Starting phenix.real_space_refine on Wed Jun 4 22:05:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yp2_33994/06_2025/7yp2_33994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yp2_33994/06_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_33994/06_2025/7yp2_33994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yp2_33994/06_2025/7yp2_33994.map" model { file = "/net/cci-nas-00/data/ceres_data/7yp2_33994/06_2025/7yp2_33994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yp2_33994/06_2025/7yp2_33994.cif" } resolution = 3.52 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.24, per 1000 atoms: 1.23 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: 0.98 Conformation dependent library (CDL) restraints added in 812.1 milliseconds 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: 0.52 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: 1.05 Time building geometry restraints manager: 1.18 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: 5.630 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- 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 : 3.19 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 (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: -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 TRP 0.014 0.002 TRP H 33 HIS 0.003 0.001 HIS A 655 PHE 0.019 0.002 PHE A 475 TYR 0.011 0.002 TYR L 38 ARG 0.003 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.31908 ( 130) hydrogen bonds : angle 11.18807 ( 345) SS BOND : bond 0.00326 ( 5) SS BOND : angle 1.38342 ( 10) covalent geometry : bond 0.00698 ( 4337) covalent geometry : angle 0.93383 ( 5887) *********************** 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 : 0.464 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: 0.1823 time to fit residues: 15.8780 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 : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.114806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095460 restraints weight = 12412.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.100406 restraints weight = 6288.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101957 restraints weight = 3583.308| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 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 = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 4342 Z= 0.168 Angle : 0.586 6.043 5897 Z= 0.310 Chirality : 0.043 0.139 670 Planarity : 0.005 0.052 748 Dihedral : 5.467 68.508 601 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.49 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 (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: -3.69 (0.31), residues: 541 helix: -2.79 (0.37), residues: 111 sheet: -1.94 (0.39), residues: 155 loop : -2.59 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 414 PHE 0.010 0.001 PHE A 475 TYR 0.010 0.001 TYR A 374 ARG 0.004 0.001 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 130) hydrogen bonds : angle 6.53557 ( 345) SS BOND : bond 0.00297 ( 5) SS BOND : angle 0.99994 ( 10) covalent geometry : bond 0.00424 ( 4337) covalent geometry : angle 0.58463 ( 5887) *********************** 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 : 0.480 Fit side-chains REVERT: A 389 TYR cc_start: 0.7695 (t80) cc_final: 0.7317 (t80) REVERT: A 474 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8631 (tt) REVERT: A 538 LEU cc_start: 0.7719 (mm) cc_final: 0.7493 (mm) REVERT: A 650 ASP cc_start: 0.8518 (t0) cc_final: 0.8201 (t0) REVERT: A 668 MET cc_start: 0.8191 (mtp) cc_final: 0.7924 (mtm) REVERT: H 3 LYS cc_start: 0.8746 (tttm) cc_final: 0.7795 (tmtt) REVERT: L 56 TRP cc_start: 0.8684 (m-10) cc_final: 0.7547 (m-10) REVERT: L 87 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7077 (tm-30) REVERT: L 88 ASP cc_start: 0.8764 (m-30) cc_final: 0.8423 (m-30) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.1705 time to fit residues: 13.7932 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 : 0.480 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.096041 restraints weight = 13537.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.100271 restraints weight = 6894.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.102148 restraints weight = 4077.560| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- 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 = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 4342 Z= 0.151 Angle : 0.542 6.202 5897 Z= 0.284 Chirality : 0.043 0.144 670 Planarity : 0.005 0.045 748 Dihedral : 5.103 64.906 601 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.13 % Allowed : 13.65 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.98 (0.33), residues: 541 helix: -1.61 (0.44), residues: 111 sheet: -1.49 (0.41), residues: 154 loop : -2.42 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.001 0.000 HIS A 414 PHE 0.007 0.001 PHE A 475 TYR 0.015 0.001 TYR H 60 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 130) hydrogen bonds : angle 5.89148 ( 345) SS BOND : bond 0.00334 ( 5) SS BOND : angle 0.93439 ( 10) covalent geometry : bond 0.00392 ( 4337) covalent geometry : angle 0.54140 ( 5887) *********************** 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 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.502 Fit side-chains REVERT: A 389 TYR cc_start: 0.7670 (t80) cc_final: 0.7291 (t80) REVERT: A 474 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8627 (tt) REVERT: A 650 ASP cc_start: 0.8541 (t0) cc_final: 0.8199 (t0) REVERT: H 3 LYS cc_start: 0.8755 (tttm) cc_final: 0.7785 (tmtt) REVERT: L 56 TRP cc_start: 0.8587 (m-10) cc_final: 0.7610 (m-10) REVERT: L 87 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7049 (tm-30) REVERT: L 88 ASP cc_start: 0.8702 (m-30) cc_final: 0.8453 (m-30) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.2044 time to fit residues: 15.9491 Evaluate side-chains 57 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 14 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.114536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.094291 restraints weight = 22157.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.098919 restraints weight = 13287.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.102245 restraints weight = 5809.478| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 4342 Z= 0.161 Angle : 0.543 6.550 5897 Z= 0.282 Chirality : 0.043 0.141 670 Planarity : 0.004 0.042 748 Dihedral : 4.965 61.828 601 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.35 % Allowed : 15.35 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.62 (0.34), residues: 541 helix: -0.98 (0.48), residues: 110 sheet: -1.33 (0.41), residues: 157 loop : -2.32 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.001 0.001 HIS A 414 PHE 0.008 0.001 PHE A 475 TYR 0.012 0.001 TYR H 60 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 130) hydrogen bonds : angle 5.58287 ( 345) SS BOND : bond 0.00239 ( 5) SS BOND : angle 0.94510 ( 10) covalent geometry : bond 0.00419 ( 4337) covalent geometry : angle 0.54220 ( 5887) *********************** 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 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.482 Fit side-chains REVERT: A 389 TYR cc_start: 0.7752 (t80) cc_final: 0.7445 (t80) REVERT: A 474 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 650 ASP cc_start: 0.8491 (t0) cc_final: 0.8094 (t0) REVERT: H 3 LYS cc_start: 0.8761 (tttm) cc_final: 0.7711 (tmtt) REVERT: L 87 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7079 (tm-30) REVERT: L 88 ASP cc_start: 0.8755 (m-30) cc_final: 0.8483 (m-30) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.1880 time to fit residues: 14.7932 Evaluate side-chains 60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 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 = 0.3147 r_free = 0.3147 target = 0.113348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.093995 restraints weight = 12828.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.098315 restraints weight = 7065.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100789 restraints weight = 3943.052| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 4342 Z= 0.189 Angle : 0.563 6.941 5897 Z= 0.291 Chirality : 0.044 0.148 670 Planarity : 0.004 0.044 748 Dihedral : 4.992 61.098 601 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.20 % Allowed : 15.35 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.49 (0.34), residues: 541 helix: -0.82 (0.48), residues: 111 sheet: -1.27 (0.41), residues: 157 loop : -2.24 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 33 HIS 0.001 0.001 HIS A 414 PHE 0.009 0.001 PHE A 475 TYR 0.016 0.002 TYR A 532 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 130) hydrogen bonds : angle 5.55847 ( 345) SS BOND : bond 0.00265 ( 5) SS BOND : angle 0.91504 ( 10) covalent geometry : bond 0.00486 ( 4337) covalent geometry : angle 0.56201 ( 5887) *********************** 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 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.487 Fit side-chains REVERT: A 389 TYR cc_start: 0.7794 (t80) cc_final: 0.7514 (t80) REVERT: A 474 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8675 (tt) REVERT: H 3 LYS cc_start: 0.8802 (tttm) cc_final: 0.7811 (tmtt) REVERT: L 87 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7046 (tm-30) REVERT: L 88 ASP cc_start: 0.8726 (m-30) cc_final: 0.8450 (m-30) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.1787 time to fit residues: 15.0661 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 51 ILE 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 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.113706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.093839 restraints weight = 22444.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.096967 restraints weight = 12699.