Starting phenix.real_space_refine on Fri Feb 14 02:39:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlj_14782/02_2025/7zlj_14782_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlj_14782/02_2025/7zlj_14782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zlj_14782/02_2025/7zlj_14782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlj_14782/02_2025/7zlj_14782.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlj_14782/02_2025/7zlj_14782_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlj_14782/02_2025/7zlj_14782_trim.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 6223 2.51 5 N 1593 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9659 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1679 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1598 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 5352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Conformer: "B" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} bond proxies already assigned to first conformer: 5464 Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Unusual residues: {'IZU': 1} Classifications: {'undetermined': 1, 'water': 9} Link IDs: {None: 9} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 214 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 214 " occ=0.50 Time building chain proxies: 8.96, per 1000 atoms: 0.93 Number of scatterers: 9659 At special positions: 0 Unit cell: (104.94, 165, 99.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1 15.00 O 1798 8.00 N 1593 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 650 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 40.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.581A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 207 removed outlier: 4.000A pdb=" N GLN H 207 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.814A pdb=" N GLN K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.592A pdb=" N LEU L 126 " --> pdb=" O ASP L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.524A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'A' and resid 25 through 55 Processing helix chain 'A' and resid 56 through 59 removed outlier: 3.720A pdb=" N LEU A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 60 through 68 removed outlier: 4.174A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 removed outlier: 4.127A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 115 through 136 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.550A pdb=" N GLY A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 241 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.563A pdb=" N ILE A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 264 through 281 removed outlier: 3.568A pdb=" N PHE A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 308 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 341 through 369 removed outlier: 3.606A pdb=" N LYS A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 4.087A pdb=" N LEU A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.876A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.874A pdb=" N LEU A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.542A pdb=" N MET A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 500 through 517 Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 534 through 548 removed outlier: 3.981A pdb=" N GLU A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.715A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.881A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.688A pdb=" N LEU A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.340A pdb=" N GLY H 13 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 139 removed outlier: 3.625A pdb=" N VAL H 184 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.117A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.761A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.772A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119 Processing sheet with id=AB2, first strand: chain 'L' and resid 150 through 151 Processing sheet with id=AB3, first strand: chain 'L' and resid 193 through 197 Processing sheet with id=AB4, first strand: chain 'A' and resid 141 through 145 removed outlier: 3.713A pdb=" N LEU A 141 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 157 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 143 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 155 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 554 through 556 removed outlier: 7.487A pdb=" N TYR A 678 " --> pdb=" O ASN A 673 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 673 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 680 " --> pdb=" O VAL A 671 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.79 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.550 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.284 9895 Z= 0.388 Angle : 0.812 41.648 13446 Z= 0.395 Chirality : 0.040 0.163 1507 Planarity : 0.005 0.105 1691 Dihedral : 13.842 87.932 3528 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 32.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1219 helix: 0.91 (0.26), residues: 456 sheet: 0.97 (0.33), residues: 223 loop : -1.07 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 PHE 0.018 0.001 PHE A 430 TYR 0.011 0.001 TYR A 164 ARG 0.009 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.954 Fit side-chains REVERT: A 561 MET cc_start: 0.8213 (mmm) cc_final: 0.7745 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2529 time to fit residues: 42.8359 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 : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 620 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.170504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134679 restraints weight = 16530.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134480 restraints weight = 35708.