Starting phenix.real_space_refine on Tue Aug 4 18:14:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.cif" model { file = "/net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oo6_17005/08_2026/8oo6_17005.map" } resolution = 4.3 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= 0.001 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: 6 Type Number sf(0) Gaussians P 54 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 3549 2.51 5 N 1042 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5890 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4782 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 28, 'TRANS': 575} Chain: "T" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "P" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.33, per 1000 atoms: 0.23 Number of scatterers: 5890 At special positions: 0 Unit cell: (86.6, 96.992, 78.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 54 15.00 Mg 1 11.99 O 1229 8.00 N 1042 7.00 C 3549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.45 Conformation dependent library (CDL) restraints added in 256.0 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 59.8% alpha, 7.5% beta 27 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 397 through 410 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.659A pdb=" N TYR A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.010A pdb=" N ILE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.755A pdb=" N ILE A 489 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 517 removed outlier: 3.587A pdb=" N ALA A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Proline residue: A 514 - end of helix Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 544 removed outlier: 4.231A pdb=" N VAL A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.886A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 621 through 644 removed outlier: 4.350A pdb=" N LYS A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 3.841A pdb=" N PHE A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.933A pdb=" N ALA A 738 " --> pdb=" O HIS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 766 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 795 through 813 removed outlier: 3.650A pdb=" N LEU A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 871 removed outlier: 3.551A pdb=" N ALA A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 923 through 928 Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.130A pdb=" N VAL A 331 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 371 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 352 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS A 416 " --> pdb=" O PHE A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 875 through 880 removed outlier: 3.548A pdb=" N ILE A 877 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 885 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN A 879 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 883 " --> pdb=" O GLN A 879 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 702 " --> pdb=" O PHE A 886 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 814 through 816 261 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1376 1.33 - 1.45: 1384 1.45 - 1.57: 3217 1.57 - 1.69: 105 1.69 - 1.81: 29 Bond restraints: 6111 Sorted by residual: bond pdb=" C3' DT P 8 " pdb=" C2' DT P 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT T 18 " pdb=" C2' DT T 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG T 25 " pdb=" C2' DG T 25 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.97e+00 bond pdb=" C1' DT P 17 " pdb=" N1 DT P 17 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.45e+00 bond pdb=" C3' DT P 9 " pdb=" C2' DT P 9 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.34e+00 ... (remaining 6106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 8140 1.71 - 3.41: 313 3.41 - 5.12: 39 5.12 - 6.83: 3 6.83 - 8.54: 4 Bond angle restraints: 8499 Sorted by residual: angle pdb=" N3 DT P 11 " pdb=" C4 DT P 11 " pdb=" O4 DT P 11 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT P 10 " pdb=" C4 DT P 10 " pdb=" O4 DT P 10 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 ... (remaining 8494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2887 17.99 - 35.98: 419 35.98 - 53.96: 215 53.96 - 71.95: 41 71.95 - 89.94: 7 Dihedral angle restraints: 3569 sinusoidal: 1806 harmonic: 1763 Sorted by residual: dihedral pdb=" CA ASP A 705 " pdb=" C ASP A 705 " pdb=" N TYR A 706 " pdb=" CA TYR A 706 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU A 346 " pdb=" C LEU A 346 " pdb=" N GLU