Starting phenix.real_space_refine on Wed Sep 17 16:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zli_14781/09_2025/7zli_14781_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zli_14781/09_2025/7zli_14781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zli_14781/09_2025/7zli_14781_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zli_14781/09_2025/7zli_14781_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zli_14781/09_2025/7zli_14781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zli_14781/09_2025/7zli_14781.map" } resolution = 2.99 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= 0.064 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 6168 2.51 5 N 1580 2.21 5 O 1789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 5 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: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5330 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 24, 'TRANS': 636} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 54 Unusual residues: {'IZY': 1} Classifications: {'undetermined': 1, 'water': 13} Link IDs: {None: 13} Time building chain proxies: 2.45, per 1000 atoms: 0.26 Number of scatterers: 9582 At special positions: 0 Unit cell: (100.32, 161.04, 97.02, 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 1789 8.00 N 1580 7.00 C 6168 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: 0.94 Conformation dependent library (CDL) restraints added in 386.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 40.4% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... 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: 4.066A pdb=" N GLN H 207 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.811A 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 Processing helix 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: 3.580A 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: 3.985A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 removed outlier: 4.119A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 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: 3.642A pdb=" N GLY A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 240 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.770A 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: 3.631A pdb=" N THR A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 3.616A 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 318 through 332 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.661A pdb=" N SER A 337 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 363 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.871A pdb=" N PHE A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.910A pdb=" N THR A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.518A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.606A pdb=" N LEU A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 464 " --> pdb=" O CYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.753A pdb=" N MET A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 499 through 527 removed outlier: 3.522A pdb=" N GLY A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 534 through 548 removed outlier: 4.383A pdb=" N GLU A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.818A pdb=" N ALA A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.544A pdb=" N LYS A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 619 through 622 Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.570A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.838A 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: 6.704A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15 removed outlier: 4.525A pdb=" N TYR H 117 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.242A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.242A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AA7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.437A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE K 98 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP K 109 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.437A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.724A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.056A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 147 through 150 removed outlier: 6.210A pdb=" N HIS L 199 " --> pdb=" O SER L 204 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER L 204 " --> pdb=" O HIS L 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.746A pdb=" N TRP A 143 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 155 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 554 through 556 removed outlier: 4.208A pdb=" N TYR A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 674 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 