Starting phenix.real_space_refine on Sun Jul 27 18:49:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zli_14781/07_2025/7zli_14781_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zli_14781/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zli_14781/07_2025/7zli_14781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zli_14781/07_2025/7zli_14781.map" model { file = "/net/cci-nas-00/data/ceres_data/7zli_14781/07_2025/7zli_14781_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zli_14781/07_2025/7zli_14781_trim.cif" } resolution = 2.99 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= 0.064 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.87, per 1000 atoms: 0.72 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: 3.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.22 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: 3.40 Time building geometry restraints manager: 2.94 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: 0.000 Normalize map: mean=0, sd=1: 4.370 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- 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 : 27.48 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 (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: 0.03 (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 TRP 0.033 0.002 TRP H 110 HIS 0.011 0.001 HIS A 297 PHE 0.045 0.002 PHE A 56 TYR 0.018 0.002 TYR A 578 ARG 0.004 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.16436 ( 470) hydrogen bonds : angle 6.64157 ( 1383) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.99589 ( 16) covalent geometry : bond 0.00730 ( 9808) covalent geometry : angle 1.01353 (13324) *********************** 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 : 1.700 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: 1.8718 time to fit residues: 227.2404 Evaluate side-chains 88 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 102 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.208054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123402 restraints weight = 9625.283| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.14 r_work: 0.3202 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9816 Z= 0.148 Angle : 0.620 8.133 13340 Z= 0.321 Chirality : 0.045 0.141 1499 Planarity : 0.004 0.037 1677 Dihedral : 6.103 55.878 1378 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 1.43 % Allowed : 8.70 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.43 (0.25), residues: 1208 helix: 0.97 (0.26), residues: 439 sheet: 0.95 (0.31), residues: 279 loop : -0.69 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 110 HIS 0.004 0.001 HIS A 105 PHE 0.020 0.002 PHE A 56 TYR 0.014 0.001 TYR H 106 ARG 0.004 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 470) hydrogen bonds : angle 4.91994 ( 1383) SS BOND : bond 0.00298 ( 8) SS BOND : angle 1.32820 ( 16) covalent geometry : bond 0.00350 ( 9808) covalent geometry : angle 0.61906 (13324) *********************** 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 103 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.998 Fit side-chains REVERT: K 83 MET cc_start: 0.4179 (mmt) cc_final: 0.2826 (mmt) REVERT: L 46 LYS cc_start: 0.8504 (ptmm) cc_final: 0.8208 (ptpp) REVERT: L 71 ASP cc_start: 0.7945 (m-30) cc_final: 0.7677 (m-30) REVERT: L 106 GLU cc_start: 0.7423 (pm20) cc_final: 0.7207 (mp0) REVERT: A 72 MET cc_start: 0.8534 (mtp) cc_final: 0.8077 (mtp) REVERT: A 328 MET cc_start: 0.8202 (tpp) cc_final: 0.7988 (tpt) REVERT: A 396 THR cc_start: 0.7295 (m) cc_final: 0.6972 (p) REVERT: A 584 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7089 (ttp80) REVERT: A 629 GLU cc_start: 0.7426 (pt0) cc_final: 0.7138 (pp20) outliers start: 15 outliers final: 3 residues processed: 96 average time/residue: 1.3210 time to fit residues: 136.1125 Evaluate side-chains 83 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 104 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 105 HIS A 577 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.211286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129787 restraints weight = 9878.508| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.01 r_work: 0.3314 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9816 Z= 0.153 Angle : 0.604 8.329 13340 Z= 0.311 Chirality : 0.044 0.144 1499 Planarity : 0.004 0.039 1677 Dihedral : 5.458 56.020 1373 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.01 % Allowed : 11.66 % Favored : 86.33 % 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: 1208 helix: 1.16 (0.26), residues: 439 sheet: 0.90 (0.31), residues: 