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135825 restraints weight = 28692.881| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 9895 Z= 0.368 Angle : 0.703 9.180 13446 Z= 0.363 Chirality : 0.048 0.164 1507 Planarity : 0.005 0.046 1691 Dihedral : 6.056 53.458 1379 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.95 % Allowed : 6.08 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1219 helix: 0.74 (0.25), residues: 457 sheet: 1.00 (0.31), residues: 244 loop : -1.14 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.005 0.001 HIS A 375 PHE 0.039 0.002 PHE A 430 TYR 0.015 0.002 TYR A 319 ARG 0.006 0.001 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.027 Fit side-chains REVERT: A 144 GLN cc_start: 0.7638 (mm110) cc_final: 0.7344 (mm110) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 0.2386 time to fit residues: 36.5007 Evaluate side-chains 105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 544 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 527 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.175238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138308 restraints weight = 20369.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140049 restraints weight = 42116.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141380 restraints weight = 19173.999| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9895 Z= 0.182 Angle : 0.599 9.195 13446 Z= 0.306 Chirality : 0.044 0.150 1507 Planarity : 0.004 0.044 1691 Dihedral : 5.809 52.788 1379 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.95 % Allowed : 8.93 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1219 helix: 1.17 (0.25), residues: 456 sheet: 1.09 (0.31), residues: 246 loop : -1.03 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 262 HIS 0.003 0.001 HIS A 375 PHE 0.035 0.001 PHE A 430 TYR 0.012 0.001 TYR A 319 ARG 0.004 0.001 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.046 Fit side-chains REVERT: L 11 SER cc_start: 0.8901 (t) cc_final: 0.8646 (m) REVERT: A 144 GLN cc_start: 0.7631 (mm110) cc_final: 0.7406 (mm110) REVERT: A 487 PHE cc_start: 0.8841 (t80) cc_final: 0.8578 (t80) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.2326 time to fit residues: 36.9408 Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 77 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.174503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136250 restraints weight = 21634.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137483 restraints weight = 47259.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140000 restraints weight = 20067.214| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9895 Z= 0.200 Angle : 0.605 8.437 13446 Z= 0.308 Chirality : 0.044 0.197 1507 Planarity : 0.004 0.042 1691 Dihedral : 5.821 55.804 1379 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.85 % Allowed : 11.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1219 helix: 1.29 (0.25), residues: 454 sheet: 1.28 (0.31), residues: 238 loop : -1.08 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.031 0.001 PHE A 430 TYR 0.012 0.001 TYR A 319 ARG 0.005 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: L 11 SER cc_start: 0.8885 (t) cc_final: 0.8616 (m) REVERT: A 144 GLN cc_start: 0.7714 (mm110) cc_final: 0.7476 (mm110) REVERT: A 273 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7635 (mp) outliers start: 9 outliers final: 4 residues processed: 104 average time/residue: 0.2341 time to fit residues: 34.7265 Evaluate side-chains 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 30.0000 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 0.0040 chunk 108 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.172833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135378 restraints weight = 20572.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137165 restraints weight = 45199.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138685 restraints weight = 18679.420| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9895 Z= 0.245 Angle : 0.616 7.796 13446 Z= 0.315 Chirality : 0.044 0.157 1507 Planarity : 0.004 0.042 1691 Dihedral : 5.892 55.531 1379 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.04 % Allowed : 10.64 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1219 helix: 1.30 (0.26), residues: 447 sheet: 1.22 (0.32), residues: 234 loop : -1.17 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.029 0.001 PHE A 430 TYR 0.013 0.001 TYR L 187 ARG 0.005 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.8993 (t) cc_final: 0.8733 (m) REVERT: A 144 GLN cc_start: 0.7736 (mm110) cc_final: 0.7491 (mm110) REVERT: A 273 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7685 (mp) outliers start: 11 outliers final: 5 residues processed: 107 average time/residue: 0.2243 time to fit residues: 34.4175 Evaluate side-chains 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 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 = 0.4147 r_free = 0.4147 target = 0.170961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132974 restraints weight = 19517.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134795 restraints weight = 41864.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135970 restraints weight = 19784.903| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9895 Z= 0.308 Angle : 0.644 7.473 13446 Z= 0.331 Chirality : 0.045 0.148 1507 Planarity : 0.004 0.042 1691 Dihedral : 6.050 55.090 1379 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.95 % Allowed : 11.68 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1219 helix: 1.09 (0.25), residues: 447 sheet: 1.15 (0.31), residues: 239 loop : -1.16 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.027 0.002 PHE A 430 TYR 0.013 0.001 TYR A 319 ARG 0.004 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.9099 (t) cc_final: 0.8782 (m) REVERT: A 144 GLN cc_start: 0.7757 (mm110) cc_final: 0.7077 (mm110) REVERT: A 273 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7759 (mp) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.2253 time to fit residues: 33.4242 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 : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 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 = 0.4168 r_free = 0.4168 target = 0.172870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141085 restraints weight = 23175.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141492 restraints weight = 49000.