A 347 " pdb=" CA GLU A 347 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLU A 611 " pdb=" C GLU A 611 " pdb=" N GLU A 612 " pdb=" CA GLU A 612 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 622 0.035 - 0.070: 217 0.070 - 0.106: 100 0.106 - 0.141: 13 0.141 - 0.176: 4 Chirality restraints: 956 Sorted by residual: chirality pdb=" CA MET A 531 " pdb=" N MET A 531 " pdb=" C MET A 531 " pdb=" CB MET A 531 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CG LEU A 884 " pdb=" CB LEU A 884 " pdb=" CD1 LEU A 884 " pdb=" CD2 LEU A 884 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA GLN A 507 " pdb=" N GLN A 507 " pdb=" C GLN A 507 " pdb=" CB GLN A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 953 not shown) Planarity restraints: 916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 465 " 0.017 2.00e-02 2.50e+03 1.47e-02 5.39e+00 pdb=" CG TRP A 465 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 465 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 465 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A 465 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 465 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 465 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 465 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 465 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 465 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 392 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 393 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 388 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C ASP A 388 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 388 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 389 " -0.011 2.00e-02 2.50e+03 ... (remaining 913 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 910 2.76 - 3.29: 5838 3.29 - 3.83: 10831 3.83 - 4.36: 12008 4.36 - 4.90: 19050 Nonbonded interactions: 48637 Sorted by model distance: nonbonded pdb=" OG1 THR A 485 " pdb=" OD1 ASN A 487 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR A 358 " pdb=" O ASN A 367 " model vdw 2.241 3.040 nonbonded pdb=" ND2 ASN A 579 " pdb=" OP1 DA T 27 " model vdw 2.241 3.120 nonbonded pdb=" O GLN A 868 " pdb=" NE2 GLN A 871 " model vdw 2.270 3.120 nonbonded pdb=" NH2 ARG A 909 " pdb=" O LEU A 910 " model vdw 2.313 3.120 ... (remaining 48632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.004 0.052 6111 Z= 0.346 Angle : 0.730 8.537 8499 Z= 0.515 Chirality : 0.043 0.176 956 Planarity : 0.004 0.054 916 Dihedral : 20.164 89.936 2429 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.09 (0.35), residues: 602 helix: 0.78 (0.29), residues: 321 sheet: -1.17 (0.85), residues: 41 loop : -0.92 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.012 0.001 TYR A 801 PHE 0.022 0.001 PHE A 762 TRP 0.034 0.003 TRP A 465 HIS 0.003 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.35 ( 6111) covalent geometry : angle 0.72988 / 0.52 ( 8499) hydrogen bonds : bond 0.11618 / 7.81 ( 331) hydrogen bonds : angle 6.09963 / 4.19 ( 911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.180 Fit side-chains REVERT: A 346 LEU cc_start: 0.9011 (mt) cc_final: 0.8644 (mt) REVERT: A 559 LEU cc_start: 0.8936 (mt) cc_final: 0.8733 (mt) REVERT: A 798 VAL cc_start: 0.9432 (t) cc_final: 0.9063 (t) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0535 time to fit residues: 2.9955 Evaluate side-chains 23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN A 456 HIS A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.042999 restraints weight = 39656.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044291 restraints weight = 22142.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045116 restraints weight = 14937.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045628 restraints weight = 11535.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046018 restraints weight = 9860.504| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6111 Z= 0.184 Angle : 0.651 6.822 8499 Z= 0.365 Chirality : 0.043 0.209 956 Planarity : 0.005 0.053 916 Dihedral : 22.616 59.895 1234 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.20 % Allowed : 6.10 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.04 (0.35), residues: 602 helix: 0.84 (0.29), residues: 331 sheet: -0.84 (0.87), residues: 41 loop : -1.09 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 835 TYR 0.012 0.002 TYR A 791 PHE 0.013 0.002 PHE A 771 TRP 0.027 0.002 TRP A 465 HIS 0.007 0.002 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 ( 6111) covalent geometry : angle 0.65108 / 0.36 ( 8499) hydrogen bonds : bond 0.05381 / 3.59 ( 331) hydrogen bonds : angle 4.97192 / 3.45 ( 911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.202 Fit side-chains REVERT: A 346 LEU cc_start: 0.8996 (mt) cc_final: 0.8593 (mt) REVERT: A 559 LEU cc_start: 0.8999 (mt) cc_final: 0.8764 (mt) REVERT: A 798 VAL cc_start: 0.9391 (t) cc_final: 0.8774 (t) REVERT: A 802 MET cc_start: 0.9136 (mpp) cc_final: 0.8888 (mpp) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0452 time to fit residues: 2.3226 Evaluate side-chains 23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.054272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.043700 restraints weight = 38810.