogen bonds : angle 4.30289 ( 1305) *********************** 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 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7712 (tppt) cc_final: 0.7506 (tptm) REVERT: H 175 THR cc_start: 0.3685 (OUTLIER) cc_final: 0.3443 (t) REVERT: L 37 TYR cc_start: 0.5846 (m-80) cc_final: 0.5588 (m-80) REVERT: L 46 LYS cc_start: 0.6997 (tmmt) cc_final: 0.6752 (ttpt) REVERT: L 71 ASP cc_start: 0.5763 (t0) cc_final: 0.5207 (t70) REVERT: A 313 MET cc_start: 0.7203 (tmm) cc_final: 0.6918 (tpp) REVERT: A 434 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.4927 (mttm) REVERT: A 471 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7344 (ttt180) REVERT: A 585 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5785 (pp20) REVERT: A 640 ASP cc_start: 0.7960 (t0) cc_final: 0.7361 (t0) outliers start: 32 outliers final: 16 residues processed: 116 average time/residue: 0.5143 time to fit residues: 64.5783 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 : 0.350 ------------------------------------------------------------------------------- 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 34 VAL 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 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 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 11 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 107 optimal weight: 0.0870 chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 overall best weight: 1.2362 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.217654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130425 restraints weight = 10537.923| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.49 r_work: 0.3323 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9723 Z= 0.145 Angle : 0.607 9.845 13215 Z= 0.315 Chirality : 0.045 0.176 1486 Planarity : 0.004 0.041 1662 Dihedral : 4.562 55.012 1312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.69 % Allowed : 14.97 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1199 helix: 1.23 (0.25), residues: 445 sheet: 0.55 (0.33), residues: 253 loop : -1.72 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 112 TYR 0.016 0.001 TYR L 50 PHE 0.020 0.001 PHE A 390 TRP 0.032 0.002 TRP H 110 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9715) covalent geometry : angle 0.60485 (13199) SS BOND : bond 0.00630 ( 8) SS BOND : angle 1.46106 ( 16) hydrogen bonds : bond 0.04428 ( 459) hydrogen bonds : angle 4.34913 ( 1305) *********************** 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: 28 poor density : 82 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7781 (tppt) cc_final: 0.7571 (tptm) REVERT: H 175 THR cc_start: 0.3650 (OUTLIER) cc_final: 0.3403 (t) REVERT: L 37 TYR cc_start: 0.5917 (m-80) cc_final: 0.5651 (m-80) REVERT: L 46 LYS cc_start: 0.7012 (tmmt) cc_final: 0.6760 (ttpt) REVERT: A 313 MET cc_start: 0.7270 (tmm) cc_final: 0.6931 (tpp) REVERT: A 434 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.4994 (mttm) REVERT: A 471 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7449 (ttt180) REVERT: A 585 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5801 (pp20) REVERT: A 640 ASP cc_start: 0.8027 (t0) cc_final: 0.7390 (t0) outliers start: 28 outliers final: 19 residues processed: 106 average time/residue: 0.5168 time to fit residues: 59.3919 Evaluate side-chains 104 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 34 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.217972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129460 restraints weight = 10485.288| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.22 r_work: 0.3364 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9723 Z= 0.140 Angle : 0.607 9.672 13215 Z= 0.315 Chirality : 0.044 0.184 1486 Planarity : 0.004 0.041 1662 Dihedral : 4.576 54.078 1312 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.50 % Allowed : 15.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1199 helix: 1.26 (0.25), residues: 445 sheet: 0.59 (0.33), residues: 248 loop : -1.79 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 112 TYR 0.016 0.001 TYR L 50 PHE 0.019 0.001 PHE A 390 TRP 0.029 0.002 TRP H 110 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9715) covalent geometry : angle 0.60442 (13199) SS BOND : bond 0.00773 ( 8) SS BOND : angle 1.62198 ( 16) hydrogen bonds : bond 0.04335 ( 459) hydrogen bonds : angle 4.37047 ( 1305) ********************** 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 109 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7754 (tppt) cc_final: 0.7543 (tptm) REVERT: H 175 THR cc_start: 0.3637 (OUTLIER) cc_final: 0.3384 (t) REVERT: L 37 TYR cc_start: 0.5970 (m-80) cc_final: 0.5711 (m-80) REVERT: L 46 LYS cc_start: 0.7038 (tmmt) cc_final: 0.6789 (ttpt) REVERT: A 313 MET cc_start: 0.7246 (tmm) cc_final: 0.6938 (tpp) REVERT: A 434 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5020 (mttm) REVERT: A 471 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7369 (ttt180) REVERT: A 585 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5806 (pp20) REVERT: A 640 ASP cc_start: 0.7988 (t0) cc_final: 0.7394 (t0) outliers start: 26 outliers final: 20 residues processed: 103 average time/residue: 0.4993 time to fit residues: 55.7839 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 : 0.404 ------------------------------------------------------------------------------- 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 34 VAL 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 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 7 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.216817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127682 restraints weight = 10500.431| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.38 r_work: 0.3335 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9723 Z= 0.165 Angle : 0.631 9.494 13215 Z= 0.329 Chirality : 0.046 0.190 1486 Planarity : 0.004 0.041 1662 Dihedral : 4.662 53.255 1312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.40 % Allowed : 15.64 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1199 helix: 1.07 (0.25), residues: 447 sheet: 0.47 (0.33), residues: 261 loop : -1.81 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 112 TYR 0.016 0.002 TYR L 50 PHE 0.022 0.002 PHE A 390 TRP 0.026 0.002 TRP H 110 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9715) covalent geometry : angle 0.62828 (13199) SS BOND : bond 0.00699 ( 8) SS BOND : angle 1.67259 ( 16) hydrogen bonds : bond 0.04815 ( 459) hydrogen bonds : angle 4.44634 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5013.72 seconds wall clock time: 85 minutes 48.09 seconds (5148.09 seconds total)