Starting phenix.real_space_refine on Fri Aug 22 14:38:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yp2_33994/08_2025/7yp2_33994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yp2_33994/08_2025/7yp2_33994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yp2_33994/08_2025/7yp2_33994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yp2_33994/08_2025/7yp2_33994.map" model { file = "/net/cci-nas-00/data/ceres_data/7yp2_33994/08_2025/7yp2_33994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yp2_33994/08_2025/7yp2_33994.cif" } resolution = 3.52 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= 0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2699 2.51 5 N 709 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2443 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 11, 'TRANS': 302} Conformer: "B" Number of residues, atoms: 314, 2443 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 11, 'TRANS': 302} bond proxies already assigned to first conformer: 2479 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Time building chain proxies: 1.41, per 1000 atoms: 0.33 Number of scatterers: 4248 At special positions: 0 Unit cell: (72.354, 80.134, 98.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 821 8.00 N 709 7.00 C 2699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 615 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " 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: 0.23 Conformation dependent library (CDL) restraints added in 224.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 8 sheets defined 24.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 369 through 383 removed outlier: 3.701A pdb=" N GLU A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.521A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 removed outlier: 3.508A pdb=" N GLY A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.537A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.544A pdb=" N LEU A 480 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 502 through 517 removed outlier: 3.617A pdb=" N ASN A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.672A pdb=" N ASP A 523 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 524 " --> pdb=" O ARG A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.660A pdb=" N LYS A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.554A pdb=" N SER A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 4.355A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 546 Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 602 removed outlier: 4.454A pdb=" N TYR A 658 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP A 623 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 628 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.568A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.835A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.579A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.599A pdb=" N THR L 80 " --> pdb=" O THR L 69 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 345 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: 0.37 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 692 1.28 - 1.41: 1091 1.41 - 1.55: 2521 1.55 - 1.68: 5 1.68 - 1.82: 28 Bond restraints: 4337 Sorted by residual: bond pdb=" C THR L 75 " pdb=" O THR L 75 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.15e-02 7.56e+03 6.04e+01 bond pdb=" C ASP L 76 " pdb=" O ASP L 76 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.21e-02 6.83e+03 5.62e+01 bond pdb=" CA THR L 75 " pdb=" CB THR L 75 " ideal model delta sigma weight residual 1.529 1.428 0.101 1.55e-02 4.16e+03 4.27e+01 bond pdb=" CA ASP L 76 " pdb=" CB ASP L 76 " ideal model delta sigma weight residual 1.528 1.449 0.080 1.49e-02 4.50e+03 2.86e+01 bond pdb=" C GLY L 72 " pdb=" O GLY L 72 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.35e-02 5.49e+03 2.58e+01 ... (remaining 4332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 5783 2.84 - 5.67: 83 5.67 - 8.51: 17 8.51 - 11.35: 2 11.35 - 14.18: 2 Bond angle restraints: 5887 Sorted by residual: angle pdb=" N THR L 75 " pdb=" CA THR L 75 " pdb=" C THR L 75 " ideal model delta sigma weight residual 111.07 125.25 -14.18 1.07e+00 8.73e-01 1.76e+02 angle pdb=" CA THR L 75 " pdb=" C THR L 75 " pdb=" N ASP L 76 " ideal model delta sigma weight residual 117.07 127.93 -10.86 1.14e+00 7.69e-01 9.07e+01 angle pdb=" O THR L 75 " pdb=" C THR L 75 " pdb=" N ASP L 76 " ideal model delta sigma weight residual 122.07 115.72 6.35 1.03e+00 