Starting phenix.real_space_refine on Thu Jul 2 02:25:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oo6_17005/07_2026/8oo6_17005.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oo6_17005/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oo6_17005/07_2026/8oo6_17005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oo6_17005/07_2026/8oo6_17005.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oo6_17005/07_2026/8oo6_17005.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oo6_17005/07_2026/8oo6_17005.cif" model { file = "/net/cci-nas-00/data/ceres_data/8oo6_17005/07_2026/8oo6_17005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oo6_17005/07_2026/8oo6_17005.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 0.95, per 1000 atoms: 0.16 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: 0.32 Conformation dependent library (CDL) restraints added in 190.6 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: 0.45 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: 0.77 Time building geometry restraints manager: 0.42 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: 8141 1.71 - 3.41: 312 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: 1.010 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.390 Find NCS groups from input model: 0.010 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.300 ------------------------------------------------------------------------------- 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 : 0.728 8.537 8499 Z= 0.513 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 0.72751 / 0.51 ( 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 : 0.193 Fit side-chains REVERT: A 346 LEU cc_start: 0.9011 (mt) cc_final: 0.8642 (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: 0.0413 time to fit residues: 2.2505 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 : 0.118 ------------------------------------------------------------------------------- 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: 9.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 A 845 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.053765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.043058 restraints weight = 39370.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.044374 restraints weight = 21909.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045181 restraints weight = 14788.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045636 restraints weight = 11473.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045765 restraints weight = 9943.706| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6111 Z= 0.187 Angle : 0.638 6.798 8499 Z= 0.361 Chirality : 0.043 0.209 956 Planarity : 0.005 0.053 916 Dihedral : 22.681 59.773 1234 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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: 0.87 (0.29), residues: 332 sheet: -0.85 (0.87), residues: 41 loop : -1.16 (0.42), residues: 229 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 0.020 0.002 TRP A 465 HIS 0.007 0.002 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 ( 6111) covalent geometry : angle 0.63791 / 0.36 ( 8499) hydrogen bonds : bond 0.05309 / 3.54 ( 331) hydrogen bonds : angle 4.97325 / 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 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 346 LEU cc_start: 0.9014 (mt) cc_final: 0.8604 (mt) REVERT: A 559 LEU cc_start: 0.9016 (mt) cc_final: 0.8774 (mt) REVERT: A 798 VAL cc_start: 0.9402 (t) cc_final: 0.8773 (t) REVERT: A 802 MET cc_start: 0.9148 (mpp) cc_final: 0.8890 (mpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0337 time to fit residues: 1.6952 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 : 0.173 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 0.0070 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.054468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.043903 restraints weight = 39106.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045182 restraints weight = 21802.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046007 restraints weight = 14726.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046452 restraints weight = 11378.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046836 restraints weight = 9832.755| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1178 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= 0.134 Angle : 0.601 6.577 8499 Z= 0.336 Chirality : 0.042 0.204 956 Planarity : 0.004 0.046 916 Dihedral : 22.646 59.914 1234 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 1.01 (0.30), residues: 329 sheet: -0.79 (0.84), residues: 41 loop : -1.23 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.008 0.001 TYR A 801 PHE 0.008 0.001 PHE A 373 TRP 0.009 0.001 TRP A 465 HIS 0.011 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 6111) covalent geometry : angle 0.60081 / 0.34 ( 8499) hydrogen bonds : bond 0.04326 / 2.87 ( 331) hydrogen bonds : angle 4.73243 / 3.28 ( 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 33 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.126 Fit side-chains REVERT: A 346 LEU cc_start: 0.8965 (mt) cc_final: 0.8527 (mt) REVERT: A 541 GLU cc_start: 0.7946 (tp30) cc_final: 0.7587 (mm-30) REVERT: A 611 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 798 VAL cc_start: 0.9422 (t) cc_final: 0.8958 (t) REVERT: A 802 MET cc_start: 0.9206 (mpp) cc_final: 0.9001 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0361 time to fit residues: 1.8984 Evaluate side-chains 25 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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: 0.0970 chunk 6 optimal weight: 0.0010 chunk 57 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.054566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.044064 restraints weight = 39046.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045360 restraints weight = 21837.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046122 restraints weight = 14658.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046718 restraints weight = 11438.