682 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE A 670 " --> pdb=" O LYS A 682 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1383 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: 1.85 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1500 1.30 - 1.43: 2785 1.43 - 1.56: 5451 1.56 - 1.69: 6 1.69 - 1.82: 66 Bond restraints: 9808 Sorted by residual: bond pdb=" C TRP A 262 " pdb=" O TRP A 262 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.26e-02 6.30e+03 2.49e+01 bond pdb=" C TYR A 75 " pdb=" O TYR A 75 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" C MET A 465 " pdb=" O MET A 465 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.15e-02 7.56e+03 2.02e+01 bond pdb=" C PHE A 264 " pdb=" O PHE A 264 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.26e-02 6.30e+03 1.93e+01 bond pdb=" C PHE A 261 " pdb=" N TRP A 262 " ideal model delta sigma weight residual 1.332 1.271 0.061 1.40e-02 5.10e+03 1.93e+01 ... (remaining 9803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.45: 13312 8.45 - 16.91: 5 16.91 - 25.36: 4 25.36 - 33.81: 2 33.81 - 42.27: 1 Bond angle restraints: 13324 Sorted by residual: angle pdb=" C03 IZY A 801 " pdb=" C02 IZY A 801 " pdb=" C04 IZY A 801 " ideal model delta sigma weight residual 121.02 163.29 -42.27 3.00e+00 1.11e-01 1.99e+02 angle pdb=" N THR A 70 " pdb=" CA THR A 70 " pdb=" C THR A 70 " ideal model delta sigma weight residual 111.07 123.64 -12.57 1.07e+00 8.73e-01 1.38e+02 angle pdb=" C THR A 70 " pdb=" CA THR A 70 " pdb=" CB THR A 70 " ideal model delta sigma weight residual 110.88 93.76 17.12 1.57e+00 4.06e-01 1.19e+02 angle pdb=" C02 IZY A 801 " pdb=" C04 IZY A 801 " pdb=" C05 IZY A 801 " ideal model delta sigma weight residual 128.13 158.83 -30.70 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C07 IZY A 801 " pdb=" C09 IZY A 801 " pdb=" C10 IZY A 801 " ideal model delta sigma weight residual 127.91 154.24 -26.33 3.00e+00 1.11e-01 7.71e+01 ... (remaining 13319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5235 17.28 - 34.55: 474 34.55 - 51.83: 67 51.83 - 69.10: 18 69.10 - 86.38: 8 Dihedral angle restraints: 5802 sinusoidal: 2257 harmonic: 3545 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 36.06 56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 145.46 -52.46 1 1.00e+01 1.00e-02 3.75e+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 47.01 45.99 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 5799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1162 0.054 - 0.109: 284 0.109 - 0.163: 38 0.163 - 0.217: 10 0.217 - 0.272: 5 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA THR A 271 " pdb=" N THR A 271 " pdb=" C THR A 271 " pdb=" CB THR A 271 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA TRP A 262 " pdb=" N TRP A 262 " pdb=" C TRP A 262 " pdb=" CB TRP A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PHE A 261 " pdb=" N PHE A 261 " pdb=" C PHE A 261 " pdb=" CB PHE A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1496 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 261 " -0.019 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE A 261 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE A 261 " -0.022 2.00e-02 2.50e+03 pdb=" N TRP A 262 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 459 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C LEU A 459 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 459 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS A 460 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP H 109 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C TRP H 109 " 0.046 2.00e-02 2.50e+03 pdb=" O TRP H 109 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP H 110 " -0.016 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 47 2.45 - 3.06: 6704 3.06 - 3.67: 13801 3.67 - 4.29: 21063 4.29 - 4.90: 36027 Nonbonded interactions: 77642 Sorted by model distance: nonbonded pdb=" O ALA A 388 " pdb=" OG1 THR A 392 " model vdw 1.834 3.040 nonbonded pdb=" NE2 GLN H 186 " pdb=" OG SER H 188 " model vdw 1.954 3.120 nonbonded pdb=" OD2 ASP K 73 " pdb=" OH TYR K 80 " model vdw 1.956 3.040 nonbonded pdb=" OG1 THR A 70 " pdb=" N GLU A 71 " model vdw 1.971 3.120 nonbonded pdb=" OG SER A 659 " pdb=" OD1 ASP A 661 " model vdw 2.008 3.040 ... (remaining 77637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.000 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.007 0.085 9816 Z= 0.371 Angle : 1.014 42.267 13340 Z= 0.536 Chirality : 0.051 0.272 1499 Planarity : 0.005 0.053 1677 Dihedral : 13.505 86.378 3504 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.54 % Favored : 93.05 % Rotamer: Outliers : 0.96 % Allowed : 0.57 % Favored : 98.47 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: 0.03 (0.25), residues: 