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044982 restraints weight = 21598.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045736 restraints weight = 14506.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046324 restraints weight = 11364.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046626 restraints weight = 9557.910| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6111 Z= 0.133 Angle : 0.602 6.564 8499 Z= 0.335 Chirality : 0.042 0.206 956 Planarity : 0.004 0.045 916 Dihedral : 22.596 59.934 1234 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.05 (0.35), residues: 602 helix: 1.03 (0.29), residues: 329 sheet: -0.78 (0.85), residues: 41 loop : -1.24 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.008 0.001 TYR A 497 PHE 0.008 0.001 PHE A 373 TRP 0.013 0.002 TRP A 465 HIS 0.011 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 6111) covalent geometry : angle 0.60217 / 0.34 ( 8499) hydrogen bonds : bond 0.04260 / 2.82 ( 331) hydrogen bonds : angle 4.69085 / 3.26 ( 911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.195 Fit side-chains REVERT: A 346 LEU cc_start: 0.8955 (mt) cc_final: 0.8520 (mt) REVERT: A 541 GLU cc_start: 0.7930 (tp30) cc_final: 0.7581 (mm-30) REVERT: A 798 VAL cc_start: 0.9431 (t) cc_final: 0.8940 (t) REVERT: A 802 MET cc_start: 0.9203 (mpp) cc_final: 0.8977 (mpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0519 time to fit residues: 2.6873 Evaluate side-chains 23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN A 845 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.051737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.041074 restraints weight = 39691.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.042364 restraints weight = 21700.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.043208 restraints weight = 14495.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.043656 restraints weight = 11128.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044092 restraints weight = 9582.787| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6111 Z= 0.204 Angle : 0.665 6.987 8499 Z= 0.373 Chirality : 0.043 0.207 956 Planarity : 0.005 0.048 916 Dihedral : 22.656 59.813 1234 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.24 (0.35), residues: 602 helix: 0.71 (0.29), residues: 332 sheet: -0.83 (0.83), residues: 41 loop : -1.28 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 631 TYR 0.013 0.002 TYR A 801 PHE 0.012 0.002 PHE A 771 TRP 0.009 0.002 TRP A 465 HIS 0.007 0.002 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 ( 6111) covalent geometry : angle 0.66500 / 0.37 ( 8499) hydrogen bonds : bond 0.05480 / 3.61 ( 331) hydrogen bonds : angle 4.76760 / 3.32 ( 911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.241 Fit side-chains REVERT: A 802 MET cc_start: 0.9278 (mpp) cc_final: 0.9031 (mpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0526 time to fit residues: 2.7219 Evaluate side-chains 21 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.038927 restraints weight = 40825.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.040090 restraints weight = 22701.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.040809 restraints weight = 15468.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.041355 restraints weight = 12149.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.041631 restraints weight = 10217.317| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6111 Z= 0.274 Angle : 0.739 7.267 8499 Z= 0.420 Chirality : 0.047 0.206 956 Planarity : 0.005 0.040 916 Dihedral : 22.886 65.182 1234 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.85 (0.34), residues: 602 helix: 0.21 (0.28), residues: 333 sheet: -0.98 (0.80), residues: 41 loop : -1.55 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 873 TYR 0.017 0.003 TYR A 431 PHE 0.014 0.003 PHE A 373 TRP 0.009 0.002 TRP A 465 HIS 0.008 0.002 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.27 ( 6111) covalent geometry : angle 0.73936 / 0.42 ( 8499) hydrogen bonds : bond 0.06351 / 4.21 ( 331) hydrogen bonds : angle 4.96486 / 3.47 ( 911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.146 Fit side-chains REVERT: A 798 VAL cc_start: 0.9415 (t) cc_final: 0.8965 (t) REVERT: A 802 MET cc_start: 0.9254 (mpp) cc_final: 0.8991 (mpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0507 time to fit residues: 2.2036 Evaluate side-chains 22 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 7 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.039213 restraints weight = 40537.