Starting phenix.real_space_refine on Fri Mar 14 06:57:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlj_14782/03_2025/7zlj_14782_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlj_14782/03_2025/7zlj_14782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2025/7zlj_14782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2025/7zlj_14782.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2025/7zlj_14782_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2025/7zlj_14782_trim.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 6223 2.51 5 N 1593 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9659 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1679 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1598 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 5352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Conformer: "B" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} bond proxies already assigned to first conformer: 5464 Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Unusual residues: {'IZU': 1} Classifications: {'undetermined': 1, 'water': 9} Link IDs: {None: 9} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 214 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 214 " occ=0.50 Time building chain proxies: 8.92, per 1000 atoms: 0.92 Number of scatterers: 9659 At special positions: 0 Unit cell: (104.94, 165, 99.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1 15.00 O 1798 8.00 N 1593 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 650 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 40.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.581A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 207 removed outlier: 4.000A pdb=" N GLN H 207 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.814A pdb=" N GLN K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.592A pdb=" N LEU L 126 " --> pdb=" O ASP L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.524A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'A' and resid 25 through 55 Processing helix chain 'A' and resid 56 through 59 removed outlier: 3.720A pdb=" N LEU A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 60 through 68 removed outlier: 4.174A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 removed outlier: 4.127A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 115 through 136 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.550A pdb=" N GLY A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 241 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.563A pdb=" N ILE A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 264 through 281 removed outlier: 3.568A pdb=" N PHE A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 308 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 341 through 369 removed outlier: 3.606A pdb=" N LYS A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 4.087A pdb=" N LEU A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.876A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.874A pdb=" N LEU A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.542A 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 485 through 489 Processing helix chain 'A' and resid 500 through 517 Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 534 through 548 removed outlier: 3.981A pdb=" N GLU A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.715A 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 631 through 639 removed outlier: 3.881A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.688A pdb=" N LEU A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.340A pdb=" N GLY H 13 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.611A 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 Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.625A pdb=" N VAL H 184 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.117A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.761A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.594A 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 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.772A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.675A 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 150 through 151 Processing sheet with id=AB3, first strand: chain 'L' and resid 193 through 197 Processing sheet with id=AB4, first strand: chain 'A' and resid 141 through 145 removed outlier: 3.713A pdb=" N LEU A 141 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 157 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 143 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 155 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 554 through 556 removed outlier: 7.487A pdb=" N TYR A 678 " --> pdb=" O ASN A 673 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 673 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 680 " --> pdb=" O VAL A 671 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1613 1.32 - 1.47: 4023 1.47 - 1.61: 4188 1.61 - 1.75: 4 1.75 - 1.90: 67 Bond restraints: 9895 Sorted by residual: bond pdb=" CG PRO H 217 " pdb=" CD PRO H 217 " ideal model delta sigma weight residual 1.503 1.219 0.284 3.40e-02 8.65e+02 6.97e+01 bond pdb=" C09 IZU A 801 " pdb=" C10 IZU A 801 " ideal model delta sigma weight residual 1.498 1.615 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C14 IZU A 801 " pdb=" C15 IZU A 801 " ideal model delta sigma weight residual 1.498 1.614 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C04 IZU A 801 " pdb=" C05 IZU A 801 " ideal model delta sigma weight residual 1.499 1.608 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C07 IZU A 801 " pdb=" C08 IZU A 801 " ideal model delta sigma