279 loop : -0.78 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 110 HIS 0.003 0.001 HIS A 479 PHE 0.015 0.001 PHE A 56 TYR 0.012 0.001 TYR H 112 ARG 0.004 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 470) hydrogen bonds : angle 4.64849 ( 1383) SS BOND : bond 0.00241 ( 8) SS BOND : angle 1.99223 ( 16) covalent geometry : bond 0.00372 ( 9808) covalent geometry : angle 0.60087 (13324) *********************** 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 108 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.071 Fit side-chains REVERT: K 83 MET cc_start: 0.3983 (mmt) cc_final: 0.2742 (mmt) REVERT: L 4 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8162 (mm-40) REVERT: L 46 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8309 (ptpp) REVERT: A 328 MET cc_start: 0.8388 (tpp) cc_final: 0.8167 (tpt) REVERT: A 524 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6326 (mp-120) REVERT: A 584 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7335 (ttp80) outliers start: 21 outliers final: 6 residues processed: 100 average time/residue: 1.3372 time to fit residues: 143.5378 Evaluate side-chains 89 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 4 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 105 HIS ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.213559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150571 restraints weight = 9711.296| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.74 r_work: 0.3350 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9816 Z= 0.159 Angle : 0.598 8.208 13340 Z= 0.307 Chirality : 0.044 0.147 1499 Planarity : 0.004 0.040 1677 Dihedral : 5.492 53.799 1373 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 2.58 % Allowed : 13.00 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1208 helix: 1.22 (0.26), residues: 439 sheet: 0.80 (0.30), residues: 293 loop : -0.83 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 110 HIS 0.003 0.001 HIS A 391 PHE 0.015 0.001 PHE A 123 TYR 0.013 0.001 TYR H 117 ARG 0.003 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 470) hydrogen bonds : angle 4.54893 ( 1383) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.42111 ( 16) covalent geometry : bond 0.00389 ( 9808) covalent geometry : angle 0.59638 (13324) *********************** 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 113 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.000 Fit side-chains REVERT: K 83 MET cc_start: 0.3882 (mmt) cc_final: 0.2578 (mmt) REVERT: L 46 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8318 (ptpp) REVERT: L 82 GLU cc_start: 0.8390 (pm20) cc_final: 0.7601 (pm20) REVERT: L 106 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: A 328 MET cc_start: 0.8354 (tpp) cc_final: 0.8135 (tpt) REVERT: A 385 THR cc_start: 0.6245 (OUTLIER) cc_final: 0.6011 (p) REVERT: A 524 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6344 (mp-120) REVERT: A 584 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7444 (ttp80) outliers start: 27 outliers final: 10 residues processed: 105 average time/residue: 1.2872 time to fit residues: 145.2334 Evaluate side-chains 97 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 106 GLU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 385 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 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 102 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 144 GLN A 479 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.215115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153985 restraints weight = 9711.459| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.75 r_work: 0.3395 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1941 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 : 0.579 8.583 13340 Z= 0.295 Chirality : 0.043 0.139 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.362 51.604 1373 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 2.49 % Allowed : 13.77 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1208 helix: 1.45 (0.26), residues: 438 sheet: 0.79 (0.30), residues: 291 loop : -0.77 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 110 HIS 0.004 0.001 HIS A 105 PHE 0.016 0.001 PHE A 123 TYR 0.012 0.001 TYR A 116 ARG 0.003 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 470) hydrogen bonds : angle 4.44130 ( 1383) SS BOND : bond 0.00586 ( 8) SS BOND : angle 2.93951 ( 16) covalent geometry : bond 0.00305 ( 9808) covalent geometry : angle 0.57063 (13324) *********************** 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 117 