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.100328 restraints weight = 6633.441| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2004 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= 0.171 Angle : 0.553 8.000 5897 Z= 0.284 Chirality : 0.043 0.155 670 Planarity : 0.004 0.042 748 Dihedral : 4.893 59.036 601 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.20 % Allowed : 16.42 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.31 (0.35), residues: 541 helix: -0.56 (0.50), residues: 111 sheet: -1.16 (0.41), residues: 158 loop : -2.18 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 56 HIS 0.001 0.001 HIS A 414 PHE 0.008 0.001 PHE A 475 TYR 0.013 0.001 TYR H 60 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 130) hydrogen bonds : angle 5.44911 ( 345) SS BOND : bond 0.00291 ( 5) SS BOND : angle 0.92751 ( 10) covalent geometry : bond 0.00447 ( 4337) covalent geometry : angle 0.55242 ( 5887) *********************** 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 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.452 Fit side-chains REVERT: A 389 TYR cc_start: 0.7811 (t80) cc_final: 0.7529 (t80) REVERT: A 474 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8690 (tt) REVERT: H 3 LYS cc_start: 0.8796 (tttm) cc_final: 0.7794 (tmtt) REVERT: H 87 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.7723 (tpm170) REVERT: L 87 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7087 (tm-30) REVERT: L 88 ASP cc_start: 0.8749 (m-30) cc_final: 0.8542 (m-30) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.1628 time to fit residues: 13.1051 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 : 0.435 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.0040 chunk 21 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.2392 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.117933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098646 restraints weight = 12159.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.103376 restraints weight = 6422.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.105248 restraints weight = 3596.292| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 4342 Z= 0.093 Angle : 0.473 6.796 5897 Z= 0.245 Chirality : 0.041 0.133 670 Planarity : 0.004 0.041 748 Dihedral : 4.372 49.214 601 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.35 % Allowed : 17.06 % 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 (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: -1.91 (0.35), residues: 541 helix: -0.01 (0.52), residues: 111 sheet: -0.76 (0.41), residues: 151 loop : -2.13 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 PHE 0.007 0.001 PHE A 475 TYR 0.013 0.001 TYR H 60 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.02598 ( 130) hydrogen bonds : angle 4.93527 ( 345) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.86584 ( 10) covalent geometry : bond 0.00251 ( 4337) covalent geometry : angle 0.47198 ( 5887) *********************** 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 60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.447 Fit side-chains REVERT: A 389 TYR cc_start: 0.7753 (t80) cc_final: 0.7386 (t80) REVERT: H 3 LYS cc_start: 0.8713 (tttm) cc_final: 0.7720 (tmtt) REVERT: H 85 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8568 (mtmt) REVERT: H 87 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.7852 (tpm170) REVERT: L 87 GLU cc_start: 0.7619 (tm-30) cc_final: 0.6968 (tm-30) outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 0.1842 time to fit residues: 13.2881 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 487 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.115749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096204 restraints weight = 11406.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.100528 restraints weight = 6567.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102360 restraints weight = 3691.665| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2213 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= 0.149 Angle : 0.521 6.700 5897 Z= 0.266 Chirality : 0.042 0.139 670 Planarity : 0.004 0.040 748 Dihedral : 4.461 49.372 601 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.41 % Allowed : 16.20 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.87 (0.35), residues: 541 helix: -0.00 (0.51), residues: 111 sheet: -0.80 (0.41), residues: 153 loop : -2.05 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 475 TYR 0.011 0.001 TYR H 60 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 130) hydrogen bonds : angle 5.02238 ( 345) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.99741 ( 10) covalent geometry : bond 0.00388 ( 4337) covalent geometry : angle 0.51979 ( 5887) *********************** 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 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.432 Fit side-chains REVERT: A 389 TYR cc_start: 0.7832 (t80) cc_final: 0.7561 (t80) REVERT: H 3 LYS cc_start: 0.8793 (tttm) cc_final: 0.7768 (tmtt) REVERT: H 85 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8565 (mtmt) REVERT: H 87 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.7851 (tpm170) outliers start: 16 outliers final: 12 residues processed: 65 average time/residue: 0.1623 time to fit residues: 13.5455 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 487 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.0040 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.116495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.097078 restraints weight = 11452.