Starting phenix.real_space_refine on Sun Jul 27 14:53:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlh_14780/07_2025/7zlh_14780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlh_14780/07_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_14780/07_2025/7zlh_14780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlh_14780/07_2025/7zlh_14780.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlh_14780/07_2025/7zlh_14780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlh_14780/07_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-5711/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: 7.16, per 1000 atoms: 0.76 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: 2.61 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: 1.19 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: 3.15 Time building geometry restraints manager: 3.08 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: 5.850 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: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.210 ------------------------------------------------------------------------------- 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 : 9.51 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 Details of bonding type rmsd hydrogen bonds : bond 0.16265 ( 459) hydrogen bonds : angle 6.50875 ( 1305) SS BOND : bond 0.00688 ( 8) SS BOND : angle 1.81409 ( 16) covalent geometry : bond 0.00521 ( 9715) covalent geometry : angle 0.80828 (13199) *********************** 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 : 0.957 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: 1.2299 time to fit residues: 141.8703 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 : 1.050 ------------------------------------------------------------------------------- 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 = 63)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127769 restraints weight = 10354.076| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.24 r_work: 0.3350 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- 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 9723 Z= 0.170 Angle : 0.657 10.542 13215 Z= 0.348 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 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 459) hydrogen bonds : angle 4.86475 ( 1305) SS BOND : bond 0.00544 ( 8) SS BOND : angle 1.86318 ( 16) covalent geometry : bond 0.00387 ( 9715) covalent geometry : angle 0.65390 (13199) *********************** 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 : 0.974 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7825 (p0) cc_final: 0.7502 (m-30) REVERT: L 37 TYR cc_start: 0.6201 (m-80) cc_final: 0.5975 (m-80) REVERT: L 46 LYS cc_start: 0.7013 (tmmt) cc_final: 0.6689 (tmtt) REVERT: L 208 LYS cc_start: 0.3123 (mmtp) cc_final: 0.2923 (ttpt) REVERT: A 585 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5930 (pm20) REVERT: A 593 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: A 640 ASP cc_start: 0.8039 (t0) cc_final: 0.7351 (t0) outliers start: 17 outliers final: 6 residues processed: 92 average time/residue: 1.1814 time to fit residues: 117.5677 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 : 1.028 ------------------------------------------------------------------------------- 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: 0.0060 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 8 optimal weight: 20.0000 chunk 21 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 46 optimal weight: 0.0370 chunk 101 optimal weight: 1.9990 overall best weight: 0.3252 ------------------------------------------------------------------------------- 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 = 0.4538 r_free = 0.4538 target = 0.221249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131624 restraints weight = 10530.031| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.26 r_work: 0.3465 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9723 Z= 0.108 Angle : 0.558 7.958 13215 Z= 0.292 Chirality : 0.043 0.247 1486 Planarity : 0.004 0.040 1662 Dihedral : 4.633 59.695 1314 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.82 % Allowed : 9.88 % Favored : 88.29 % 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: 0.05 (0.25), residues: 1199 helix: 1.42 (0.26), residues: 445 sheet: 0.52 (0.32), residues: 266 loop : -1.61 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 262 HIS 0.005 0.001 HIS A 391 PHE 0.015 0.001 PHE A 387 TYR 0.022 0.001 TYR L 50 ARG 0.003 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 459) hydrogen bonds : angle 4.36665 ( 1305) SS BOND : bond 0.00346 ( 8) SS BOND : angle 1.43870 ( 16) covalent geometry : bond 0.00218 ( 9715) covalent geometry : angle 0.55647 (13199) *********************** 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: 19 poor density : 93 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.5363 (mmm-85) cc_final: 0.4651 (mmt180) REVERT: L 37 TYR cc_start: 0.6014 (m-80) cc_final: 0.5767 (m-80) REVERT: L 46 LYS cc_start: 0.7010 (tmmt) cc_final: 0.6632 (tmtt) REVERT: A 434 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.4767 (mttm) REVERT: A 471 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7329 (ttt180) REVERT: A 585 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5833 (pp20) REVERT: A 626 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.5007 (ppt170) REVERT: A 640 ASP cc_start: 0.7817 (t0) cc_final: 0.7315 (t0) outliers start: 19 outliers final: 5 residues processed: 102 average time/residue: 1.9311 time to fit residues: 215.3972 Evaluate side-chains 96 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 407 SER 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: 6.9990 chunk 3 optimal weight: 2.9990 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: 2.9990 chunk 35 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.214733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123856 restraints weight = 10401.165| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.21 r_work: 0.3343 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9723 Z= 0.248 Angle : 0.715 9.497 13215 Z= 0.377 Chirality : 0.051 0.240 1486 Planarity : 0.005 0.040 1662 Dihedral : 4.919 58.306 1312 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 2.59 % Allowed : 11.80 % Favored : 85.60 % 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: -0.44 (0.24), residues: 1199 helix: 0.66 (0.25), residues: 447 sheet: 0.53 (0.32), residues: 259 loop : -1.65 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 109 HIS 0.006 0.002 HIS A 479 PHE 0.029 0.002 PHE A 390 TYR 0.019 0.002 TYR A 345 ARG 0.003 0.001 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.06020 ( 459) hydrogen bonds : angle 4.71820 ( 1305) SS BOND : bond 0.00804 ( 8) SS BOND : angle 1.88846 ( 16) covalent geometry : bond 0.00594 ( 9715) covalent geometry : angle 0.71196 (13199) *********************** 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: 27 poor density : 84 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7834 (p0) cc_final: 0.7524 (m-30) REVERT: L 25 ARG cc_start: 0.5512 (mmm-85) cc_final: 0.4794 (mmt180) REVERT: L 37 TYR cc_start: 0.6155 (m-80) cc_final: 0.5864 (m-80) REVERT: L 46 LYS cc_start: 0.7028 (tmmt) cc_final: 0.6744 (ttpt) REVERT: A 70 THR cc_start: 0.8476 (t) cc_final: 0.8254 (m) REVERT: A 434 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5208 (mttm) REVERT: A 471 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7515 (ttt180) REVERT: A 585 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5934 (pm20) REVERT: A 626 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.4042 (ppt170) REVERT: A 640 ASP cc_start: 0.8102 (t0) cc_final: 0.7318 (t0) outliers start: 27 outliers final: 11 residues processed: 101 average time/residue: 1.2150 time to fit residues: 132.7813 Evaluate side-chains 96 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.0140 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.217156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128910 restraints weight = 10441.455| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.23 r_work: 0.3369 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9723 Z= 0.133 Angle : 0.593 10.014 13215 Z= 0.310 Chirality : 0.045 0.196 1486 Planarity : 0.004 0.043 1662 Dihedral : 4.659 58.027 1312 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.21 % Allowed : 13.24 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1199 helix: 1.10 (0.25), residues: 446 sheet: 0.53 (0.32), residues: 261 loop : -1.59 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 110 HIS 0.005 0.001 HIS A 391 PHE 0.018 0.001 PHE A 390 TYR 0.018 0.001 TYR L 50 ARG 0.002 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 459) hydrogen bonds : angle 4.42089 ( 1305) SS BOND : bond 0.00439 ( 8) SS BOND : angle 1.59740 ( 16) covalent geometry : bond 0.00293 ( 9715) covalent geometry : angle 0.59092 (13199) *********************** 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 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7798 (p0) cc_final: 0.7563 (m-30) REVERT: H 68 LYS cc_start: 0.7750 (tppt) cc_final: 0.7540 (tptm) REVERT: H 175 THR cc_start: 0.3641 (OUTLIER) cc_final: 0.3403 (t) REVERT: L 37 TYR cc_start: 0.6122 (m-80) cc_final: 0.5885 (m-80) REVERT: L 