weight residual 1.504 1.595 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 9890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.33: 13435 8.33 - 16.66: 8 16.66 - 24.99: 1 24.99 - 33.32: 0 33.32 - 41.65: 2 Bond angle restraints: 13446 Sorted by residual: angle pdb=" C12 IZU A 801 " pdb=" C14 IZU A 801 " pdb=" C15 IZU A 801 " ideal model delta sigma weight residual 127.14 168.79 -41.65 3.00e+00 1.11e-01 1.93e+02 angle pdb=" C07 IZU A 801 " pdb=" C09 IZU A 801 " pdb=" C10 IZU A 801 " ideal model delta sigma weight residual 128.54 165.07 -36.53 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N PRO H 217 " pdb=" CD PRO H 217 " pdb=" CG PRO H 217 " ideal model delta sigma weight residual 103.20 86.80 16.40 1.50e+00 4.44e-01 1.20e+02 angle pdb=" CA PRO H 217 " pdb=" N PRO H 217 " pdb=" CD PRO H 217 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 angle pdb=" O28 IZU A 801 " pdb=" P27 IZU A 801 " pdb=" O29 IZU A 801 " ideal model delta sigma weight residual 119.05 101.92 17.13 3.00e+00 1.11e-01 3.26e+01 ... (remaining 13441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5279 17.59 - 35.17: 453 35.17 - 52.76: 84 52.76 - 70.35: 16 70.35 - 87.93: 10 Dihedral angle restraints: 5842 sinusoidal: 2271 harmonic: 3571 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 34.10 58.90 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual 93.00 44.99 48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CB CYS A 621 " pdb=" SG CYS A 621 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -43.53 -42.47 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 5839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 983 0.033 - 0.065: 371 0.065 - 0.098: 105 0.098 - 0.131: 45 0.131 - 0.163: 3 Chirality restraints: 1507 Sorted by residual: chirality pdb=" C22 IZU A 801 " pdb=" C21 IZU A 801 " pdb=" C23 IZU A 801 " pdb=" C24 IZU A 801 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ARG K 19 " pdb=" N ARG K 19 " pdb=" C ARG K 19 " pdb=" CB ARG K 19 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA PRO A 641 " pdb=" N PRO A 641 " pdb=" C PRO A 641 " pdb=" CB PRO A 641 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1504 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 216 " -0.074 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO H 217 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO H 217 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 217 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 640 " 0.062 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 641 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 163 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO H 164 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 164 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 164 " -0.031 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 113 2.61 - 3.18: 8939 3.18 - 3.75: 14245 3.75 - 4.33: 20161 4.33 - 4.90: 33295 Nonbonded interactions: 76753 Sorted by model distance: nonbonded pdb=" OG SER K 17 " pdb=" O MET K 83 " model vdw 2.033 3.040 nonbonded pdb=" NH1 ARG K 53 " pdb=" OG SER K 54 " model vdw 2.070 3.120 nonbonded pdb=" O ILE A 95 " pdb=" OG1 THR A 109 " model vdw 2.083 3.040 nonbonded pdb=" OG1 THR L 130 " pdb=" O LEU L 182 " model vdw 2.086 3.040 nonbonded pdb=" O LYS L 146 " pdb=" OG1 THR L 198 " model vdw 2.102 3.040 ... (remaining 76748 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.290 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: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.240 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.006 0.284 9895 Z= 0.388 Angle : 0.812 41.648 13446 Z= 0.395 Chirality : 0.040 0.163 1507 Planarity : 0.005 0.105 1691 Dihedral : 13.842 87.932 3528 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 32.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.10 (0.25), residues: 1219 helix: 0.91 (0.26), residues: 456 sheet: 0.97 (0.33), residues: 223 loop : -1.07 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 PHE 0.018 0.001 PHE A 430 TYR 0.011 0.001 TYR A 164 ARG 0.009 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.868 Fit side-chains REVERT: A 561 MET cc_start: 0.8213 (mmm) cc_final: 0.7745 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2361 time to fit residues: 40.0465 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 620 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.170504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134679 restraints weight = 16530.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134480 restraints weight = 35708.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135826 restraints weight = 28692.786| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 9895 Z= 0.368 Angle : 0.703 9.180 13446 Z= 0.363 Chirality : 0.048 0.164 1507 Planarity : 0.005 0.046 1691 Dihedral : 6.056 53.458 1379 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.95 % Allowed : 6.08 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1219 helix: 0.74 (0.25), residues: 457 sheet: 1.00 (0.31), residues: 244 loop : -1.14 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.005 0.001 HIS A 375 PHE 0.039 0.002 PHE A 430 TYR 0.015 0.002 TYR A 319 ARG 0.006 0.001 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.228 Fit side-chains REVERT: A 144 GLN cc_start: 0.7638 (mm110) cc_final: 0.7344 (mm110) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 0.2569 time to fit residues: 39.3858 Evaluate side-chains 105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 544 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 527 ASN ** A 662 ASN ** 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 = 0.4185 r_free = 0.4185 target = 0.174687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135697 restraints weight = 20365.