1208 helix: 0.55 (0.26), residues: 427 sheet: 0.83 (0.32), residues: 278 loop : -0.86 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 67 TYR 0.018 0.002 TYR A 578 PHE 0.045 0.002 PHE A 56 TRP 0.033 0.002 TRP H 110 HIS 0.011 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00730 ( 9808) covalent geometry : angle 1.01353 (13324) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.99589 ( 16) hydrogen bonds : bond 0.16436 ( 470) hydrogen bonds : angle 6.64157 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: L 82 GLU cc_start: 0.7990 (pm20) cc_final: 0.7599 (pm20) REVERT: A 328 MET cc_start: 0.7180 (tpp) cc_final: 0.6919 (tpt) REVERT: A 549 LYS cc_start: 0.7694 (pttp) cc_final: 0.7483 (pmtt) REVERT: A 584 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7323 (ttp80) outliers start: 10 outliers final: 3 residues processed: 114 average time/residue: 0.7236 time to fit residues: 87.3489 Evaluate side-chains 87 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN H 87 ASN ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.207534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120582 restraints weight = 9663.054| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.80 r_work: 0.3216 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9816 Z= 0.183 Angle : 0.651 8.089 13340 Z= 0.337 Chirality : 0.046 0.153 1499 Planarity : 0.004 0.038 1677 Dihedral : 6.219 56.287 1378 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 1.53 % Allowed : 8.89 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.26 (0.25), residues: 1208 helix: 0.79 (0.25), residues: 439 sheet: 0.86 (0.31), residues: 280 loop : -0.74 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 393 TYR 0.015 0.002 TYR H 106 PHE 0.024 0.002 PHE A 56 TRP 0.019 0.002 TRP H 110 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9808) covalent geometry : angle 0.65006 (13324) SS BOND : bond 0.00279 ( 8) SS BOND : angle 1.34029 ( 16) hydrogen bonds : bond 0.04748 ( 470) hydrogen bonds : angle 4.98723 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.387 Fit side-chains REVERT: K 83 MET cc_start: 0.4124 (mmt) cc_final: 0.2756 (mmt) REVERT: L 46 LYS cc_start: 0.8522 (ptmm) cc_final: 0.8191 (ptpp) REVERT: L 71 ASP cc_start: 0.7967 (m-30) cc_final: 0.7691 (m-30) REVERT: A 584 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7138 (ttp80) outliers start: 16 outliers final: 5 residues processed: 97 average time/residue: 0.6462 time to fit residues: 66.8659 Evaluate side-chains 87 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 30.0000 chunk 31 optimal weight: 40.0000 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 HIS ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.210453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123113 restraints weight = 9777.594| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.17 r_work: 0.3308 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9816 Z= 0.164 Angle : 0.612 8.450 13340 Z= 0.316 Chirality : 0.045 0.151 1499 Planarity : 0.004 0.040 1677 Dihedral : 5.512 54.298 1374 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.68 % Allowed : 11.66 % Favored : 85.66 % 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 aren not related in a simple way. whole: 0.35 (0.25), residues: 1208 helix: 1.00 (0.26), residues: 439 sheet: 0.87 (0.31), residues: 279 loop : -0.82 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.012 0.001 TYR H 106 PHE 0.015 0.001 PHE A 305 TRP 0.012 0.002 TRP H 110 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9808) covalent geometry : angle 0.61014 (13324) SS BOND : bond 0.00225 ( 8) SS BOND : angle 1.61567 ( 16) hydrogen bonds : bond 0.04392 ( 470) hydrogen bonds : angle 4.66960 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.375 Fit side-chains REVERT: K 83 MET cc_start: 0.3972 (mmt) cc_final: 0.2716 (mmt) REVERT: L 46 LYS cc_start: 0.8616 (ptmm) cc_final: 0.8331 (ptpp) REVERT: A 72 MET cc_start: 0.8703 (mtp) cc_final: 0.8238 (mtp) REVERT: A 366 LYS cc_start: 0.7423 (ttpp) cc_final: 0.7180 (ttpp) REVERT: A 524 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6380 (mp-120) REVERT: A 584 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7390 (ttp80) outliers start: 28 outliers final: 11 residues processed: 106 average time/residue: 0.6342 time to fit residues: 71.9083 Evaluate side-chains 96 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.207082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122497 restraints weight = 9879.176| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.11 r_work: 0.3204 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9816 Z= 0.254 Angle : 0.681 8.627 13340 Z= 0.350 Chirality : 0.048 0.192 1499 Planarity : 0.004 0.042 1677 Dihedral : 5.850 54.235 1373 