Starting phenix.real_space_refine on Tue Aug 4 15:11:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6r_62133/08_2026/9k6r_62133.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6r_62133/08_2026/9k6r_62133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6r_62133/08_2026/9k6r_62133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6r_62133/08_2026/9k6r_62133.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6r_62133/08_2026/9k6r_62133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6r_62133/08_2026/9k6r_62133.cif" } resolution = 2.7 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= 0.041 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 29 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 2675 2.51 5 N 796 2.21 5 O 883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 4405 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3791 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 29, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 315 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 9} 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: 1.20, per 1000 atoms: 0.27 Number of scatterers: 4405 At special positions: 0 Unit cell: (72.96, 79.8, 80.94, 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 21 16.00 P 29 15.00 Mg 1 11.99 O 883 8.00 N 796 7.00 C 2675 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: 0.41 Conformation dependent library (CDL) restraints added in 142.8 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 894 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 39.0% alpha, 16.5% beta 7 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 430 through 434 removed outlier: 4.195A pdb=" N GLY A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.612A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 4.279A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.801A pdb=" N ARG A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.588A pdb=" N ARG A 583 " --> pdb=" O PRO A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.738A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.882A pdb=" N VAL A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.572A pdb=" N ARG A 723 " --> pdb=" O LYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 821 removed outlier: 3.909A pdb=" N GLU A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 838 through 847 Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.024A pdb=" N ARG A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 632 removed outlier: 4.853A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 592 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR A 667 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 594 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA A 669 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA A 596 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 664 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE A 705 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE A 666 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 707 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG A 668 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 494 removed outlier: 6.534A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1216 1.34 - 1.45: 924 1.45 - 1.57: 2339 1.57 - 1.69: 56 1.69 - 1.81: 30 Bond restraints: 4565 Sorted by residual: bond pdb=" P A C 4 " pdb=" O5' A C 4 " ideal model delta sigma weight residual 1.593 1.627 -0.034 1.00e-02 1.00e+04 1.19e+01 bond pdb=" P U B 12 " pdb=" O5' U B 12 " ideal model delta sigma weight residual 1.593 1.620 -0.027 1.00e-02 1.00e+04 7.44e+00 bond pdb=" C HIS A 600 " pdb=" N PRO A 601 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.18e-02 7.18e+03 7.36e+00 bond pdb=" P G C 5 " pdb=" O5' G C 5 " ideal model delta sigma weight residual 1.593 1.619 -0.026 1.00e-02 1.00e+04 6.73e+00 bond pdb=" N GLU A 637 " pdb=" CA GLU A 637 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.28e-02 6.10e+03 6.59e+00 ... (remaining 4560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6021 1.66 - 3.31: 248 3.31 - 4.97: 28 4.97 - 6.63: 20 6.63 - 8.29: 6 Bond angle restraints: 6323 Sorted by residual: angle pdb=" C3' A C 4 " pdb=" C2' A C 4 " pdb=" C1' A C 4 " ideal model delta sigma weight residual 101.50 94.78 6.72 8.00e-01 1.56e+00 7.05e+01 angle pdb=" C4' A C 4 " pdb=" O4' A C 4 " pdb=" C1' A C 4 " ideal model delta sigma weight residual 109.70 104.45 5.25 7.00e-01 2.04e+00 5.62e+01 angle pdb=" C1' C B 9 " pdb=" N1 C B 9 " pdb=" C2 C B 9 " ideal model delta sigma weight residual 118.80 126.46 -7.66 1.10e+00 8.26e-01 4.85e+01 angle pdb=" C1' U B 11 " pdb=" N1 U B 11 " pdb=" C2 U B 11 " ideal model delta sigma weight residual 117.70 125.54 -7.84 1.20e+00 6.94e-01 4.27e+01 angle pdb=" O4' A C 4 " pdb=" C1' A C 4 " pdb=" N9 A C 4 " ideal model delta sigma weight residual 108.20 113.37 -5.17 8.00e-01 1.56e+00 4.18e+01 ... (remaining 6318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.13: 2491 27.13 - 54.26: 225 54.26 - 81.40: 56 81.40 - 108.53: 7 108.53 - 135.66: 1 Dihedral angle restraints: 2780 sinusoidal: 1391 harmonic: 1389 Sorted by residual: dihedral pdb=" CA TYR A 790 " pdb=" C TYR A 790 " pdb=" N VAL A 791 " pdb=" CA VAL A 791 " ideal model delta harmonic sigma weight residual 180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR A 738 " pdb=" C THR A 738 " pdb=" N LYS A 739 " pdb=" CA LYS A 739 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' A C 4 " pdb=" O4' A C 4 " pdb=" C1' A C 4 " pdb=" C2' A C 4 " ideal model delta sinusoidal sigma weight residual -21.00 -46.48 25.48 1 8.00e+00 1.56e-02 1.46e+01 ... (remaining 2777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 681 0.111 - 0.222: 40 0.222 - 0.333: 2 0.333 - 0.443: 1 0.443 - 0.554: 2 Chirality restraints: 726 Sorted by residual: chirality pdb=" P U B 12 " pdb=" OP1 U B 12 " pdb=" OP2 U B 12 " pdb=" O5' U B 12 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" P A C 4 " pdb=" OP1 A C 4 " pdb=" OP2 A C 4 " pdb=" O5' A C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" P G C 5 " pdb=" OP1 G C 5 " pdb=" OP2 G C 5 " pdb=" O5' G C 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.80 -0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 723 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 11 " -0.024 2.00e-02 2.50e+03 1.43e-02 4.63e+00 pdb=" N1 U B 11 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 11 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U B 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 11 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 11 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U B 11 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U B 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 3 " 0.026 2.00e-02 2.50e+03 1.18e-02 3.83e+00 pdb=" N9 A C 3 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A C 3 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 3 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A C 3 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 3 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 3 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A C 3 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A C 3 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 2 " -0.026 2.00e-02 2.50e+03 1.12e-02 3.42e+00 pdb=" N9 A B 2 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A B 2 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 2 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A B 2 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 2 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 2 " 0.006 2.00e-02 2.50e+03 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 740 2.77 - 3.30: 4047 3.30 - 3.83: 8256 3.83 - 4.37: 9458 4.37 - 4.90: 15636 Nonbonded interactions: 38137 Sorted by model distance: nonbonded pdb=" OG SER A 752 " pdb=" O VAL A 797 " model vdw 2.235 3.040 nonbonded pdb=" N2 G B 6 " pdb=" O2 C C 9 " model vdw 2.267 2.496 nonbonded pdb=" O CYS A 462 " pdb=" OH TYR A 494 " model vdw 2.291 3.040 nonbonded pdb=" O HIS A 507 " pdb=" OG1 THR A 511 " model vdw 2.322 3.040 nonbonded pdb=" O2 C B 3 " pdb=" N2 G C 12 " model vdw 2.326 2.496 ... (remaining 38132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.770 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 0.038 4565 Z= 0.239 Angle : 0.810 8.286 6323 Z= 0.590 Chirality : 0.061 0.554 726 Planarity : 0.005 0.038 715 Dihedral : 20.507 135.658 1886 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.49 % Allowed : 20.44 % Favored : 79.08 % 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: -0.70 (0.36), residues: 476 helix: 0.48 (0.40), residues: 159 sheet: -0.59 (0.47), residues: 112 loop : -1.04 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 761 TYR 0.013 0.001 TYR A 784 PHE 0.022 0.002 PHE A 491 TRP 0.007 0.002 TRP A 435 HIS 0.004 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.24 ( 4565) covalent geometry : angle 0.81034 / 0.59 ( 6323) hydrogen bonds : bond 0.16231 / 12.40 ( 180) hydrogen bonds : angle 6.76507 / 4.68 ( 482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.167 Fit side-chains REVERT: A 645 MET cc_start: 0.8698 (mtp) cc_final: 0.8284 (mtp) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.7819 time to fit residues: 38.6639 Evaluate side-chains 46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144680 restraints weight = 4587.196| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.75 r_work: 0.3560 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4565 Z= 0.126 Angle : 0.589 11.055 