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.040405 restraints weight = 22471.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041202 restraints weight = 15260.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041592 restraints weight = 11883.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.041972 restraints weight = 10343.875| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6111 Z= 0.146 Angle : 0.623 6.751 8499 Z= 0.351 Chirality : 0.044 0.201 956 Planarity : 0.004 0.041 916 Dihedral : 22.821 66.463 1234 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.43 (0.34), residues: 602 helix: 0.57 (0.29), residues: 331 sheet: -0.85 (0.80), residues: 41 loop : -1.38 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.011 0.002 TYR A 497 PHE 0.007 0.001 PHE A 373 TRP 0.005 0.001 TRP A 465 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 6111) covalent geometry : angle 0.62263 / 0.35 ( 8499) hydrogen bonds : bond 0.04732 / 3.15 ( 331) hydrogen bonds : angle 4.67446 / 3.26 ( 911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.197 Fit side-chains REVERT: A 798 VAL cc_start: 0.9392 (t) cc_final: 0.9002 (t) REVERT: A 802 MET cc_start: 0.9297 (mpp) cc_final: 0.8991 (mpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0493 time to fit residues: 2.2324 Evaluate side-chains 21 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.040545 restraints weight = 39838.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.041736 restraints weight = 21855.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042555 restraints weight = 14777.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.043089 restraints weight = 11339.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.043358 restraints weight = 9551.008| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6111 Z= 0.132 Angle : 0.616 6.802 8499 Z= 0.342 Chirality : 0.042 0.192 956 Planarity : 0.005 0.078 916 Dihedral : 22.743 67.046 1234 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.09 (0.35), residues: 602 helix: 0.89 (0.29), residues: 328 sheet: -0.53 (0.83), residues: 41 loop : -1.30 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.012 0.001 TYR A 497 PHE 0.008 0.001 PHE A 727 TRP 0.017 0.002 TRP A 342 HIS 0.003 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 6111) covalent geometry : angle 0.61586 / 0.34 ( 8499) hydrogen bonds : bond 0.04305 / 2.86 ( 331) hydrogen bonds : angle 4.49840 / 3.11 ( 911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.206 Fit side-chains REVERT: A 342 TRP cc_start: 0.8669 (t-100) cc_final: 0.8468 (t60) REVERT: A 798 VAL cc_start: 0.9391 (t) cc_final: 0.8960 (t) REVERT: A 802 MET cc_start: 0.9316 (mpp) cc_final: 0.9017 (mpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0542 time to fit residues: 2.6251 Evaluate side-chains 24 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.039974 restraints weight = 40339.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.041140 restraints weight = 22535.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.041856 restraints weight = 15453.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042372 restraints weight = 12228.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042645 restraints weight = 10484.769| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6111 Z= 0.134 Angle : 0.622 9.123 8499 Z= 0.343 Chirality : 0.042 0.187 956 Planarity : 0.004 0.067 916 Dihedral : 22.708 67.800 1234 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.03 (0.35), residues: 602 helix: 0.98 (0.29), residues: 328 sheet: -0.43 (0.81), residues: 41 loop : -1.26 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.010 0.001 TYR A 497 PHE 0.007 0.001 PHE A 771 TRP 0.007 0.001 TRP A 465 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 6111) covalent geometry : angle 0.62204 / 0.34 ( 8499) hydrogen bonds : bond 0.04329 / 2.86 ( 331) hydrogen bonds : angle 4.49761 / 3.16 ( 911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.139 Fit side-chains REVERT: A 798 VAL cc_start: 0.9389 (t) cc_final: 0.8994 (t) REVERT: A 802 MET cc_start: 0.9341 (mpp) cc_final: 0.9059 (mpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0493 time to fit residues: 2.3793 Evaluate side-chains 23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.050378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.039888 restraints weight = 40812.