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047081 restraints weight = 9630.792| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6111 Z= 0.124 Angle : 0.580 6.488 8499 Z= 0.325 Chirality : 0.042 0.203 956 Planarity : 0.004 0.048 916 Dihedral : 22.611 59.830 1234 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 0.10 (0.35), residues: 602 helix: 1.03 (0.29), residues: 329 sheet: -0.73 (0.84), residues: 41 loop : -1.13 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.008 0.001 TYR A 497 PHE 0.007 0.001 PHE A 373 TRP 0.012 0.001 TRP A 465 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 6111) covalent geometry : angle 0.57984 / 0.32 ( 8499) hydrogen bonds : bond 0.03979 / 2.64 ( 331) hydrogen bonds : angle 4.57091 / 3.18 ( 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 31 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.117 Fit side-chains REVERT: A 343 ILE cc_start: 0.8587 (pt) cc_final: 0.8315 (pt) REVERT: A 346 LEU cc_start: 0.8950 (mt) cc_final: 0.8478 (mt) REVERT: A 798 VAL cc_start: 0.9423 (t) cc_final: 0.8906 (t) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0366 time to fit residues: 1.8273 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 : 0.175 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.053960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043254 restraints weight = 39634.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044539 restraints weight = 22249.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045392 restraints weight = 15093.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045778 restraints weight = 11662.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045778 restraints weight = 10130.272| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6111 Z= 0.127 Angle : 0.568 6.601 8499 Z= 0.319 Chirality : 0.041 0.204 956 Planarity : 0.004 0.050 916 Dihedral : 22.579 59.323 1234 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 0.98 (0.29), residues: 330 sheet: -0.54 (0.85), residues: 41 loop : -1.15 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.011 0.001 TYR A 630 PHE 0.008 0.001 PHE A 373 TRP 0.006 0.001 TRP A 465 HIS 0.003 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 6111) covalent geometry : angle 0.56831 / 0.32 ( 8499) hydrogen bonds : bond 0.03990 / 2.65 ( 331) hydrogen bonds : angle 4.46655 / 3.10 ( 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 30 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.113 Fit side-chains REVERT: A 798 VAL cc_start: 0.9430 (t) cc_final: 0.8949 (t) REVERT: A 802 MET cc_start: 0.9273 (mpp) cc_final: 0.9008 (mpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0342 time to fit residues: 1.7083 Evaluate side-chains 20 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.053379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042875 restraints weight = 40059.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044129 restraints weight = 22417.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044975 restraints weight = 15244.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045412 restraints weight = 11762.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.045875 restraints weight = 10129.244| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6111 Z= 0.144 Angle : 0.594 6.658 8499 Z= 0.330 Chirality : 0.042 0.204 956 Planarity : 0.004 0.043 916 Dihedral : 22.589 60.276 1234 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 0.99 (0.29), residues: 329 sheet: -0.48 (0.84), residues: 41 loop : -1.15 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 631 TYR 0.009 0.001 TYR A 795 PHE 0.007 0.001 PHE A 771 TRP 0.013 0.001 TRP A 465 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 6111) covalent geometry : angle 0.59400 / 0.33 ( 8499) hydrogen bonds : bond 0.04212 / 2.79 ( 331) hydrogen bonds : angle 4.51867 / 3.13 ( 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 29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.118 Fit side-chains REVERT: A 798 VAL cc_start: 0.9440 (t) cc_final: 0.8906 (t) REVERT: A 802 MET cc_start: 0.9234 (mpp) cc_final: 0.8985 (mpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0321 time to fit residues: 1.5416 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 : 0.122 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.051659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.041097 restraints weight = 40153.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042330 restraints weight = 22455.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.043181 restraints weight = 15215.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043623 restraints weight = 11600.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044069 restraints weight = 9967.502| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6111 Z= 0.177 Angle : 0.620 6.818 8499 Z= 0.351 Chirality : 0.042 0.203 956 Planarity : 0.005 0.079 916 Dihedral : 22.661 63.174 1234 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -0.11 (0.35), residues: 602 helix: 0.74 (0.29), residues: 335 sheet: -0.40 (0.82), residues: 41 loop : -1.18 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.012 0.002 TYR A 630 PHE 0.010 0.001 PHE A 771 TRP 0.014 0.002 TRP A 465 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 ( 6111) covalent geometry : angle 0.62026 / 0.35 ( 8499) hydrogen bonds : bond 0.04799 / 3.18 ( 331) hydrogen bonds : angle 4.62665 / 3.21 ( 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 29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.132 Fit side-chains REVERT: A 798 VAL cc_start: 0.9397 (t) cc_final: 0.8959 (t) REVERT: A 802 MET cc_start: 0.9271 (mpp) cc_final: 0.8951 (mpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0339 time to fit residues: 1.6194 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 : 0.155 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.052155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.041666 restraints weight = 39729.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.042920 restraints weight = 22178.