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 3.63 % Allowed : 12.81 % Favored : 83.56 % 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 aren not related in a simple way. whole: 0.05 (0.24), residues: 1208 helix: 0.65 (0.25), residues: 445 sheet: 0.68 (0.30), residues: 293 loop : -0.92 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 67 TYR 0.014 0.002 TYR A 116 PHE 0.019 0.002 PHE A 305 TRP 0.023 0.002 TRP H 110 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 9808) covalent geometry : angle 0.67816 (13324) SS BOND : bond 0.00709 ( 8) SS BOND : angle 1.76920 ( 16) hydrogen bonds : bond 0.05312 ( 470) hydrogen bonds : angle 4.78534 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.390 Fit side-chains REVERT: H 116 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8618 (p0) REVERT: K 83 MET cc_start: 0.3887 (mmt) cc_final: 0.2549 (mmt) REVERT: L 46 LYS cc_start: 0.8712 (ptmm) cc_final: 0.8411 (ptpp) REVERT: L 82 GLU cc_start: 0.8296 (pm20) cc_final: 0.7511 (pm20) REVERT: L 83 ASP cc_start: 0.8310 (m-30) cc_final: 0.8078 (m-30) REVERT: L 89 CYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8504 (p) REVERT: A 72 MET cc_start: 0.8709 (mtp) cc_final: 0.8311 (mtp) REVERT: A 366 LYS cc_start: 0.7551 (ttpp) cc_final: 0.7340 (ttpp) REVERT: A 385 THR cc_start: 0.6064 (OUTLIER) cc_final: 0.5743 (p) REVERT: A 524 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6533 (mp-120) REVERT: A 584 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7128 (tpt90) outliers start: 38 outliers final: 21 residues processed: 113 average time/residue: 0.5950 time to fit residues: 72.2182 Evaluate side-chains 108 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.211680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151444 restraints weight = 9825.353| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.80 r_work: 0.3371 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9816 Z= 0.124 Angle : 0.580 8.657 13340 Z= 0.296 Chirality : 0.043 0.138 1499 Planarity : 0.004 0.040 1677 Dihedral : 5.502 50.089 1373 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 2.39 % Allowed : 14.91 % Favored : 82.70 % 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 aren not related in a simple way. whole: 0.47 (0.25), residues: 1208 helix: 1.26 (0.26), residues: 438 sheet: 0.77 (0.30), residues: 291 loop : -0.84 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 22 TYR 0.011 0.001 TYR A 116 PHE 0.015 0.001 PHE A 123 TRP 0.022 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9808) covalent geometry : angle 0.57542 (13324) SS BOND : bond 0.00439 ( 8) SS BOND : angle 2.23418 ( 16) hydrogen bonds : bond 0.03737 ( 470) hydrogen bonds : angle 4.46513 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.408 Fit side-chains REVERT: K 83 MET cc_start: 0.3943 (mmt) cc_final: 0.2630 (mmt) REVERT: L 46 LYS cc_start: 0.8590 (ptmm) cc_final: 0.8344 (ptpp) REVERT: L 82 GLU cc_start: 0.8302 (pm20) cc_final: 0.7496 (pm20) REVERT: A 366 LYS cc_start: 0.7446 (ttpp) cc_final: 0.7197 (ttpp) REVERT: A 524 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6225 (mp-120) REVERT: A 584 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7177 (tpt90) outliers start: 25 outliers final: 14 residues processed: 110 average time/residue: 0.6381 time to fit residues: 75.2709 Evaluate side-chains 107 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN A 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.208691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118663 restraints weight = 9812.237| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.15 r_work: 0.3241 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9816 Z= 0.199 Angle : 0.640 8.996 13340 Z= 0.328 Chirality : 0.046 0.166 1499 Planarity : 0.004 0.043 1677 Dihedral : 5.727 51.459 1373 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 3.35 % Allowed : 15.49 % Favored : 81.17 % 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 aren not related in a simple way. whole: 0.28 (0.25), residues: 1208 helix: 0.97 (0.25), residues: 445 sheet: 0.71 (0.30), residues: 293 loop : -0.87 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 143 TYR 0.015 0.002 TYR H 112 PHE 0.017 0.002 PHE A 123 TRP 0.034 0.002 TRP H 110 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9808) covalent geometry : angle 0.63347 (13324) SS BOND : bond 0.00459 ( 8) SS BOND : angle 2.76874 ( 16) hydrogen bonds : bond 0.04734 ( 470) hydrogen bonds : angle 4.59126 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.376 Fit side-chains REVERT: K 83 MET cc_start: 0.3936 (mmt) cc_final: 0.2623 (mmt) REVERT: L 12 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7089 (tt) REVERT: L 46 LYS cc_start: 0.8667 (ptmm) cc_final: 0.8391 (ptpp) REVERT: L 82 GLU