9.43e-01 3.80e+01 angle pdb=" CA ASP L 76 " pdb=" C ASP L 76 " pdb=" N PHE L 77 " ideal model delta sigma weight residual 116.23 123.91 -7.68 1.30e+00 5.92e-01 3.49e+01 angle pdb=" N ASP L 76 " pdb=" CA ASP L 76 " pdb=" C ASP L 76 " ideal model delta sigma weight residual 109.76 118.93 -9.17 1.59e+00 3.96e-01 3.33e+01 ... (remaining 5882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 2281 16.54 - 33.07: 244 33.07 - 49.61: 62 49.61 - 66.14: 8 66.14 - 82.68: 6 Dihedral angle restraints: 2601 sinusoidal: 1017 harmonic: 1584 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 615 " pdb=" CB CYS A 615 " ideal model delta sinusoidal sigma weight residual 93.00 153.55 -60.55 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CA ALA H 92 " pdb=" C ALA H 92 " pdb=" N LEU H 93 " pdb=" CA LEU H 93 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA CYS A 612 " pdb=" C CYS A 612 " pdb=" N ILE A 613 " pdb=" CA ILE A 613 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 2598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 611 0.092 - 0.184: 56 0.184 - 0.276: 2 0.276 - 0.368: 0 0.368 - 0.460: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" CA THR L 75 " pdb=" N THR L 75 " pdb=" C THR L 75 " pdb=" CB THR L 75 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB VAL A 381 " pdb=" CA VAL A 381 " pdb=" CG1 VAL A 381 " pdb=" CG2 VAL A 381 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA PRO H 53 " pdb=" N PRO H 53 " pdb=" C PRO H 53 " pdb=" CB PRO H 53 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 667 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP L 76 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ASP L 76 " -0.065 2.00e-02 2.50e+03 pdb=" O ASP L 76 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE L 77 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 74 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY L 74 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY L 74 " 0.021 2.00e-02 2.50e+03 pdb=" N THR L 75 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO A 441 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.041 5.00e-02 4.00e+02 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1311 2.82 - 3.34: 3363 3.34 - 3.86: 6466 3.86 - 4.38: 7467 4.38 - 4.90: 13573 Nonbonded interactions: 32180 Sorted by model distance: nonbonded pdb=" N GLY L 72 " pdb=" O GLY L 72 " model vdw 2.294 2.496 nonbonded pdb=" O SER A 556 " pdb=" OG SER A 556 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP H 28 " pdb=" OG SER H 30 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 373 " pdb=" OG1 THR A 420 " model vdw 2.345 3.040 nonbonded pdb=" OD2 ASP A 650 " pdb=" OH TYR L 98 " model vdw 2.372 3.040 ... (remaining 32175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.700 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.101 4342 Z= 0.379 Angle : 0.935 14.183 5897 Z= 0.563 Chirality : 0.055 0.460 670 Planarity : 0.007 0.074 748 Dihedral : 14.655 82.677 1576 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.80 (0.28), residues: 541 helix: -4.68 (0.16), residues: 109 sheet: -2.48 (0.37), residues: 166 loop : -2.92 (0.30), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 430 TYR 0.011 0.002 TYR L 38 PHE 0.019 0.002 PHE A 475 TRP 0.014 0.002 TRP H 33 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 4337) covalent geometry : angle 0.93383 ( 5887) SS BOND : bond 0.00326 ( 5) SS BOND : angle 1.38342 ( 10) hydrogen bonds : bond 0.31908 ( 130) hydrogen bonds : angle 11.18807 ( 345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.128 Fit side-chains REVERT: A 389 TYR cc_start: 0.7781 (t80) cc_final: 0.7560 (t80) REVERT: A 475 PHE cc_start: 0.8496 (t80) cc_final: 0.7865 (t80) REVERT: A 575 SER cc_start: 0.9076 (t) cc_final: 0.8728 (m) REVERT: A 650 ASP cc_start: 0.8309 (t0) cc_final: 0.8103 (t0) REVERT: H 3 LYS cc_start: 0.8732 (tttm) cc_final: 0.7997 (tmtt) REVERT: L 56 TRP cc_start: 0.8578 (m-10) cc_final: 0.7591 (m-10) REVERT: L 58 SER cc_start: 0.8674 (m) cc_final: 0.8362 (p) REVERT: L 88 ASP cc_start: 0.8542 (m-30) cc_final: 0.8311 (m-30) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0830 time to fit residues: 7.2020 Evaluate side-chains 54 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN A 604 ASN A 640 GLN H 39 GLN L 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.094780 restraints weight = 16186.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.099411 restraints weight = 7269.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.100194 restraints weight = 4483.