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135871 restraints weight = 40227.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138048 restraints weight = 23930.924| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9895 Z= 0.186 Angle : 0.602 9.318 13446 Z= 0.308 Chirality : 0.044 0.150 1507 Planarity : 0.004 0.043 1691 Dihedral : 5.827 52.900 1379 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.85 % Allowed : 8.93 % Favored : 90.22 % 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: 0.35 (0.25), residues: 1219 helix: 1.15 (0.25), residues: 455 sheet: 1.08 (0.31), residues: 246 loop : -1.04 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 262 HIS 0.003 0.001 HIS A 375 PHE 0.035 0.001 PHE A 430 TYR 0.012 0.001 TYR A 319 ARG 0.004 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.996 Fit side-chains REVERT: H 20 SER cc_start: 0.8271 (t) cc_final: 0.8065 (m) REVERT: A 144 GLN cc_start: 0.7761 (mm110) cc_final: 0.7523 (mm110) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.2476 time to fit residues: 39.5588 Evaluate side-chains 105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 77 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 662 ASN ** 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 = 0.4158 r_free = 0.4158 target = 0.171955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133498 restraints weight = 20430.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133666 restraints weight = 48565.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136249 restraints weight = 22518.963| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9895 Z= 0.304 Angle : 0.646 8.879 13446 Z= 0.331 Chirality : 0.046 0.222 1507 Planarity : 0.004 0.041 1691 Dihedral : 5.966 54.783 1379 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.33 % Allowed : 10.73 % Favored : 87.94 % 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: 1219 helix: 1.09 (0.25), residues: 446 sheet: 1.13 (0.31), residues: 238 loop : -1.07 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.031 0.002 PHE A 430 TYR 0.014 0.001 TYR A 319 ARG 0.004 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: L 11 SER cc_start: 0.8992 (t) cc_final: 0.8675 (m) REVERT: A 144 GLN cc_start: 0.7822 (mm110) cc_final: 0.7533 (mm110) REVERT: A 273 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7583 (mp) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.2180 time to fit residues: 33.6976 Evaluate side-chains 106 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 40.0000 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 74 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** 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 = 0.4202 r_free = 0.4202 target = 0.176785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148346 restraints weight = 19770.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149157 restraints weight = 47537.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149271 restraints weight = 23248.685| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9895 Z= 0.165 Angle : 0.587 7.790 13446 Z= 0.298 Chirality : 0.043 0.167 1507 Planarity : 0.004 0.044 1691 Dihedral : 5.842 55.565 1379 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.85 % Allowed : 11.40 % Favored : 87.75 % 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: 1219 helix: 1.43 (0.26), residues: 451 sheet: 1.27 (0.32), residues: 234 loop : -1.17 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 PHE 0.029 0.001 PHE A 430 TYR 0.012 0.001 TYR L 187 ARG 0.004 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.8731 (t) cc_final: 0.8424 (m) REVERT: A 273 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7669 (mp) outliers start: 9 outliers final: 3 residues processed: 111 average time/residue: 0.2227 time to fit residues: 35.2165 Evaluate side-chains 100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.0570 chunk 25 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.175365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139545 restraints weight = 19147.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135433 restraints weight = 17199.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136347 restraints weight = 24267.227| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9895 Z= 0.186 Angle : 0.586 7.927 13446 Z= 0.299 Chirality : 0.043 0.144 1507 Planarity : 0.004 0.042 1691 Dihedral : 5.810 55.525 1379 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.95 % Allowed : 11.68 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1219 helix: 1.52 (0.26), residues: 448 sheet: 1.28 (0.32), residues: 234 loop : -1.11 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.027 0.001 PHE A 430 TYR 0.011 0.001 TYR A 319 ARG 0.004 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 79 LYS cc_start: 0.8643 (ptmm) cc_final: 0.8420 (ptmm) REVERT: L 144 GLU cc_start: 0.8290 (mp0) cc_final: 0.7508 (tm-30) REVERT: A 273 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7557 (mp) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.2365 time to fit residues: 36.1560 Evaluate side-chains 105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 0.0030 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 115 optimal weight: 0.0980 chunk 49 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** 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 = 0.4172 r_free = 0.4172 target = 0.173784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135468 restraints weight = 22867.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136554 restraints weight = 34400.