cc_start: 0.8240 (pm20) cc_final: 0.7353 (pm20) REVERT: L 83 ASP cc_start: 0.8279 (m-30) cc_final: 0.8046 (m-30) REVERT: A 366 LYS cc_start: 0.7484 (ttpp) cc_final: 0.7235 (ttpp) REVERT: A 524 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6446 (mp-120) REVERT: A 584 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7086 (tpt90) outliers start: 35 outliers final: 20 residues processed: 114 average time/residue: 0.6166 time to fit residues: 75.4102 Evaluate side-chains 107 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 58 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** 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 = 0.4394 r_free = 0.4394 target = 0.212351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151192 restraints weight = 9723.238| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.72 r_work: 0.3389 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9816 Z= 0.140 Angle : 0.605 10.088 13340 Z= 0.307 Chirality : 0.043 0.145 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.552 49.348 1373 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 2.87 % Allowed : 15.77 % Favored : 81.36 % 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 aren not related in a simple way. whole: 0.46 (0.25), residues: 1208 helix: 1.22 (0.26), residues: 444 sheet: 0.73 (0.31), residues: 291 loop : -0.82 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 676 TYR 0.013 0.001 TYR A 116 PHE 0.019 0.001 PHE A 123 TRP 0.031 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9808) covalent geometry : angle 0.59288 (13324) SS BOND : bond 0.00664 ( 8) SS BOND : angle 3.50690 ( 16) hydrogen bonds : bond 0.03910 ( 470) hydrogen bonds : angle 4.46543 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.363 Fit side-chains REVERT: K 83 MET cc_start: 0.3948 (mmt) cc_final: 0.2628 (mmt) REVERT: L 12 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7289 (tt) REVERT: L 46 LYS cc_start: 0.8570 (ptmm) cc_final: 0.8315 (ptpp) REVERT: L 82 GLU cc_start: 0.8246 (pm20) cc_final: 0.7417 (pm20) REVERT: A 524 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6218 (mp-120) REVERT: A 584 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7167 (tpt90) outliers start: 30 outliers final: 17 residues processed: 111 average time/residue: 0.5830 time to fit residues: 69.6263 Evaluate side-chains 107 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN A 527 ASN A 617 GLN A 673 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.214971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125338 restraints weight = 9678.224| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.31 r_work: 0.3297 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9816 Z= 0.129 Angle : 0.590 8.947 13340 Z= 0.299 Chirality : 0.043 0.142 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.437 48.056 1373 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 2.68 % Allowed : 17.02 % Favored : 80.31 % 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 aren not related in a simple way. whole: 0.57 (0.25), residues: 1208 helix: 1.36 (0.26), residues: 444 sheet: 0.83 (0.31), residues: 288 loop : -0.84 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 22 TYR 0.013 0.001 TYR A 116 PHE 0.021 0.001 PHE A 123 TRP 0.027 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9808) covalent geometry : angle 0.58048 (13324) SS BOND : bond 0.00571 ( 8) SS BOND : angle 3.02273 ( 16) hydrogen bonds : bond 0.03696 ( 470) hydrogen bonds : angle 4.38435 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.390 Fit side-chains REVERT: K 83 MET cc_start: 0.3958 (mmt) cc_final: 0.2642 (mmt) REVERT: L 12 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7080 (tt) REVERT: L 46 LYS cc_start: 0.8588 (ptmm) cc_final: 0.8331 (ptpp) REVERT: L 82 GLU cc_start: 0.8207 (pm20) cc_final: 0.7224 (pm20) REVERT: L 83 ASP cc_start: 0.8215 (m-30) cc_final: 0.7991 (m-30) REVERT: A 524 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6186 (mp-120) REVERT: A 584 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7147 (tpt90) REVERT: A 619 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6797 (pmm) outliers start: 28 outliers final: 19 residues processed: 109 average time/residue: 0.5969 time to fit residues: 69.9553 Evaluate side-chains 111 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 36 optimal weight: 4.