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.101175 restraints weight = 3263.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102571 restraints weight = 2686.781| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 4342 Z= 0.174 Angle : 0.595 5.963 5897 Z= 0.316 Chirality : 0.044 0.142 670 Planarity : 0.005 0.052 748 Dihedral : 5.529 69.284 601 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.07 % Allowed : 13.43 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.71 (0.31), residues: 541 helix: -2.76 (0.37), residues: 111 sheet: -1.96 (0.38), residues: 155 loop : -2.61 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.010 0.001 TYR A 374 PHE 0.010 0.001 PHE A 475 TRP 0.011 0.001 TRP H 33 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 4337) covalent geometry : angle 0.59415 ( 5887) SS BOND : bond 0.00301 ( 5) SS BOND : angle 0.94854 ( 10) hydrogen bonds : bond 0.04543 ( 130) hydrogen bonds : angle 6.65605 ( 345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.181 Fit side-chains REVERT: A 389 TYR cc_start: 0.7703 (t80) cc_final: 0.7340 (t80) REVERT: A 474 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 538 LEU cc_start: 0.7702 (mm) cc_final: 0.7472 (mm) REVERT: A 650 ASP cc_start: 0.8506 (t0) cc_final: 0.8201 (t0) REVERT: A 668 MET cc_start: 0.8183 (mtp) cc_final: 0.7913 (mtm) REVERT: H 3 LYS cc_start: 0.8763 (tttm) cc_final: 0.7830 (tmtt) REVERT: L 56 TRP cc_start: 0.8691 (m-10) cc_final: 0.7484 (m-10) REVERT: L 87 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7075 (tm-30) REVERT: L 88 ASP cc_start: 0.8757 (m-30) cc_final: 0.8366 (m-30) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.0686 time to fit residues: 5.5006 Evaluate side-chains 55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.113289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.093605 restraints weight = 22023.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.097453 restraints weight = 11115.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.100714 restraints weight = 5999.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101909 restraints weight = 3359.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.104585 restraints weight = 2583.783| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 4342 Z= 0.199 Angle : 0.583 6.065 5897 Z= 0.305 Chirality : 0.044 0.149 670 Planarity : 0.005 0.048 748 Dihedral : 5.305 67.212 601 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.56 % Allowed : 13.65 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.11 (0.33), residues: 541 helix: -1.71 (0.44), residues: 110 sheet: -1.62 (0.40), residues: 155 loop : -2.48 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.015 0.002 TYR H 60 PHE 0.009 0.002 PHE A 578 TRP 0.011 0.001 TRP H 33 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 4337) covalent geometry : angle 0.58251 ( 5887) SS BOND : bond 0.00343 ( 5) SS BOND : angle 0.92046 ( 10) hydrogen bonds : bond 0.03925 ( 130) hydrogen bonds : angle 6.05486 ( 345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.174 Fit side-chains REVERT: A 389 TYR cc_start: 0.7714 (t80) cc_final: 0.7354 (t80) REVERT: A 474 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8623 (tt) REVERT: A 538 LEU cc_start: 0.7693 (mm) cc_final: 0.7491 (mm) REVERT: A 650 ASP cc_start: 0.8535 (t0) cc_final: 0.8207 (t0) REVERT: H 3 LYS cc_start: 0.8775 (tttm) cc_final: 0.7902 (tmtt) REVERT: L 56 TRP cc_start: 0.8616 (m-10) cc_final: 0.7600 (m-10) REVERT: L 87 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7035 (tm-30) REVERT: L 88 ASP cc_start: 0.8716 (m-30) cc_final: 0.8423 (m-30) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.0723 time to fit residues: 6.3022 Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN L 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.096939 restraints weight = 15823.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.101304 restraints weight = 7531.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102986 restraints weight = 4504.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.104194 restraints weight = 3096.