Starting phenix.real_space_refine on Wed Mar 4 00:54:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlj_14782/03_2026/7zlj_14782_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlj_14782/03_2026/7zlj_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2026/7zlj_14782_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2026/7zlj_14782_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2026/7zlj_14782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlj_14782/03_2026/7zlj_14782.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.27, per 1000 atoms: 0.34 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: 0.77 Conformation dependent library (CDL) restraints added in 591.6 milliseconds 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: 0.34 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: 1.62 Time building geometry restraints manager: 1.02 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: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.060 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- 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 9903 Z= 0.246 Angle : 0.812 41.648 13462 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 : 32.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (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 ARG 0.009 0.000 ARG K 19 TYR 0.011 0.001 TYR A 164 PHE 0.018 0.001 PHE A 430 TRP 0.014 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 9895) covalent geometry : angle 0.81168 (13446) SS BOND : bond 0.00264 ( 8) SS BOND : angle 0.67503 ( 16) hydrogen bonds : bond 0.16211 ( 458) hydrogen bonds : angle 6.46385 ( 1308) *********************** 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 : 0.332 Fit side-chains REVERT: A 561 MET cc_start: 0.8213 (mmm) cc_final: 0.7746 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1013 time to fit residues: 17.2215 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 50.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 455 ASN A 458 GLN A 577 HIS A 620 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.174711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141790 restraints weight = 21109.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142535 restraints weight = 51071.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143660 restraints weight = 22478.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144009 restraints weight = 13049.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144563 restraints weight = 11547.073| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9903 Z= 0.146 Angle : 0.646 9.307 13462 Z= 0.330 Chirality : 0.045 0.158 1507 Planarity : 0.005 0.048 1691 Dihedral : 5.896 52.930 1379 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.66 % Allowed : 5.89 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1219 helix: 1.12 (0.25), residues: 457 sheet: 1.11 (0.31), residues: 244 loop : -1.03 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 143 TYR 0.013 0.001 TYR A 319 PHE 0.039 0.002 PHE A 487 TRP 0.011 0.001 TRP A 262 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9895) covalent geometry : angle 0.64526 (13446) SS BOND : bond 0.00396 ( 8) SS BOND : angle 1.16757 ( 16) hydrogen bonds : bond 0.04203 ( 458) hydrogen bonds : angle 4.67226 ( 1308) *********************** 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 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.332 Fit side-chains REVERT: H 20 SER cc_start: 0.8161 (t) cc_final: 0.7938 (m) REVERT: A 144 GLN cc_start: 0.7622 (mm110) cc_final: 0.7407 (mm110) outliers start: 7 outliers final: 3 residues processed: 110 average time/residue: 0.0923 time to fit residues: 14.3200 Evaluate side-chains 100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 120 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 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 = 0.173944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136210 restraints weight = 30274.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135651 restraints weight = 38744.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137532 restraints weight = 17953.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137397 restraints weight = 17158.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137398 restraints weight = 11595.316| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9903 Z= 0.149 Angle : 0.613 8.846 13462 Z= 0.316 Chirality : 0.044 0.148 1507 Planarity : 0.005 0.050 1691 Dihedral : 5.720 52.086 1379 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.04 % Allowed : 8.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1219 helix: 1.15 (0.25), residues: 456 sheet: 1.10 (0.31), residues: 245 loop : -1.07 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.012 0.001 TYR A 319 PHE 0.035 0.001 PHE A 430 TRP 0.019 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9895) covalent geometry : angle 0.61056 (13446) SS BOND : bond 0.00442 ( 8) SS BOND : angle 1.71430 ( 16) hydrogen bonds : bond 0.04001 ( 458) hydrogen bonds : angle 4.46782 ( 1308) *********************** 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: 11 poor density : 105 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: H 20 SER cc_start: 0.8410 (t) cc_final: 0.8176 (m) REVERT: L 11 SER cc_start: 0.9014 (t) cc_final: 0.8755 (m) REVERT: A 144 GLN cc_start: 0.8106 (mm110) cc_final: 0.7858 (mm110) REVERT: A 487 PHE cc_start: 0.8846 (t80) cc_final: 0.8597 (t80) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.0963 time to fit residues: 14.5851 Evaluate side-chains 102 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 347 LEU 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 86 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 50.0000 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 0.0270 chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 92 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 297 HIS 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 = 0.4174 r_free = 0.4174 target = 0.173505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136024 restraints weight = 17230.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134414 restraints weight = 32796.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136373 restraints weight = 26115.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136658 restraints weight = 14344.