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.061 Fit side-chains REVERT: H 14 LEU cc_start: 0.7894 (tt) cc_final: 0.7678 (tm) REVERT: H 193 LEU cc_start: 0.6970 (pp) cc_final: 0.6614 (pt) REVERT: K 83 MET cc_start: 0.3937 (mmt) cc_final: 0.2649 (mmt) REVERT: L 12 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7180 (tt) REVERT: L 46 LYS cc_start: 0.8559 (ptmm) cc_final: 0.8292 (ptpp) REVERT: L 82 GLU cc_start: 0.8318 (pm20) cc_final: 0.7513 (pm20) REVERT: L 106 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 328 MET cc_start: 0.8317 (tpp) cc_final: 0.8104 (tpt) REVERT: A 385 THR cc_start: 0.6307 (OUTLIER) cc_final: 0.6101 (p) REVERT: A 524 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6189 (mp-120) REVERT: A 584 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7185 (tpt90) outliers start: 26 outliers final: 11 residues processed: 108 average time/residue: 1.2266 time to fit residues: 142.5307 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 : 1.008 ------------------------------------------------------------------------------- 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 12 LEU Chi-restraints excluded: chain L residue 106 GLU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** A 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.215358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154496 restraints weight = 9712.397| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.81 r_work: 0.3369 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9816 Z= 0.126 Angle : 0.572 8.872 13340 Z= 0.291 Chirality : 0.043 0.140 1499 Planarity : 0.004 0.042 1677 Dihedral : 5.311 50.859 1373 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.58 % Allowed : 14.53 % Favored : 82.89 % 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: 0.70 (0.25), residues: 1208 helix: 1.55 (0.26), residues: 437 sheet: 0.82 (0.31), residues: 291 loop : -0.75 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 110 HIS 0.004 0.001 HIS A 105 PHE 0.017 0.001 PHE A 123 TYR 0.013 0.001 TYR A 116 ARG 0.004 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 470) hydrogen bonds : angle 4.38093 ( 1383) SS BOND : bond 0.00382 ( 8) SS BOND : angle 2.23137 ( 16) covalent geometry : bond 0.00297 ( 9808) covalent geometry : angle 0.56712 (13324) *********************** 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 117 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.991 Fit side-chains REVERT: K 83 MET cc_start: 0.3951 (mmt) cc_final: 0.2647 (mmt) REVERT: L 12 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7288 (tt) REVERT: L 46 LYS cc_start: 0.8582 (ptmm) cc_final: 0.8336 (ptpp) REVERT: L 82 GLU cc_start: 0.8330 (pm20) cc_final: 0.7459 (pm20) REVERT: L 106 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 328 MET cc_start: 0.8383 (tpp) cc_final: 0.8176 (tpt) REVERT: A 385 THR cc_start: 0.6300 (OUTLIER) cc_final: 0.6085 (p) REVERT: A 524 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6271 (mp-120) REVERT: A 584 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7192 (tpt90) outliers start: 27 outliers final: 14 residues processed: 110 average time/residue: 1.1813 time to fit residues: 139.9773 Evaluate side-chains 106 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 385 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 105 HIS A 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.213490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152221 restraints weight = 9709.291| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.81 r_work: 0.3365 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9816 Z= 0.125 Angle : 0.574 9.021 13340 Z= 0.291 Chirality : 0.043 0.142 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.277 50.135 1373 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 2.68 % Allowed : 15.11 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1208 helix: 1.57 (0.26), residues: 439 sheet: 0.93 (0.31), residues: 289 loop : -0.77 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 110 HIS 0.005 0.001 HIS A 105 PHE 0.020 0.001 PHE A 123 TYR 0.020 0.001 TYR H 83 ARG 0.004 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 470) hydrogen bonds : angle 4.35906 ( 1383) SS BOND : bond 0.00488 ( 8) SS BOND : angle 2.49022 ( 16) covalent geometry : bond 0.00295 ( 9808) covalent geometry : angle 0.56812 (13324) *********************** 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 121 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.991 Fit side-chains REVERT: K 83 MET cc_start: 0.3976 (mmt) cc_final: 0.2661 (mmt) REVERT: L 12 