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.105468 restraints weight = 2606.836| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 4342 Z= 0.120 Angle : 0.510 6.549 5897 Z= 0.266 Chirality : 0.042 0.153 670 Planarity : 0.004 0.044 748 Dihedral : 4.838 59.991 601 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.35 % Allowed : 15.99 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.61 (0.34), residues: 541 helix: -0.98 (0.48), residues: 110 sheet: -1.27 (0.41), residues: 155 loop : -2.34 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.014 0.001 TYR A 532 PHE 0.008 0.001 PHE A 475 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4337) covalent geometry : angle 0.50950 ( 5887) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.88855 ( 10) hydrogen bonds : bond 0.03034 ( 130) hydrogen bonds : angle 5.49597 ( 345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.126 Fit side-chains REVERT: A 389 TYR cc_start: 0.7711 (t80) cc_final: 0.7320 (t80) REVERT: A 650 ASP cc_start: 0.8497 (t0) cc_final: 0.8114 (t0) REVERT: H 3 LYS cc_start: 0.8753 (tttm) cc_final: 0.7761 (tmtt) REVERT: L 87 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6987 (tm-30) REVERT: L 88 ASP cc_start: 0.8642 (m-30) cc_final: 0.8413 (m-30) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.0666 time to fit residues: 5.3069 Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN L 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.096112 restraints weight = 9280.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.099113 restraints weight = 5431.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.101146 restraints weight = 3796.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102646 restraints weight = 2967.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.103581 restraints weight = 2492.065| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.004 0.115 4342 Z= 0.148 Angle : 0.523 6.983 5897 Z= 0.271 Chirality : 0.042 0.152 670 Planarity : 0.004 0.042 748 Dihedral : 4.766 58.163 601 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.20 % Allowed : 16.20 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.37 (0.34), residues: 541 helix: -0.70 (0.48), residues: 111 sheet: -1.11 (0.41), residues: 155 loop : -2.24 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.013 0.001 TYR A 532 PHE 0.008 0.001 PHE A 475 TRP 0.008 0.001 TRP H 33 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4337) covalent geometry : angle 0.52157 ( 5887) SS BOND : bond 0.00279 ( 5) SS BOND : angle 0.92739 ( 10) hydrogen bonds : bond 0.03141 ( 130) hydrogen bonds : angle 5.38017 ( 345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.165 Fit side-chains REVERT: A 389 TYR cc_start: 0.7773 (t80) cc_final: 0.7476 (t80) REVERT: A 474 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 650 ASP cc_start: 0.8518 (t0) cc_final: 0.8131 (t0) REVERT: H 3 LYS cc_start: 0.8744 (tttm) cc_final: 0.7788 (tmtt) REVERT: H 87 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.7854 (tpm170) REVERT: L 87 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6971 (tm-30) REVERT: L 88 ASP cc_start: 0.8656 (m-30) cc_final: 0.8423 (m-30) outliers start: 15 outliers final: 11 residues processed: 66 average time/residue: 0.0685 time to fit residues: 5.7488 Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.114593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.094959 restraints weight = 12272.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.099186 restraints weight = 6865.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.101244 restraints weight = 3875.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.101682 restraints weight = 3081.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101883 restraints weight = 2792.290| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 4342 Z= 0.161 Angle : 0.537 7.646 5897 Z= 0.275 Chirality : 0.043 0.141 670 Planarity : 0.004 0.042 748 Dihedral : 4.741 56.635 601 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.77 % Allowed : 15.99 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.20 (0.35), residues: 541 helix: -0.51 (0.49), residues: 111 sheet: -0.84 (0.42), residues: 148 loop : -2.24 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.016 0.001 TYR A 532 PHE 0.008 0.001 PHE A 475 TRP 0.008 0.001 TRP H 33 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4337) covalent geometry : angle 0.53600 ( 5887) SS BOND : bond 0.00307 ( 5) SS BOND : angle 0.98656 ( 10) hydrogen bonds : bond 0.03148 ( 130) hydrogen bonds : angle 5.31752 ( 345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.141 Fit side-chains REVERT: A 389 TYR cc_start: 0.7788 (t80) cc_final: 0.7507 (t80) REVERT: A 474 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8670 (tt) REVERT: A 650 ASP cc_start: 0.8522 (t0) cc_final: 0.8103 (t0) REVERT: H 3 LYS cc_start: 0.8774 (tttm) cc_final: 0.7785 (tmtt) REVERT: H 85 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8557 (mtmt) REVERT: H 87 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.7817 (tpm170) REVERT: L 87 GLU cc_start: 0.7622 (tm-30) cc_final: 0.6977 (tm-30) REVERT: L 88 ASP cc_start: 0.8698 (m-30) cc_final: 0.8429 (m-30) outliers start: 13 outliers final: 11 residues processed: 60 average time/residue: 0.0754 time to fit residues: 5.5584 Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 0.0970 chunk 2 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.097889 restraints weight = 17923.