6323 Z= 0.327 Chirality : 0.044 0.295 726 Planarity : 0.004 0.043 715 Dihedral : 18.415 136.136 970 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.92 % Allowed : 21.90 % Favored : 75.18 % 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: -0.32 (0.36), residues: 476 helix: 0.97 (0.41), residues: 164 sheet: -0.58 (0.46), residues: 111 loop : -0.90 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.011 0.001 TYR A 784 PHE 0.018 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 4565) covalent geometry : angle 0.58857 / 0.33 ( 6323) hydrogen bonds : bond 0.08219 / 5.39 ( 180) hydrogen bonds : angle 5.25922 / 3.67 ( 482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.103 Fit side-chains REVERT: A 504 MET cc_start: 0.6602 (ttp) cc_final: 0.6267 (ttm) REVERT: A 645 MET cc_start: 0.8853 (mtp) cc_final: 0.8496 (mtp) REVERT: A 648 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: A 678 GLN cc_start: 0.7398 (mp10) cc_final: 0.6872 (mp10) outliers start: 12 outliers final: 1 residues processed: 55 average time/residue: 0.6068 time to fit residues: 34.3582 Evaluate side-chains 47 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 831 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 ASN A 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.181664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140465 restraints weight = 4483.429| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.71 r_work: 0.3507 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4565 Z= 0.164 Angle : 0.600 8.792 6323 Z= 0.326 Chirality : 0.044 0.279 726 Planarity : 0.005 0.045 715 Dihedral : 18.433 135.097 968 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.92 % Allowed : 22.14 % Favored : 74.94 % 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: -0.28 (0.37), residues: 476 helix: 1.03 (0.41), residues: 164 sheet: -0.46 (0.47), residues: 111 loop : -0.96 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 423 TYR 0.007 0.001 TYR A 784 PHE 0.023 0.002 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4565) covalent geometry : angle 0.59989 / 0.33 ( 6323) hydrogen bonds : bond 0.07796 / 5.10 ( 180) hydrogen bonds : angle 5.23239 / 3.66 ( 482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.156 Fit side-chains REVERT: A 504 MET cc_start: 0.6835 (ttp) cc_final: 0.6539 (ttm) REVERT: A 645 MET cc_start: 0.8822 (mtp) cc_final: 0.8515 (mtp) REVERT: A 648 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: A 678 GLN cc_start: 0.7413 (mp10) cc_final: 0.6973 (mp10) outliers start: 12 outliers final: 5 residues processed: 54 average time/residue: 0.5993 time to fit residues: 33.4143 Evaluate side-chains 54 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN A 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.182879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142766 restraints weight = 4460.110| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.87 r_work: 0.3519 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4565 Z= 0.127 Angle : 0.551 7.417 6323 Z= 0.300 Chirality : 0.042 0.258 726 Planarity : 0.004 0.044 715 Dihedral : 18.435 134.691 968 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.19 % Allowed : 23.84 % Favored : 73.97 % 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: -0.22 (0.37), residues: 476 helix: 1.15 (0.41), residues: 164 sheet: -0.57 (0.47), residues: 109 loop : -0.91 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.027 0.001 TYR A 698 PHE 0.019 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 4565) covalent geometry : angle 0.55128 / 0.30 ( 6323) hydrogen bonds : bond 0.07111 / 4.61 ( 180) hydrogen bonds : angle 5.02495 / 3.51 ( 482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.104 Fit side-chains REVERT: A 504 MET cc_start: 0.6815 (ttp) cc_final: 0.6536 (ttm) REVERT: A 641 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: A 645 MET cc_start: 0.8851 (mtp) cc_final: 0.8511 (mtp) REVERT: A 648 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6776 (tt0) REVERT: A 678 GLN cc_start: 0.7413 (mp10) cc_final: 0.6993 (mp10) outliers start: 9 outliers final: 2 residues processed: 52 average time/residue: 0.7064 time to fit residues: 37.7931 Evaluate side-chains 47 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 672 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 3 optimal weight: 0.0010 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143146 restraints weight = 4489.371| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.66 r_work: 0.3514 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4565 Z= 0.139 Angle : 0.553 6.615 6323 Z= 0.298 Chirality : 0.042 0.220 726 Planarity : 0.004 0.044 715 Dihedral : 18.507 134.332 968 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.68 % Allowed : 23.36 % Favored : 73.97 % 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: -0.22 (0.37), residues: 476 helix: 1.16 (0.41), residues: 163 sheet: -0.60 (0.47), residues: 110 loop : -0.88 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.018 0.001 TYR A 698 PHE 0.021 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4565) covalent geometry : angle 0.55263 / 0.30 ( 6323) hydrogen bonds : bond 0.07082 / 4.64 ( 180) hydrogen bonds : angle 5.02778 / 3.52 ( 482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.160 Fit side-chains REVERT: A 504 MET cc_start: 0.6872 (ttp) cc_final: 0.6595 (ttm) REVERT: A 645 MET cc_start: 0.8872 (mtp) cc_final: 0.8540 (mtp) REVERT: A 648 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: A 678 GLN cc_start: 0.7419 (mp10) cc_final: 0.7181 (mp10) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 0.7573 time to fit residues: 41.2859 Evaluate side-chains 51 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 831 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN A 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.183407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142182 restraints weight = 4540.550| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.73 r_work: 0.3529 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4565 Z= 0.119 Angle : 0.531 6.547 6323 Z= 0.286 Chirality : 0.041 0.202 726 Planarity : 0.004 0.042 715 Dihedral : 18.524 133.810 968 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.70 % Allowed : 24.33 % Favored : 73.97 % 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 (0.37), residues: 476 helix: 1.19 (0.41), residues: 164 sheet: -0.55 (0.47), residues: 109 loop : -0.85 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.016 0.001 TYR A 698 PHE 0.019 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4565) covalent geometry : angle 0.53108 / 0.29 ( 6323) hydrogen bonds : bond 0.06816 / 4.44 ( 180) hydrogen bonds : angle 4.93456 / 3.46 ( 482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.158 Fit side-chains REVERT: A 504 MET cc_start: 0.6846 (ttp) cc_final: 0.6564 (ttm) REVERT: A 641 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: A 645 MET cc_start: 0.8879 (mtp) cc_final: 0.8453 (mtp) REVERT: A 648 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6693 (tt0) REVERT: A 678 GLN cc_start: 0.7414 (mp10) cc_final: 0.7203 (mp10) REVERT: A 739 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7781 (ttmt) REVERT: A 784 TYR cc_start: 0.7945 (t80) cc_final: 0.7675 (t80) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.8265 time to fit residues: 42.4851 Evaluate side-chains 53 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN A 623 ASN A 847 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143499 restraints weight = 4472.923| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.72 r_work: 0.3549 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4565 Z= 0.107 Angle : 0.510 6.372 6323 Z= 0.274 Chirality : 0.040 0.168 726 Planarity : 0.004 0.042 715 Dihedral : 18.480 132.826 968 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.70 % Allowed : 24.57 % Favored : 73.72 % 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 (0.37), residues: 476 helix: 1.28 (0.41), residues: 164 sheet: -0.57 (0.47), residues: 109 loop : -0.76 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.013 0.001 TYR A 698 PHE 0.017 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.002 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 4565) covalent geometry : angle 0.51033 / 0.27 ( 6323) hydrogen bonds : bond 0.06654 / 4.35 ( 180) hydrogen bonds : angle 4.80092 / 3.36 ( 482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.095 Fit side-chains REVERT: A 504 MET cc_start: 0.6840 (ttp) cc_final: 0.6532 (ttm) REVERT: A 645 MET cc_start: 0.8883 (mtp) cc_final: 0.8423 (mtp) REVERT: A 648 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: A 678 GLN cc_start: 0.7356 (mp10) cc_final: 0.7144 (mp10) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.6784 time to fit residues: 34.9018 Evaluate side-chains 53 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.182544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141332 restraints weight = 4485.627| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.72 r_work: 0.3520 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4565 Z= 0.138 Angle : 0.541 6.476 6323 Z= 0.287 Chirality : 0.041 0.162 726 Planarity : 0.004 0.042 715 Dihedral : 18.469 133.495 968 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.19 % Allowed : 25.06 % Favored : 72.75 % 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: -0.12 (0.37), residues: 476 helix: 1.18 (0.41), residues: 164 sheet: -0.50 (0.47), residues: 109 loop : -0.79 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 