46 LYS cc_start: 0.7038 (tmmt) cc_final: 0.6722 (ttpt) REVERT: L 71 ASP cc_start: 0.5867 (t0) cc_final: 0.5352 (t70) REVERT: L 136 LEU cc_start: 0.2978 (mm) cc_final: 0.2776 (tp) REVERT: A 422 LEU cc_start: 0.7822 (mp) cc_final: 0.7609 (mt) REVERT: A 434 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5016 (mttm) REVERT: A 471 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7446 (ttt180) REVERT: A 585 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5821 (pp20) REVERT: A 640 ASP cc_start: 0.7986 (t0) cc_final: 0.7336 (t0) outliers start: 23 outliers final: 8 residues processed: 105 average time/residue: 1.2534 time to fit residues: 142.8339 Evaluate side-chains 96 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 63 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** A 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.216803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127394 restraints weight = 10436.986| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.29 r_work: 0.3347 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9723 Z= 0.157 Angle : 0.612 9.786 13215 Z= 0.320 Chirality : 0.045 0.190 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.675 57.937 1312 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.21 % Allowed : 14.59 % Favored : 83.21 % 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: 1.04 (0.25), residues: 446 sheet: 0.49 (0.32), residues: 261 loop : -1.63 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 110 HIS 0.005 0.001 HIS A 391 PHE 0.022 0.002 PHE A 390 TYR 0.017 0.002 TYR L 50 ARG 0.004 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 459) hydrogen bonds : angle 4.43529 ( 1305) SS BOND : bond 0.00639 ( 8) SS BOND : angle 1.58586 ( 16) covalent geometry : bond 0.00362 ( 9715) covalent geometry : angle 0.60986 (13199) *********************** 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 107 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7794 (p0) cc_final: 0.7557 (m-30) REVERT: H 68 LYS cc_start: 0.7743 (tppt) cc_final: 0.7538 (tptm) REVERT: H 175 THR cc_start: 0.3693 (OUTLIER) cc_final: 0.3460 (t) REVERT: L 37 TYR cc_start: 0.6094 (m-80) cc_final: 0.5849 (m-80) REVERT: L 46 LYS cc_start: 0.7017 (tmmt) cc_final: 0.6688 (ttpt) REVERT: L 136 LEU cc_start: 0.3102 (mm) cc_final: 0.2893 (tp) REVERT: A 422 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7563 (mt) REVERT: A 434 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5110 (mttm) REVERT: A 471 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7390 (ttt180) REVERT: A 585 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5773 (pp20) REVERT: A 626 ARG cc_start: 0.5616 (OUTLIER) cc_final: 0.4044 (ppt170) REVERT: A 640 ASP cc_start: 0.8034 (t0) cc_final: 0.7338 (t0) outliers start: 23 outliers final: 12 residues processed: 100 average time/residue: 1.2031 time to fit residues: 130.2474 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 : 1.020 ------------------------------------------------------------------------------- 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 70 THR 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 422 LEU 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 626 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 22 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 92 optimal weight: 0.0060 chunk 35 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 overall best weight: 2.4160 ------------------------------------------------------------------------------- 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 = 0.4475 r_free = 0.4475 target = 0.214495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123728 restraints weight = 10523.027| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.30 r_work: 0.3310 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9723 Z= 0.218 Angle : 0.678 10.048 13215 Z= 0.357 Chirality : 0.048 0.222 1486 Planarity : 0.005 0.042 1662 Dihedral : 4.907 56.392 1312 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.09 % Favored : 93.74 % Rotamer: Outliers : 2.69 % Allowed : 14.40 % Favored : 82.92 % 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: -0.46 (0.24), residues: 1199 helix: 0.69 (0.25), residues: 444 sheet: 0.50 (0.32), residues: 257 loop : -1.67 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 109 HIS 0.006 0.002 HIS A 546 PHE 0.026 0.002 PHE A 390 TYR 0.018 0.002 TYR A 345 ARG 0.004 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.05666 ( 459) hydrogen bonds : angle 4.61083 ( 1305) SS BOND : bond 0.00656 ( 8) SS BOND : angle 1.82468 ( 16) covalent geometry : bond 0.00520 ( 9715) covalent geometry : angle 0.67527 (13199) *********************** 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 115 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7774 (p0) cc_final: 0.7496 (m-30) REVERT: H 68 LYS cc_start: 0.7762 (tppt) cc_final: 0.7549 (tptm) REVERT: H 175 THR cc_start: 0.3669 (OUTLIER) cc_final: 0.3416 (t) REVERT: L 37 TYR cc_start: 0.6181 (m-80) cc_final: 0.5966 (m-80) REVERT: L 46 LYS cc_start: 0.6997 (tmmt) cc_final: 0.6670 (ttpt) REVERT: L 136 LEU cc_start: 0.3078 (mm) cc_final: 0.2867 (tp) REVERT: A 422 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7584 (mt) REVERT: A 434 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5204 (mttm) REVERT: A 471 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7449 (ttt180) REVERT: A 585 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5825 (pp20) REVERT: A 640 ASP cc_start: 0.8108 (t0) cc_final: 0.7354 (t0) outliers start: 28 outliers final: 16 residues processed: 105 average time/residue: 1.1303 time to fit residues: 128.6405 Evaluate side-chains 107 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 188 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 422 LEU 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 537 GLN 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: 10.0000 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.216818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128066 restraints weight = 10578.458| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.36 r_work: 0.3351 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1802 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= 0.150 Angle : 0.605 9.932 13215 Z= 0.317 Chirality : 0.045 0.192 1486 Planarity : 0.004 0.044 1662 Dihedral : 4.680 56.021 1312 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.69 % Allowed : 14.78 % Favored : 82.53 % 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: -0.27 (0.24), residues: 1199 helix: 0.95 (0.25), residues: 447 sheet: 0.47 (0.32), residues: 261 loop : -1.63 (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 0.019 0.002 PHE A 390 TYR 0.016 0.001 TYR L 50 ARG 0.003 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 459) hydrogen bonds : angle 4.39599 ( 1305) SS BOND : bond 0.00523 ( 8) SS BOND : angle 1.61048 ( 16) covalent geometry : bond 0.00347 ( 9715) covalent geometry : angle 0.60260 (13199) *********************** 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 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: H 65 ASP cc_start: 0.7782 (p0) cc_final: 0.7565 (m-30) REVERT: H 68 LYS cc_start: 0.7728 (tppt) cc_final: 0.7524 (tptm) REVERT: H 175 THR cc_start: 0.3683 (OUTLIER) cc_final: 0.3433 (t) REVERT: L 37 TYR cc_start: 0.6133 (m-80) cc_final: 0.5890 (m-80) REVERT: L 46 LYS cc_start: 0.7015 (tmmt) cc_final: 0.6665 (ttpt) REVERT: L 136 LEU cc_start: 0.3047 (mm) cc_final: 0.2839 (tp) REVERT: A 313 MET cc_start: 0.7265 (tmm) cc_final: 0.6934 (tpp) REVERT: A 422 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 434 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5065 (mttm) REVERT: A 471 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7410 (ttt180) REVERT: A 585 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5835 (pp20) REVERT: A 640 ASP cc_start: 0.8080 (t0) cc_final: 0.7388 (t0) outliers start: 28 outliers final: 16 residues processed: 105 average time/residue: 1.1914 time to fit residues: 135.6506 Evaluate side-chains 105 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 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 407 SER Chi-restraints excluded: chain A residue 422 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 overall best weight: 1.0880 ------------------------------------------------------------------------------- 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** 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 = 0.217593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126783 restraints weight = 10492.261| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.28 r_work: 0.3378 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9723 Z= 0.138 Angle : 0.599 9.821 13215 Z= 0.313 Chirality : 0.044 0.179 1486 Planarity : 0.004 0.043 1662 Dihedral : 4.634 55.696 1312 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.11 % Allowed : 15.74 % Favored : 82.15 % 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 (0.25), residues: 1199 helix: 1.12 (0.25), residues: 445 sheet: 0.46 (0.32), residues: 263 loop : -1.63 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 110 HIS 0.006 0.001 HIS A 391 PHE 0.018 0.001 PHE A 390 TYR 0.016 0.001 TYR L 50 ARG 0.004 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 459) hydrogen