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.043707 restraints weight = 14952.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.044273 restraints weight = 11635.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044452 restraints weight = 9813.875| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6111 Z= 0.134 Angle : 0.589 6.507 8499 Z= 0.329 Chirality : 0.042 0.201 956 Planarity : 0.004 0.069 916 Dihedral : 22.643 64.378 1234 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: 0.02 (0.35), residues: 602 helix: 0.89 (0.29), residues: 332 sheet: -0.33 (0.83), residues: 41 loop : -1.18 (0.42), residues: 229 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 0.006 0.001 PHE A 771 TRP 0.006 0.001 TRP A 465 HIS 0.002 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 6111) covalent geometry : angle 0.58943 / 0.33 ( 8499) hydrogen bonds : bond 0.04162 / 2.77 ( 331) hydrogen bonds : angle 4.51431 / 3.15 ( 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 29 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.123 Fit side-chains REVERT: A 713 ILE cc_start: 0.9029 (mm) cc_final: 0.8793 (mt) REVERT: A 798 VAL cc_start: 0.9387 (t) cc_final: 0.8960 (t) REVERT: A 802 MET cc_start: 0.9318 (mpp) cc_final: 0.8950 (mpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0457 time to fit residues: 2.0990 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 : 0.120 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.051721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.041348 restraints weight = 40398.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.042545 restraints weight = 22635.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.043317 restraints weight = 15456.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.043701 restraints weight = 12045.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.044149 restraints weight = 10488.329| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6111 Z= 0.139 Angle : 0.591 6.726 8499 Z= 0.330 Chirality : 0.041 0.194 956 Planarity : 0.004 0.060 916 Dihedral : 22.626 65.555 1234 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: 0.07 (0.35), residues: 602 helix: 0.92 (0.29), residues: 333 sheet: -0.27 (0.83), residues: 41 loop : -1.15 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.009 0.001 TYR A 706 PHE 0.007 0.001 PHE A 771 TRP 0.005 0.001 TRP A 924 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 6111) covalent geometry : angle 0.59115 / 0.33 ( 8499) hydrogen bonds : bond 0.04281 / 2.84 ( 331) hydrogen bonds : angle 4.48497 / 3.12 ( 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 27 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.125 Fit side-chains REVERT: A 713 ILE cc_start: 0.9045 (mm) cc_final: 0.8784 (mt) REVERT: A 798 VAL cc_start: 0.9368 (t) cc_final: 0.8886 (t) REVERT: A 802 MET cc_start: 0.9345 (mpp) cc_final: 0.8987 (mpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0360 time to fit residues: 1.5810 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 : 0.118 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 49 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.2960 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.051914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.041508 restraints weight = 40194.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042735 restraints weight = 22478.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043519 restraints weight = 15182.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043986 restraints weight = 11770.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044403 restraints weight = 10106.336| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6111 Z= 0.128 Angle : 0.579 6.311 8499 Z= 0.323 Chirality : 0.041 0.199 956 Planarity : 0.004 0.053 916 Dihedral : 22.579 67.452 1234 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.19 (0.35), residues: 602 helix: 1.05 (0.29), residues: 333 sheet: -0.20 (0.82), residues: 41 loop : -1.17 (0.43), residues: 228 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 0.006 0.001 PHE A 886 TRP 0.004 0.001 TRP A 924 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 6111) covalent geometry : angle 0.57885 / 0.32 ( 8499) hydrogen bonds : bond 0.03938 / 2.60 ( 331) hydrogen bonds : angle 4.36225 / 3.02 ( 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 27 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.120 Fit side-chains REVERT: A 802 MET cc_start: 0.9333 (mpp) cc_final: 0.8936 (mpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0380 time to fit residues: 1.6798 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 : 0.119 ------------------------------------------------------------------------------- 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: 0.7980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.051733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.041364 restraints weight = 40002.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.042587 restraints weight = 22240.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043406 restraints weight = 15032.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.043845 restraints weight = 11576.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044255 restraints weight = 9942.127| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6111 Z= 0.131 Angle : 0.580 6.740 8499 Z= 0.322 Chirality : 0.041 0.192 956 Planarity : 0.004 0.047 916 Dihedral : 22.573 68.264 1234 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.16 (0.35), residues: 602 helix: 0.99 (0.29), residues: 336 sheet: -0.13 (0.83), residues: 41 loop : -1.16 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.010 0.001 TYR A 706 PHE 0.007 0.001 PHE A 771 TRP 0.004 0.001 TRP A 924 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 6111) covalent geometry : angle 0.58000 / 0.32 ( 8499) hydrogen bonds : bond 0.04061 / 2.70 ( 331) hydrogen bonds : angle 4.33100 / 3.00 ( 911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 704.11 seconds wall clock time: 12 minutes 52.56 seconds (772.56 seconds total)