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137525 restraints weight = 12210.053| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9903 Z= 0.146 Angle : 0.611 8.118 13462 Z= 0.312 Chirality : 0.044 0.145 1507 Planarity : 0.004 0.042 1691 Dihedral : 5.757 53.710 1379 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.95 % Allowed : 10.35 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1219 helix: 1.21 (0.25), residues: 458 sheet: 1.21 (0.31), residues: 238 loop : -1.15 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 72 TYR 0.012 0.001 TYR A 319 PHE 0.031 0.001 PHE A 430 TRP 0.015 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9895) covalent geometry : angle 0.61054 (13446) SS BOND : bond 0.00414 ( 8) SS BOND : angle 1.00760 ( 16) hydrogen bonds : bond 0.03847 ( 458) hydrogen bonds : angle 4.34204 ( 1308) *********************** 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 106 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.8951 (t) cc_final: 0.8693 (m) REVERT: A 144 GLN cc_start: 0.7734 (mm110) cc_final: 0.7486 (mm110) REVERT: A 273 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 561 MET cc_start: 0.7731 (tpp) cc_final: 0.7482 (tpp) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.1001 time to fit residues: 14.2561 Evaluate side-chains 95 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 273 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.174394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138848 restraints weight = 26004.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140062 restraints weight = 38598.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139934 restraints weight = 14592.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140346 restraints weight = 21657.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140350 restraints weight = 11926.335| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9903 Z= 0.148 Angle : 0.611 7.595 13462 Z= 0.309 Chirality : 0.044 0.146 1507 Planarity : 0.004 0.045 1691 Dihedral : 5.757 54.296 1379 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.23 % Allowed : 10.64 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1219 helix: 1.27 (0.26), residues: 451 sheet: 1.12 (0.32), residues: 234 loop : -1.14 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 72 TYR 0.012 0.001 TYR A 319 PHE 0.028 0.001 PHE A 430 TRP 0.011 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9895) covalent geometry : angle 0.61017 (13446) SS BOND : bond 0.00407 ( 8) SS BOND : angle 1.03458 ( 16) hydrogen bonds : bond 0.03801 ( 458) hydrogen bonds : angle 4.27215 ( 1308) *********************** 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 110 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.8974 (t) cc_final: 0.8684 (m) REVERT: A 144 GLN cc_start: 0.7969 (mm110) cc_final: 0.7714 (mm110) REVERT: A 273 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7654 (mp) outliers start: 13 outliers final: 7 residues processed: 105 average time/residue: 0.0894 time to fit residues: 13.3525 Evaluate side-chains 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 544 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 50.0000 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 620 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.176521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147424 restraints weight = 17665.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146843 restraints weight = 35398.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146681 restraints weight = 28999.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146428 restraints weight = 16203.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147383 restraints weight = 12879.305| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9903 Z= 0.115 Angle : 0.583 10.485 13462 Z= 0.293 Chirality : 0.043 0.144 1507 Planarity : 0.004 0.044 1691 Dihedral : 5.667 54.526 1379 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.66 % Allowed : 11.68 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1219 helix: 1.50 (0.26), residues: 452 sheet: 1.06 (0.31), residues: 247 loop : -1.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 143 TYR 0.010 0.001 TYR A 319 PHE 0.027 0.001 PHE A 430 TRP 0.010 0.001 TRP H 110 HIS 0.004 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9895) covalent geometry : angle 0.58281 (13446) SS BOND : bond 0.00354 ( 8) SS BOND : angle 0.88575 ( 16) hydrogen bonds : bond 0.03306 ( 458) hydrogen bonds : angle 4.12347 ( 1308) *********************** 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 113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.8746 (t) cc_final: 0.8479 (m) REVERT: A 273 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7770 (mp) outliers start: 7 outliers final: 4 residues processed: 110 average time/residue: 0.0932 time to fit residues: 14.3418 Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.172758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129978 restraints weight = 23035.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128637 restraints weight = 30022.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131169 restraints weight = 14374.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131944 restraints weight = 9048.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132805 restraints weight = 7755.693| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9903 Z= 0.135 Angle : 0.599 8.991 13462 Z= 0.303 Chirality : 0.043 0.145 1507 Planarity : 0.004 0.042 1691 Dihedral : 5.682 54.719 1379 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.04 % Allowed : 11.87 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.25), residues: 1219 helix: 1.47 (0.26), residues: 452 sheet: 1.22 (0.32), residues: 236 loop : -1.07 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 143 TYR 0.010 0.001 TYR A 319 PHE 0.026 0.001 PHE A 430 TRP 0.009 0.001 TRP A 262 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9895) covalent geometry : angle 0.59830 (13446) SS BOND : bond 0.00358 ( 8) SS BOND : angle 0.95884 ( 16) hydrogen bonds : bond 0.03497 ( 458) hydrogen bonds : angle 4.12601 ( 1308) *********************** 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 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 12 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7734 (tt) REVERT: L 144 GLU cc_start: 0.8146 (mp0) cc_final: 0.7560 (tm-30) REVERT: A 273 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7638 (mp) REVERT: A 328 MET cc_start: 0.7674 (ppp) cc_final: 0.7415 (ppp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.0969 time to fit residues: 14.5939 Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 12 LEU 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 210 THR 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 6 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 61 optimal weight: 0.0000 chunk 116 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 37 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.174879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129936 restraints weight = 17062.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126628 restraints weight = 17077.