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136539 restraints weight = 19119.978| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9895 Z= 0.231 Angle : 0.619 11.976 13446 Z= 0.312 Chirality : 0.044 0.145 1507 Planarity : 0.004 0.040 1691 Dihedral : 5.869 54.736 1379 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.85 % Allowed : 12.16 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1219 helix: 1.47 (0.26), residues: 447 sheet: 1.23 (0.33), residues: 230 loop : -1.13 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.026 0.001 PHE A 430 TYR 0.014 0.001 TYR L 187 ARG 0.004 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7592 (mp) outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 0.2337 time to fit residues: 34.2178 Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 42 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 62 optimal weight: 0.0020 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 4 optimal weight: 0.3980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** 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 = 0.4182 r_free = 0.4182 target = 0.174674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138581 restraints weight = 18776.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132645 restraints weight = 16390.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132935 restraints weight = 27651.408| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9895 Z= 0.195 Angle : 0.599 10.593 13446 Z= 0.303 Chirality : 0.043 0.143 1507 Planarity : 0.004 0.041 1691 Dihedral : 5.823 54.950 1379 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.14 % Allowed : 12.73 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1219 helix: 1.56 (0.26), residues: 447 sheet: 1.31 (0.33), residues: 228 loop : -1.08 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.025 0.001 PHE A 430 TYR 0.011 0.001 TYR L 187 ARG 0.005 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: A 273 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7669 (mp) REVERT: A 328 MET cc_start: 0.7623 (ppp) cc_final: 0.7405 (ppp) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 0.2382 time to fit residues: 36.7921 Evaluate side-chains 107 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** 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 = 0.4156 r_free = 0.4156 target = 0.172416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140856 restraints weight = 17305.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139685 restraints weight = 37741.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141163 restraints weight = 29438.671| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9895 Z= 0.288 Angle : 0.640 9.936 13446 Z= 0.326 Chirality : 0.045 0.146 1507 Planarity : 0.004 0.052 1691 Dihedral : 5.997 54.312 1379 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.95 % Allowed : 12.63 % Favored : 86.42 % 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 (0.25), residues: 1219 helix: 1.36 (0.26), residues: 443 sheet: 1.26 (0.33), residues: 228 loop : -1.06 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 636 HIS 0.005 0.001 HIS A 375 PHE 0.026 0.002 PHE A 430 TYR 0.015 0.001 TYR L 187 ARG 0.013 0.001 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: A 273 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7770 (mp) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.2266 time to fit residues: 33.4483 Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.174689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142147 restraints weight = 23839.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142652 restraints weight = 47789.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142842 restraints weight = 13537.773| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9895 Z= 0.203 Angle : 0.605 9.605 13446 Z= 0.307 Chirality : 0.043 0.144 1507 Planarity : 0.004 0.059 1691 Dihedral : 5.911 55.917 1379 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.04 % Allowed : 13.01 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1219 helix: 1.55 (0.26), residues: 443 sheet: 1.24 (0.33), residues: 230 loop : -1.02 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.025 0.001 PHE A 430 TYR 0.015 0.001 TYR L 187 ARG 0.014 0.000 ARG L 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 273 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7576 (mp) REVERT: A 328 MET cc_start: 0.7682 (ppp) cc_final: 0.7427 (ppp) REVERT: A 546 HIS cc_start: 0.6402 (m170) cc_final: 0.6187 (m170) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.2279 time to fit residues: 34.2957 Evaluate side-chains 103 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 0.0000 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.176564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140205 restraints weight = 22817.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141227 restraints weight = 38705.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141244 restraints weight = 16739.107| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9895 Z= 0.167 Angle : 0.588 9.167 13446 Z= 0.298 Chirality : 0.043 0.144 1507 Planarity : 0.004 0.058 1691 Dihedral : 5.781 57.058 1379 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 1.04 % Allowed : 13.20 % Favored : 85.75 % 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: 0.75 (0.25), residues: 1219 helix: 1.80 (0.26), residues: 440 sheet: 1.25 (0.33), residues: 229 loop : -0.95 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 PHE 0.029 0.001 PHE A 430 TYR 0.017 0.001 TYR L 187 ARG 0.013 0.000 ARG L 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3678.41 seconds wall clock time: 64 minutes 48.77 seconds (3888.77 seconds total)