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101582 restraints weight = 6534.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.103161 restraints weight = 3698.208| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 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 = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 4342 Z= 0.128 Angle : 0.505 6.400 5897 Z= 0.259 Chirality : 0.042 0.146 670 Planarity : 0.004 0.040 748 Dihedral : 4.358 46.213 601 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.20 % Allowed : 17.06 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.74 (0.35), residues: 541 helix: 0.18 (0.51), residues: 111 sheet: -0.67 (0.42), residues: 152 loop : -2.03 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 475 TYR 0.013 0.001 TYR H 60 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.02820 ( 130) hydrogen bonds : angle 4.97053 ( 345) SS BOND : bond 0.00227 ( 5) SS BOND : angle 1.00796 ( 10) covalent geometry : bond 0.00346 ( 4337) covalent geometry : angle 0.50401 ( 5887) *********************** 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 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.500 Fit side-chains REVERT: A 389 TYR cc_start: 0.7797 (t80) cc_final: 0.7519 (t80) REVERT: H 3 LYS cc_start: 0.8785 (tttm) cc_final: 0.7769 (tmtt) REVERT: H 85 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8552 (mtmt) REVERT: H 87 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.7856 (tpm170) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.1720 time to fit residues: 14.0440 Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 487 THR 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 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.115803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.096201 restraints weight = 16421.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.099875 restraints weight = 8791.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102361 restraints weight = 4864.939| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 4342 Z= 0.144 Angle : 0.522 6.373 5897 Z= 0.268 Chirality : 0.042 0.139 670 Planarity : 0.004 0.040 748 Dihedral : 4.360 44.055 601 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.99 % Allowed : 17.27 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.73 (0.35), residues: 541 helix: 0.26 (0.51), residues: 111 sheet: -0.76 (0.41), residues: 153 loop : -1.99 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 56 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 475 TYR 0.013 0.001 TYR H 60 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 130) hydrogen bonds : angle 4.96658 ( 345) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.93220 ( 10) covalent geometry : bond 0.00381 ( 4337) covalent geometry : angle 0.52127 ( 5887) ********************** 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 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.421 Fit side-chains REVERT: A 389 TYR cc_start: 0.7814 (t80) cc_final: 0.7549 (t80) REVERT: H 3 LYS cc_start: 0.8608 (tttm) cc_final: 0.7616 (tmtt) REVERT: H 85 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8543 (mtmt) REVERT: H 87 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.7858 (tpm170) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.1781 time to fit residues: 14.2800 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 487 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3176 r_free = 0.3176 target = 0.115391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.096242 restraints weight = 11894.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.100800 restraints weight = 6352.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102324 restraints weight = 3767.750| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 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 = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 4342 Z= 0.159 Angle : 0.540 8.221 5897 Z= 0.277 Chirality : 0.043 0.173 670 Planarity : 0.004 0.041 748 Dihedral : 4.410 42.755 601 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.77 % Allowed : 17.70 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.72 (0.35), residues: 541 helix: 0.26 (0.51), residues: 111 sheet: -0.76 (0.41), residues: 153 loop : -1.99 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 56 HIS 0.001 0.001 HIS A 414 PHE 0.010 0.001 PHE A 475 TYR 0.013 0.001 TYR H 60 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 130) hydrogen bonds : angle 5.03016 ( 345) SS BOND : bond 0.00251 ( 5) SS BOND : angle 0.90298 ( 10) covalent geometry : bond 0.00422 ( 4337) covalent geometry : angle 0.53935 ( 5887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2393.87 seconds wall clock time: 42 minutes 13.36 seconds (2533.36 seconds total)