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.128385 restraints weight = 17674.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129364 restraints weight = 10330.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130025 restraints weight = 8885.296| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9903 Z= 0.112 Angle : 0.584 11.486 13462 Z= 0.294 Chirality : 0.042 0.143 1507 Planarity : 0.004 0.042 1691 Dihedral : 5.599 55.272 1379 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 1.14 % Allowed : 12.25 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1219 helix: 1.67 (0.26), residues: 452 sheet: 1.31 (0.33), residues: 229 loop : -0.97 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 143 TYR 0.010 0.001 TYR K 110 PHE 0.024 0.001 PHE A 430 TRP 0.010 0.001 TRP H 109 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9895) covalent geometry : angle 0.58416 (13446) SS BOND : bond 0.00408 ( 8) SS BOND : angle 0.81651 ( 16) hydrogen bonds : bond 0.03033 ( 458) hydrogen bonds : angle 3.99902 ( 1308) *********************** 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 115 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 139 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.3846 (mt) REVERT: L 168 ASP cc_start: 0.7795 (t0) cc_final: 0.7566 (t0) REVERT: A 273 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 328 MET cc_start: 0.7635 (ppp) cc_final: 0.7388 (ppp) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.0944 time to fit residues: 14.7410 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 139 LEU 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 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 53 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.171708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127597 restraints weight = 19598.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126667 restraints weight = 21898.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127680 restraints weight = 16793.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129079 restraints weight = 9302.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129779 restraints weight = 7637.946| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9903 Z= 0.161 Angle : 0.626 10.916 13462 Z= 0.317 Chirality : 0.044 0.145 1507 Planarity : 0.004 0.055 1691 Dihedral : 5.730 54.230 1379 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 1.14 % Allowed : 12.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1219 helix: 1.55 (0.26), residues: 441 sheet: 1.17 (0.33), residues: 232 loop : -0.91 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 143 TYR 0.014 0.001 TYR L 187 PHE 0.024 0.001 PHE A 430 TRP 0.031 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9895) covalent geometry : angle 0.62573 (13446) SS BOND : bond 0.00394 ( 8) SS BOND : angle 1.05191 ( 16) hydrogen bonds : bond 0.03767 ( 458) hydrogen bonds : angle 4.15871 ( 1308) *********************** 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 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 139 LEU cc_start: 0.4685 (OUTLIER) cc_final: 0.3764 (mp) REVERT: A 56 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: A 273 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 328 MET cc_start: 0.7689 (ppp) cc_final: 0.7457 (ppp) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.0920 time to fit residues: 13.8166 Evaluate side-chains 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU 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 103 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 50.0000 chunk 50 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.174153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130470 restraints weight = 18238.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130710 restraints weight = 20747.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130815 restraints weight = 17987.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132060 restraints weight = 8897.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133475 restraints weight = 7234.774| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9903 Z= 0.115 Angle : 0.588 10.900 13462 Z= 0.296 Chirality : 0.043 0.144 1507 Planarity : 0.004 0.057 1691 Dihedral : 5.658 56.651 1379 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 1.04 % Allowed : 12.63 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1219 helix: 1.77 (0.26), residues: 438 sheet: 1.28 (0.33), residues: 229 loop : -0.88 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 143 TYR 0.016 0.001 TYR L 187 PHE 0.024 0.001 PHE A 430 TRP 0.030 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9895) covalent geometry : angle 0.58791 (13446) SS BOND : bond 0.00374 ( 8) SS BOND : angle 0.85334 ( 16) hydrogen bonds : bond 0.03150 ( 458) hydrogen bonds : angle 4.01794 ( 1308) ********************** 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 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 139 LEU cc_start: 0.4338 (OUTLIER) cc_final: 0.3486 (mp) REVERT: A 273 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 328 MET cc_start: 0.7618 (ppp) cc_final: 0.7392 (ppp) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 0.0949 time to fit residues: 14.1368 Evaluate side-chains 105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 139 LEU 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 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 55 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.172313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129340 restraints weight = 21978.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128093 restraints weight = 30504.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131297 restraints weight = 15518.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131409 restraints weight = 9733.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132742 restraints weight = 8024.525| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9903 Z= 0.152 Angle : 0.614 10.657 13462 Z= 0.311 Chirality : 0.044 0.145 1507 Planarity : 0.004 0.062 1691 Dihedral : 5.718 55.297 1379 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 1.04 % Allowed : 12.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1219 helix: 1.62 (0.26), residues: 437 sheet: 1.21 (0.33), residues: 232 loop : -0.93 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 143 TYR 0.016 0.001 TYR L 187 PHE 0.029 0.001 PHE A 430 TRP 0.027 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9895) covalent geometry : angle 0.61323 (13446) SS BOND : bond 0.00387 ( 8) SS BOND : angle 1.01311 ( 16) hydrogen bonds : bond 0.03608 ( 458) hydrogen bonds : angle 4.11111 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.65 seconds wall clock time: 32 minutes 39.86 seconds (1959.86 seconds total)