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101384 restraints weight = 8516.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.104404 restraints weight = 4848.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.105575 restraints weight = 3174.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.106961 restraints weight = 2626.623| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 4342 Z= 0.100 Angle : 0.477 6.504 5897 Z= 0.246 Chirality : 0.041 0.134 670 Planarity : 0.004 0.041 748 Dihedral : 4.358 49.243 601 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.56 % Allowed : 16.42 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.91 (0.35), residues: 541 helix: -0.03 (0.51), residues: 111 sheet: -0.76 (0.42), residues: 152 loop : -2.12 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.013 0.001 TYR H 60 PHE 0.007 0.001 PHE A 475 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4337) covalent geometry : angle 0.47563 ( 5887) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.86696 ( 10) hydrogen bonds : bond 0.02649 ( 130) hydrogen bonds : angle 4.94376 ( 345) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.192 Fit side-chains REVERT: A 389 TYR cc_start: 0.7750 (t80) cc_final: 0.7386 (t80) REVERT: A 650 ASP cc_start: 0.8484 (t0) cc_final: 0.8061 (t0) REVERT: H 3 LYS cc_start: 0.8728 (tttm) cc_final: 0.7744 (tmtt) REVERT: H 87 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.7899 (tpm170) REVERT: L 87 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6908 (tm-30) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.0716 time to fit residues: 5.3794 Evaluate side-chains 59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 43 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.116953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097803 restraints weight = 12680.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102009 restraints weight = 6595.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103805 restraints weight = 4059.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.104600 restraints weight = 2922.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.105807 restraints weight = 2595.211| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 0.105 4342 Z= 0.121 Angle : 0.496 6.299 5897 Z= 0.253 Chirality : 0.042 0.136 670 Planarity : 0.004 0.039 748 Dihedral : 4.288 46.015 601 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.56 % Allowed : 16.42 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.77 (0.35), residues: 541 helix: 0.18 (0.51), residues: 111 sheet: -0.69 (0.42), residues: 152 loop : -2.07 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.012 0.001 TYR H 60 PHE 0.010 0.001 PHE A 475 TRP 0.015 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4337) covalent geometry : angle 0.49564 ( 5887) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.85134 ( 10) hydrogen bonds : bond 0.02781 ( 130) hydrogen bonds : angle 4.89987 ( 345) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.166 Fit side-chains REVERT: A 389 TYR cc_start: 0.7767 (t80) cc_final: 0.7395 (t80) REVERT: A 650 ASP cc_start: 0.8482 (t0) cc_final: 0.8060 (t0) REVERT: H 3 LYS cc_start: 0.8756 (tttm) cc_final: 0.7755 (tmtt) REVERT: H 87 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.7863 (tpm170) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.0738 time to fit residues: 5.5253 Evaluate side-chains 59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 49 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.116540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.097686 restraints weight = 10494.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.102024 restraints weight = 5995.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.103932 restraints weight = 3492.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.104368 restraints weight = 2664.