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041056 restraints weight = 22709.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041770 restraints weight = 15448.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042310 restraints weight = 12210.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.042565 restraints weight = 10383.162| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6111 Z= 0.139 Angle : 0.602 6.600 8499 Z= 0.336 Chirality : 0.042 0.183 956 Planarity : 0.004 0.060 916 Dihedral : 22.677 68.720 1234 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.01 (0.35), residues: 602 helix: 0.94 (0.29), residues: 331 sheet: -0.29 (0.81), residues: 41 loop : -1.29 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.009 0.001 TYR A 497 PHE 0.008 0.001 PHE A 771 TRP 0.014 0.002 TRP A 465 HIS 0.002 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 6111) covalent geometry : angle 0.60153 / 0.34 ( 8499) hydrogen bonds : bond 0.04300 / 2.85 ( 331) hydrogen bonds : angle 4.49368 / 3.15 ( 911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.126 Fit side-chains REVERT: A 798 VAL cc_start: 0.9365 (t) cc_final: 0.9046 (t) REVERT: A 802 MET cc_start: 0.9319 (mpp) cc_final: 0.8957 (mpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0467 time to fit residues: 2.3402 Evaluate side-chains 22 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 2 optimal weight: 0.0370 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.040404 restraints weight = 40176.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.041554 restraints weight = 22463.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042259 restraints weight = 15416.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.042816 restraints weight = 12248.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043073 restraints weight = 10341.171| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6111 Z= 0.128 Angle : 0.623 6.575 8499 Z= 0.342 Chirality : 0.042 0.185 956 Planarity : 0.004 0.052 916 Dihedral : 22.643 69.236 1234 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.08 (0.35), residues: 602 helix: 1.02 (0.29), residues: 328 sheet: -0.21 (0.80), residues: 41 loop : -1.28 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.009 0.001 TYR A 497 PHE 0.011 0.001 PHE A 526 TRP 0.014 0.001 TRP A 342 HIS 0.002 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 6111) covalent geometry : angle 0.62349 / 0.34 ( 8499) hydrogen bonds : bond 0.04127 / 2.73 ( 331) hydrogen bonds : angle 4.46724 / 3.10 ( 911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 342 TRP cc_start: 0.8740 (t-100) cc_final: 0.8483 (t60) REVERT: A 713 ILE cc_start: 0.9048 (mm) cc_final: 0.8820 (mt) REVERT: A 798 VAL cc_start: 0.9354 (t) cc_final: 0.8996 (t) REVERT: A 802 MET cc_start: 0.9338 (mpp) cc_final: 0.8987 (mpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0384 time to fit residues: 1.8936 Evaluate side-chains 23 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.049605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.038984 restraints weight = 40896.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.040115 restraints weight = 22920.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040848 restraints weight = 15792.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041209 restraints weight = 12440.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.041573 restraints weight = 10966.647| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6111 Z= 0.185 Angle : 0.629 6.708 8499 Z= 0.352 Chirality : 0.043 0.170 956 Planarity : 0.004 0.051 916 Dihedral : 22.673 70.869 1234 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.13 (0.35), residues: 602 helix: 0.80 (0.29), residues: 332 sheet: -0.18 (0.81), residues: 41 loop : -1.34 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 873 TYR 0.013 0.002 TYR A 706 PHE 0.011 0.002 PHE A 771 TRP 0.014 0.002 TRP A 465 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 6111) covalent geometry : angle 0.62920 / 0.35 ( 8499) hydrogen bonds : bond 0.04957 / 3.29 ( 331) hydrogen bonds : angle 4.61020 / 3.22 ( 911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 927.14 seconds wall clock time: 16 minutes 45.03 seconds (1005.03 seconds total)