bonds : angle 4.38845 ( 1305) SS BOND : bond 0.00657 ( 8) SS BOND : angle 1.52046 ( 16) covalent geometry : bond 0.00315 ( 9715) covalent geometry : angle 0.59752 (13199) *********************** 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 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7714 (tppt) cc_final: 0.7510 (tptm) REVERT: H 175 THR cc_start: 0.3636 (OUTLIER) cc_final: 0.3388 (t) REVERT: L 46 LYS cc_start: 0.7040 (tmmt) cc_final: 0.6759 (ttpt) REVERT: A 313 MET cc_start: 0.7240 (tmm) cc_final: 0.6935 (tpp) REVERT: A 422 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7540 (mt) REVERT: A 434 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5061 (mttm) REVERT: A 471 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7442 (ttt180) REVERT: A 585 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5778 (pp20) REVERT: A 640 ASP cc_start: 0.8020 (t0) cc_final: 0.7376 (t0) outliers start: 22 outliers final: 16 residues processed: 106 average time/residue: 1.1287 time to fit residues: 129.7710 Evaluate side-chains 108 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 104 LYS 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 173 VAL 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 422 LEU 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: 10.0000 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN A 97 HIS ** 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 = 0.4489 r_free = 0.4489 target = 0.216137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127197 restraints weight = 10581.832| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.33 r_work: 0.3329 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9723 Z= 0.183 Angle : 0.649 9.576 13215 Z= 0.340 Chirality : 0.046 0.199 1486 Planarity : 0.004 0.042 1662 Dihedral : 4.783 54.862 1312 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.69 % Allowed : 15.55 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1199 helix: 0.90 (0.25), residues: 444 sheet: 0.56 (0.33), residues: 257 loop : -1.68 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 109 HIS 0.006 0.001 HIS A 391 PHE 0.023 0.002 PHE A 390 TYR 0.016 0.002 TYR H 117 ARG 0.004 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 459) hydrogen bonds : angle 4.52722 ( 1305) SS BOND : bond 0.00715 ( 8) SS BOND : angle 1.57262 ( 16) covalent geometry : bond 0.00432 ( 9715) covalent geometry : angle 0.64704 (13199) ********************** 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: 28 poor density : 83 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: H 68 LYS cc_start: 0.7746 (tppt) cc_final: 0.7522 (tptm) REVERT: H 175 THR cc_start: 0.3649 (OUTLIER) cc_final: 0.3398 (t) REVERT: L 46 LYS cc_start: 0.7001 (tmmt) cc_final: 0.6759 (ttpt) REVERT: A 422 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7548 (mt) REVERT: A 434 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5163 (mttm) REVERT: A 471 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7520 (ttt180) REVERT: A 585 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5779 (pp20) REVERT: A 640 ASP cc_start: 0.8085 (t0) cc_final: 0.7371 (t0) outliers start: 28 outliers final: 19 residues processed: 102 average time/residue: 1.1357 time to fit residues: 125.2790 Evaluate side-chains 107 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 104 LYS Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LYS 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: 0.0670 chunk 46 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.218830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130807 restraints weight = 10513.976| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.38 r_work: 0.3343 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2039 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= 0.124 Angle : 0.596 10.574 13215 Z= 0.310 Chirality : 0.044 0.179 1486 Planarity : 0.004 0.044 1662 Dihedral : 4.602 54.396 1312 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.92 % Allowed : 16.41 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1199 helix: 1.24 (0.25), residues: 445 sheet: 0.57 (0.32), residues: 264 loop : -1.76 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.006 0.001 HIS A 391 PHE 0.016 0.001 PHE A 390 TYR 0.015 0.001 TYR L 50 ARG 0.004 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 459) hydrogen bonds : angle 4.37803 ( 1305) SS BOND : bond 0.00659 ( 8) SS BOND : angle 1.70409 ( 16) covalent geometry : bond 0.00271 ( 9715) covalent geometry : angle 0.59367 (13199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11203.70 seconds wall clock time: 197 minutes 42.81 seconds (11862.81 seconds total)