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140124 restraints weight = 15245.129| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9895 Z= 0.209 Angle : 0.604 12.167 13446 Z= 0.306 Chirality : 0.043 0.143 1507 Planarity : 0.004 0.043 1691 Dihedral : 5.929 55.983 1379 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.14 % Allowed : 12.16 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1219 helix: 1.43 (0.26), residues: 441 sheet: 1.23 (0.32), residues: 228 loop : -1.00 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.026 0.001 PHE A 430 TYR 0.011 0.001 TYR A 319 ARG 0.004 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.8982 (t) cc_final: 0.8683 (m) REVERT: A 56 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 144 GLN cc_start: 0.7605 (mm110) cc_final: 0.7381 (mm110) REVERT: A 273 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7747 (mp) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.2191 time to fit residues: 33.7956 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 : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 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 42 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.171742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133714 restraints weight = 18482.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134316 restraints weight = 39187.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.136174 restraints weight = 23803.812| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9895 Z= 0.255 Angle : 0.626 10.721 13446 Z= 0.318 Chirality : 0.044 0.144 1507 Planarity : 0.004 0.040 1691 Dihedral : 5.946 55.711 1379 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.23 % Allowed : 12.25 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1219 helix: 1.38 (0.26), residues: 441 sheet: 1.24 (0.33), residues: 228 loop : -1.00 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.025 0.001 PHE A 430 TYR 0.011 0.001 TYR A 319 ARG 0.007 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 SER cc_start: 0.9063 (t) cc_final: 0.8750 (m) REVERT: L 12 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7924 (tt) REVERT: A 56 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: A 144 GLN cc_start: 0.7749 (mm110) cc_final: 0.7521 (mm110) REVERT: A 273 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7751 (mp) REVERT: A 328 MET cc_start: 0.7699 (ppp) cc_final: 0.7484 (ppp) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.2176 time to fit residues: 33.7776 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 : 1.027 ------------------------------------------------------------------------------- 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 L residue 198 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.169604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132792 restraints weight = 17484.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126211 restraints weight = 15449.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128198 restraints weight = 16772.199| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9895 Z= 0.347 Angle : 0.675 10.000 13446 Z= 0.346 Chirality : 0.046 0.148 1507 Planarity : 0.005 0.040 1691 Dihedral : 6.178 55.497 1379 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.23 % Allowed : 12.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1219 helix: 1.01 (0.25), residues: 447 sheet: 1.00 (0.32), residues: 239 loop : -1.11 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 262 HIS 0.005 0.001 HIS A 375 PHE 0.026 0.002 PHE A 430 TYR 0.014 0.002 TYR L 187 ARG 0.008 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 56 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: A 144 GLN cc_start: 0.8329 (mm110) cc_final: 0.7552 (mm110) REVERT: A 273 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7715 (mp) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.2212 time to fit residues: 33.5705 Evaluate side-chains 100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.172964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135011 restraints weight = 23765.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135688 restraints weight = 34325.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135780 restraints weight = 19550.392| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9895 Z= 0.193 Angle : 0.610 9.713 13446 Z= 0.311 Chirality : 0.043 0.141 1507 Planarity : 0.004 0.051 1691 Dihedral : 5.978 57.033 1379 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 0.95 % Allowed : 12.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1219 helix: 1.43 (0.26), residues: 440 sheet: 1.18 (0.33), residues: 225 loop : -0.98 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.025 0.001 PHE A 430 TYR 0.014 0.001 TYR L 187 ARG 0.007 0.000 ARG L 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: L 11 SER cc_start: 0.9165 (t) cc_final: 0.8817 (m) REVERT: A 56 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: A 144 GLN cc_start: 0.8154 (mm110) cc_final: 0.7929 (mm110) REVERT: A 273 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7637 (mp) REVERT: A 328 MET cc_start: 0.7665 (ppp) cc_final: 0.7429 (ppp) outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 0.2252 time to fit residues: 35.9657 Evaluate side-chains 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 0.0060 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 ** 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 = 0.4188 r_free = 0.4188 target = 0.175558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147127 restraints weight = 20381.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.147056 restraints weight = 51110.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146013 restraints weight = 22470.645| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9895 Z= 0.184 Angle : 0.606 9.258 13446 Z= 0.308 Chirality : 0.043 0.140 1507 Planarity : 0.004 0.042 1691 Dihedral : 5.885 56.614 1379 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1219 helix: 1.57 (0.26), residues: 444 sheet: 1.20 (0.34), residues: 225 loop : -0.97 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.030 0.001 PHE A 430 TYR 0.010 0.001 TYR K 110 ARG 0.007 0.000 ARG L 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.43 seconds wall clock time: 63 minutes 33.48 seconds (3813.48 seconds total)