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.104614 restraints weight = 2461.705| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 4342 Z= 0.133 Angle : 0.505 5.970 5897 Z= 0.259 Chirality : 0.042 0.142 670 Planarity : 0.004 0.039 748 Dihedral : 4.275 42.545 601 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.77 % Allowed : 16.20 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.75 (0.35), residues: 541 helix: 0.27 (0.51), residues: 111 sheet: -0.79 (0.41), residues: 154 loop : -2.01 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.012 0.001 TYR H 60 PHE 0.009 0.001 PHE A 475 TRP 0.014 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4337) covalent geometry : angle 0.50402 ( 5887) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.95396 ( 10) hydrogen bonds : bond 0.02864 ( 130) hydrogen bonds : angle 4.92112 ( 345) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.148 Fit side-chains REVERT: A 389 TYR cc_start: 0.7791 (t80) cc_final: 0.7499 (t80) REVERT: H 3 LYS cc_start: 0.8790 (tttm) cc_final: 0.7791 (tmtt) REVERT: H 87 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.7843 (tpm170) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.0717 time to fit residues: 6.0127 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.0010 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.0060 chunk 9 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 overall best weight: 0.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.119187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.099853 restraints weight = 15836.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.103589 restraints weight = 7535.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.106161 restraints weight = 4437.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107322 restraints weight = 3112.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.108577 restraints weight = 2460.722| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 4342 Z= 0.094 Angle : 0.475 6.262 5897 Z= 0.245 Chirality : 0.041 0.142 670 Planarity : 0.004 0.039 748 Dihedral : 3.981 33.893 601 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.71 % Allowed : 17.48 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.49 (0.36), residues: 541 helix: 0.69 (0.52), residues: 111 sheet: -0.60 (0.42), residues: 153 loop : -1.96 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.011 0.001 TYR H 60 PHE 0.009 0.001 PHE A 475 TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4337) covalent geometry : angle 0.47385 ( 5887) SS BOND : bond 0.00209 ( 5) SS BOND : angle 0.89921 ( 10) hydrogen bonds : bond 0.02507 ( 130) hydrogen bonds : angle 4.66197 ( 345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.106 Fit side-chains REVERT: A 389 TYR cc_start: 0.7756 (t80) cc_final: 0.7387 (t80) REVERT: H 3 LYS cc_start: 0.8543 (tttm) cc_final: 0.7563 (tmtt) REVERT: H 87 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.7976 (tpm170) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.0779 time to fit residues: 5.5082 Evaluate side-chains 54 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 chunk 5 optimal weight: 0.0770 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN L 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.103181 restraints weight = 14528.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107000 restraints weight = 7440.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.108031 restraints weight = 5129.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.109162 restraints weight = 3735.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.110600 restraints weight = 3039.974| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 4342 Z= 0.097 Angle : 0.485 8.309 5897 Z= 0.246 Chirality : 0.041 0.158 670 Planarity : 0.004 0.038 748 Dihedral : 3.854 28.052 601 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.28 % Allowed : 18.55 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.34 (0.36), residues: 541 helix: 0.88 (0.53), residues: 111 sheet: -0.51 (0.42), residues: 153 loop : -1.90 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.015 0.001 TYR A 532 PHE 0.008 0.001 PHE A 475 TRP 0.012 0.001 TRP L 56 HIS 0.002 0.000 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4337) covalent geometry : angle 0.48354 ( 5887) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.90163 ( 10) hydrogen bonds : bond 0.02541 ( 130) hydrogen bonds : angle 4.57268 ( 345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1018.55 seconds wall clock time: 18 minutes 10.16 seconds (1090.16 seconds total)