723 TYR 0.019 0.001 TYR A 784 PHE 0.020 0.001 PHE A 491 TRP 0.005 0.001 TRP A 435 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 4565) covalent geometry : angle 0.54100 / 0.29 ( 6323) hydrogen bonds : bond 0.06817 / 4.46 ( 180) hydrogen bonds : angle 4.92495 / 3.45 ( 482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.193 Fit side-chains REVERT: A 504 MET cc_start: 0.6858 (ttp) cc_final: 0.6599 (ttm) REVERT: A 645 MET cc_start: 0.8885 (mtp) cc_final: 0.8466 (mtp) REVERT: A 648 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6728 (tt0) REVERT: A 678 GLN cc_start: 0.7421 (mp10) cc_final: 0.7189 (mp10) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.7745 time to fit residues: 40.6479 Evaluate side-chains 52 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN A 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.181730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140596 restraints weight = 4490.358| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.70 r_work: 0.3514 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4565 Z= 0.141 Angle : 0.541 6.538 6323 Z= 0.288 Chirality : 0.041 0.147 726 Planarity : 0.004 0.041 715 Dihedral : 18.423 133.781 968 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.22 % Allowed : 26.28 % Favored : 72.51 % 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: -0.12 (0.37), residues: 476 helix: 1.20 (0.41), residues: 163 sheet: -0.51 (0.47), residues: 110 loop : -0.81 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.011 0.001 TYR A 698 PHE 0.021 0.001 PHE A 491 TRP 0.005 0.001 TRP A 435 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 4565) covalent geometry : angle 0.54133 / 0.29 ( 6323) hydrogen bonds : bond 0.06803 / 4.44 ( 180) hydrogen bonds : angle 4.98376 / 3.49 ( 482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.157 Fit side-chains REVERT: A 504 MET cc_start: 0.6870 (ttp) cc_final: 0.6605 (ttm) REVERT: A 645 MET cc_start: 0.8872 (mtp) cc_final: 0.8541 (mtp) REVERT: A 648 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6721 (tt0) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.7614 time to fit residues: 37.5733 Evaluate side-chains 51 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN A 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.183527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142721 restraints weight = 4447.601| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.70 r_work: 0.3537 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4565 Z= 0.112 Angle : 0.519 6.435 6323 Z= 0.276 Chirality : 0.040 0.120 726 Planarity : 0.004 0.041 715 Dihedral : 18.338 132.931 968 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.22 % Allowed : 26.28 % Favored : 72.51 % 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 (0.37), residues: 476 helix: 1.18 (0.40), residues: 164 sheet: -0.54 (0.48), residues: 109 loop : -0.75 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 814 TYR 0.012 0.001 TYR A 784 PHE 0.017 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.002 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 4565) covalent geometry : angle 0.51882 / 0.28 ( 6323) hydrogen bonds : bond 0.06603 / 4.32 ( 180) hydrogen bonds : angle 4.82004 / 3.37 ( 482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.154 Fit side-chains REVERT: A 504 MET cc_start: 0.6839 (ttp) cc_final: 0.6519 (ttm) REVERT: A 645 MET cc_start: 0.8893 (mtp) cc_final: 0.8446 (mtp) REVERT: A 648 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6663 (tt0) REVERT: A 739 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7804 (ttmt) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.8563 time to fit residues: 41.3574 Evaluate side-chains 51 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142198 restraints weight = 4506.127| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.71 r_work: 0.3533 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4565 Z= 0.117 Angle : 0.518 6.400 6323 Z= 0.274 Chirality : 0.040 0.126 726 Planarity : 0.004 0.041 715 Dihedral : 18.214 132.690 968 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.22 % Allowed : 26.28 % Favored : 72.51 % 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 (0.37), residues: 476 helix: 1.24 (0.41), residues: 164 sheet: -0.55 (0.47), residues: 109 loop : -0.75 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 411 TYR 0.010 0.001 TYR A 698 PHE 0.018 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.002 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 4565) covalent geometry : angle 0.51789 / 0.27 ( 6323) hydrogen bonds : bond 0.06623 / 4.35 ( 180) hydrogen bonds : angle 4.80748 / 3.36 ( 482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.56 seconds wall clock time: 30 minutes 31.70 seconds (1831.70 seconds total)