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN A 527 ASN A 673 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.212475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125931 restraints weight = 9731.318| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.17 r_work: 0.3235 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9816 Z= 0.187 Angle : 0.641 9.283 13340 Z= 0.325 Chirality : 0.045 0.162 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.611 50.697 1373 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 2.58 % Allowed : 17.30 % Favored : 80.11 % 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 aren not related in a simple way. whole: 0.40 (0.25), residues: 1208 helix: 1.15 (0.25), residues: 445 sheet: 0.74 (0.31), residues: 290 loop : -0.85 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 676 TYR 0.015 0.001 TYR A 116 PHE 0.023 0.002 PHE A 123 TRP 0.044 0.002 TRP H 110 HIS 0.003 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9808) covalent geometry : angle 0.63148 (13324) SS BOND : bond 0.00505 ( 8) SS BOND : angle 3.25059 ( 16) hydrogen bonds : bond 0.04416 ( 470) hydrogen bonds : angle 4.49969 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.411 Fit side-chains REVERT: K 83 MET cc_start: 0.3973 (mmt) cc_final: 0.2635 (mmt) REVERT: L 12 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7119 (tt) REVERT: L 46 LYS cc_start: 0.8656 (ptmm) cc_final: 0.8393 (ptpp) REVERT: L 82 GLU cc_start: 0.8185 (pm20) cc_final: 0.7856 (pm20) REVERT: A 524 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6326 (mp-120) REVERT: A 580 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.6314 (m90) REVERT: A 584 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7095 (tpt90) outliers start: 27 outliers final: 19 residues processed: 110 average time/residue: 0.6090 time to fit residues: 71.9171 Evaluate side-chains 111 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN A 527 ASN A 673 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.214354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152592 restraints weight = 9697.195| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.73 r_work: 0.3368 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9816 Z= 0.138 Angle : 0.609 9.278 13340 Z= 0.309 Chirality : 0.043 0.144 1499 Planarity : 0.004 0.042 1677 Dihedral : 5.538 54.056 1373 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 2.39 % Allowed : 17.50 % Favored : 80.11 % 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 aren not related in a simple way. whole: 0.52 (0.25), residues: 1208 helix: 1.31 (0.25), residues: 445 sheet: 0.78 (0.31), residues: 290 loop : -0.84 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 676 TYR 0.013 0.001 TYR A 116 PHE 0.027 0.001 PHE A 123 TRP 0.047 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9808) covalent geometry : angle 0.60017 (13324) SS BOND : bond 0.00511 ( 8) SS BOND : angle 3.07203 ( 16) hydrogen bonds : bond 0.03829 ( 470) hydrogen bonds : angle 4.42982 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.300 Fit side-chains REVERT: K 83 MET cc_start: 0.3987 (mmt) cc_final: 0.2706 (mmt) REVERT: L 12 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7300 (tt) REVERT: L 46 LYS cc_start: 0.8581 (ptmm) cc_final: 0.8341 (ptpp) REVERT: L 82 GLU cc_start: 0.8236 (pm20) cc_final: 0.7961 (pm20) REVERT: A 524 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6277 (mp-120) REVERT: A 580 HIS cc_start: 0.6698 (OUTLIER) cc_final: 0.6207 (m90) REVERT: A 584 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7074 (tpt90) REVERT: A 585 GLU cc_start: 0.7479 (tp30) cc_final: 0.7048 (tp30) outliers start: 25 outliers final: 16 residues processed: 109 average time/residue: 0.5552 time to fit residues: 65.0527 Evaluate side-chains 109 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 31 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 23 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN H 186 GLN A 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.207159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121105 restraints weight = 9582.881| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.00 r_work: 0.3195 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9816 Z= 0.146 Angle : 0.617 9.902 13340 Z= 0.312 Chirality : 0.044 0.146 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.548 59.230 1373 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 2.29 % Allowed : 17.69 % Favored : 80.02 % 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 aren not related in a simple way. whole: 0.53 (0.25), residues: 1208 helix: 1.33 (0.25), residues: 445 sheet: 0.77 (0.31), residues: 290 loop : -0.84 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 676 TYR 0.014 0.001 TYR A 116 PHE 0.028 0.001 PHE A 123 TRP 0.042 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9808) covalent geometry : angle 0.60861 (13324) SS BOND : bond 0.00470 ( 8) SS BOND : angle 2.99026 ( 16) hydrogen bonds : bond 0.03915 ( 470) hydrogen bonds : angle 4.43885 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4262.06 seconds wall clock time: 73 minutes 21.57 seconds (4401.57 seconds total)