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7233 (tt) REVERT: L 46 LYS cc_start: 0.8573 (ptmm) cc_final: 0.8327 (ptpp) REVERT: L 82 GLU cc_start: 0.8322 (pm20) cc_final: 0.7420 (pm20) REVERT: L 83 ASP cc_start: 0.8256 (m-30) cc_final: 0.8033 (m-30) REVERT: L 106 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: L 164 VAL cc_start: 0.7685 (t) cc_final: 0.7223 (p) REVERT: A 328 MET cc_start: 0.8376 (tpp) cc_final: 0.8161 (tpt) REVERT: A 385 THR cc_start: 0.6287 (OUTLIER) cc_final: 0.6058 (p) REVERT: A 524 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6273 (mp-120) REVERT: A 584 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7205 (tpt90) REVERT: A 585 GLU cc_start: 0.7471 (tp30) cc_final: 0.7252 (tp30) outliers start: 28 outliers final: 18 residues processed: 112 average time/residue: 1.2669 time to fit residues: 153.0811 Evaluate side-chains 112 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 261 PHE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 474 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 55 HIS A 105 HIS A 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.210029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147790 restraints weight = 9852.356| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.79 r_work: 0.3298 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 9816 Z= 0.261 Angle : 0.701 9.179 13340 Z= 0.358 Chirality : 0.048 0.184 1499 Planarity : 0.004 0.043 1677 Dihedral : 5.887 53.321 1373 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.87 % Rotamer: Outliers : 3.25 % Allowed : 15.11 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1208 helix: 0.82 (0.25), residues: 446 sheet: 0.73 (0.30), residues: 292 loop : -0.90 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 109 HIS 0.004 0.001 HIS A 206 PHE 0.021 0.002 PHE A 123 TYR 0.020 0.002 TYR H 83 ARG 0.004 0.001 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 470) hydrogen bonds : angle 4.70908 ( 1383) SS BOND : bond 0.00515 ( 8) SS BOND : angle 2.63722 ( 16) covalent geometry : bond 0.00658 ( 9808) covalent geometry : angle 0.69519 (13324) *********************** 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 124 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 1.033 Fit side-chains REVERT: K 83 MET cc_start: 0.3971 (mmt) cc_final: 0.2658 (mmt) REVERT: L 12 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7371 (tt) REVERT: L 46 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8419 (ptpp) REVERT: L 82 GLU cc_start: 0.8305 (pm20) cc_final: 0.8066 (pm20) REVERT: L 106 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 72 MET cc_start: 0.8784 (mtp) cc_final: 0.8402 (mtp) REVERT: A 524 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6581 (mp-120) REVERT: A 584 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7158 (tpt90) outliers start: 34 outliers final: 20 residues processed: 113 average time/residue: 1.2504 time to fit residues: 151.7153 Evaluate side-chains 107 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 H residue 185 LEU 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 47 TYR 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 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 609 MET Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A 105 HIS A 617 GLN A 673 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.211087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122253 restraints weight = 9741.204| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.27 r_work: 0.3302 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9816 Z= 0.128 Angle : 0.595 9.330 13340 Z= 0.301 Chirality : 0.043 0.141 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.554 49.639 1373 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 2.39 % Allowed : 15.97 % Favored : 81.64 % 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: 1208 helix: 1.26 (0.26), residues: 445 sheet: 0.79 (0.31), residues: 290 loop : -0.82 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 110 HIS 0.003 0.001 HIS A 105 PHE 0.025 0.001 PHE A 123 TYR 0.020 0.001 TYR H 83 ARG 0.004 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 470) hydrogen bonds : angle 4.42161 ( 1383) SS BOND : bond 0.00558 ( 8) SS BOND : angle 2.57736 ( 16) covalent geometry : bond 0.00300 ( 9808) covalent geometry : angle 0.58832 (13324) *********************** 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 121 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.050 Fit side-chains REVERT: K 83 MET cc_start: 0.3964 (mmt) cc_final: 0.2695 (mmt) REVERT: L 12 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7226 (tt) REVERT: L 46 LYS cc_start: 0.8623 (ptmm) cc_final: 0.8366 (ptpp) REVERT: L 82 GLU cc_start: 0.8229 (pm20) cc_final: 0.7946 (pm20) REVERT: L 106 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 385 THR cc_start: 0.6066 (OUTLIER) cc_final: 0.5775 (p) REVERT: A 524 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6213 (mp-120) REVERT: A 580 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.6160 (m90) REVERT: A 584 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7154 (tpt90) REVERT: A 585 GLU cc_start: 0.7525 (tp30) cc_final: 0.7010 (tp30) outliers start: 25 outliers final: 13 residues processed: 111 average time/residue: 1.2287 time to fit residues: 146.7100 Evaluate side-chains 106 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 H residue 185 LEU 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 385 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 524 GLN 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 44 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** A 527 ASN A 673 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.208479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120438 restraints weight = 9865.003| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.29 r_work: 0.3238 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9816 Z= 0.216 Angle : 0.672 9.839 13340 Z= 0.342 Chirality : 0.046 0.207 1499 Planarity : 0.004 0.043 1677 Dihedral : 5.757 51.417 1373 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.87 % Rotamer: Outliers : 2.29 % Allowed : 16.25 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.25), residues: 1208 helix: 1.00 (0.25), residues: 445 sheet: 0.71 (0.30), residues: 290 loop : -0.88 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 110 HIS 0.003 0.001 HIS A 206 PHE 0.027 0.002 PHE A 123 TYR 0.021 0.002 TYR H 83 ARG 0.006 0.001 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 470) hydrogen bonds : angle 4.56870 ( 1383) SS BOND : bond 0.00510 ( 8) SS BOND : angle 2.82760 ( 16) covalent geometry : bond 0.00544 ( 9808) covalent geometry : angle 0.66558 (13324) ********************** 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 112 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.047 Fit side-chains REVERT: K 83 MET cc_start: 0.3861 (mmt) cc_final: 0.2558 (mmt) REVERT: L 12 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7100 (tt) REVERT: L 46 LYS cc_start: 0.8676 (ptmm) cc_final: 0.8400 (ptpp) REVERT: L 82 GLU cc_start: 0.8191 (pm20) cc_final: 0.7905 (pm20) REVERT: L 106 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 72 MET cc_start: 0.8697 (mtp) cc_final: 0.8314 (mtp) REVERT: A 385 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5737 (p) REVERT: A 524 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6377 (mp-120) REVERT: A 584 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7050 (tpt90) REVERT: A 585 GLU cc_start: 0.7549 (tp30) cc_final: 0.6993 (tp30) REVERT: A 619 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6709 (pmm) outliers start: 24 outliers final: 15 residues processed: 104 average time/residue: 1.2452 time to fit residues: 139.3162 Evaluate side-chains 108 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 H residue 185 LEU 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 385 THR Chi-restraints excluded: chain A residue 474 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** A 105 HIS 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 = 0.4363 r_free = 0.4363 target = 0.210959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121376 restraints weight = 9761.283| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.20 r_work: 0.3292 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9816 Z= 0.134 Angle : 0.612 9.803 13340 Z= 0.309 Chirality : 0.043 0.180 1499 Planarity : 0.004 0.041 1677 Dihedral : 5.563 54.299 1373 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 2.01 % Allowed : 16.44 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1208 helix: 1.26 (0.25), residues: 446 sheet: 0.74 (0.31), residues: 290 loop : -0.82 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 110 HIS 0.003 0.001 HIS A 479 PHE 0.028 0.001 PHE A 123 TYR 0.021 0.001 TYR H 83 ARG 0.005 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 470) hydrogen bonds : angle 4.39725 ( 1383) SS BOND : bond 0.00455 ( 8) SS BOND : angle 2.54205 ( 16) covalent geometry : bond 0.00318 ( 9808) covalent geometry : angle 0.60592 (13324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8952.66 seconds wall clock time: 154 minutes 28.99 seconds (9268.99 seconds total)