Starting phenix.real_space_refine on Wed Jul 23 21:09:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6r_62133/07_2025/9k6r_62133.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6r_62133/07_2025/9k6r_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_62133/07_2025/9k6r_62133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6r_62133/07_2025/9k6r_62133.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6r_62133/07_2025/9k6r_62133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6r_62133/07_2025/9k6r_62133.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.40, per 1000 atoms: 0.77 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: 1.23 Conformation dependent library (CDL) restraints added in 490.4 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: 1.54 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: 1.53 Time building geometry restraints manager: 1.46 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=" 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=" 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 bond pdb=" O5' G C 5 " pdb=" C5' G C 5 " ideal model delta sigma weight residual 1.420 1.455 -0.035 1.50e-02 4.44e+03 5.43e+00 bond pdb=" P A C 4 " pdb=" O5' A C 4 " ideal model delta sigma weight residual 1.593 1.627 -0.034 1.50e-02 4.44e+03 5.29e+00 bond pdb=" N ALA A 603 " pdb=" CA ALA A 603 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.37e-02 5.33e+03 5.21e+00 ... (remaining 4560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6077 1.66 - 3.31: 194 3.31 - 4.97: 26 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 1.00e+00 1.00e+00 4.52e+01 angle pdb=" O3' A C 3 " pdb=" P A C 4 " pdb=" O5' A C 4 " ideal model delta sigma weight residual 104.00 111.93 -7.93 1.50e+00 4.44e-01 2.80e+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 1.00e+00 1.00e+00 2.75e+01 angle pdb=" O3' A C 4 " pdb=" C3' A C 4 " pdb=" C2' A C 4 " ideal model delta sigma weight residual 109.50 102.08 7.42 1.50e+00 4.44e-01 2.45e+01 angle pdb=" O4' A C 4 " pdb=" C1' A C 4 " pdb=" C2' A C 4 " ideal model delta sigma weight residual 105.80 101.16 4.64 1.00e+00 1.00e+00 2.15e+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: 699 0.111 - 0.222: 22 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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= 0.207 Angle : 0.772 8.286 6323 Z= 0.438 Chirality : 0.057 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.002 TRP A 435 HIS 0.004 0.001 HIS A 807 PHE 0.022 0.002 PHE A 491 TYR 0.013 0.001 TYR A 784 ARG 0.005 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.16231 ( 180) hydrogen bonds : angle 6.76507 ( 482) covalent geometry : bond 0.00391 ( 4565) covalent geometry : angle 0.77193 ( 6323) *********************** 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 : 0.434 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: 1.6254 time to fit residues: 80.4461 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 : 0.478 ------------------------------------------------------------------------------- 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 42 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.182041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140770 restraints weight = 4531.803| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.74 r_work: 0.3513 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1059 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= 0.167 Angle : 0.636 6.987 6323 Z= 0.328 Chirality : 0.044 0.223 726 Planarity : 0.005 0.042 715 Dihedral : 18.486 138.825 970 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.92 % Allowed : 21.65 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.36), residues: 476 helix: 1.07 (0.41), residues: 158 sheet: -0.54 (0.47), residues: 110 loop : -1.09 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 435 HIS 0.003 0.001 HIS A 822 PHE 0.023 0.001 PHE A 491 TYR 0.006 0.001 TYR A 749 ARG 0.002 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.07229 ( 180) hydrogen bonds : angle 5.30244 ( 482) covalent geometry : bond 0.00365 ( 4565) covalent geometry : angle 0.63626 ( 6323) *********************** 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 : 0.431 Fit side-chains REVERT: A 504 MET cc_start: 0.6772 (ttp) cc_final: 0.6555 (ttm) REVERT: A 645 MET cc_start: 0.8800 (mtp) cc_final: 0.8477 (mtp) REVERT: A 648 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6449 (tt0) REVERT: A 678 GLN cc_start: 0.7456 (mp10) cc_final: 0.7208 (mp10) outliers start: 12 outliers final: 3 residues processed: 56 average time/residue: 1.5037 time to fit residues: 87.0185 Evaluate side-chains 50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 672 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 0.0010 chunk 46 optimal weight: 0.8980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4103 r_free = 0.4103 target = 0.182878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142631 restraints weight = 4519.321| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.69 r_work: 0.3530 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1282 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= 0.132 Angle : 0.601 6.532 6323 Z= 0.305 Chirality : 0.042 0.189 726 Planarity : 0.004 0.042 715 Dihedral : 18.474 136.128 968 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.16 % Allowed : 22.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.37), residues: 476 helix: 1.03 (0.41), residues: 164 sheet: -0.54 (0.47), residues: 109 loop : -0.87 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 435 HIS 0.003 0.001 HIS A 634 PHE 0.020 0.001 PHE A 491 TYR 0.026 0.001 TYR A 698 ARG 0.003 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06652 ( 180) hydrogen bonds : angle 5.04626 ( 482) covalent geometry : bond 0.00292 ( 4565) covalent geometry : angle 0.60134 ( 6323) *********************** 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 59 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.472 Fit side-chains REVERT: A 504 MET cc_start: 0.6764 (ttp) cc_final: 0.6503 (ttm) REVERT: A 645 MET cc_start: 0.8826 (mtp) cc_final: 0.8469 (mtp) REVERT: A 648 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6633 (tt0) REVERT: A 678 GLN cc_start: 0.7464 (mp10) cc_final: 0.7245 (mp10) outliers start: 13 outliers final: 4 residues processed: 55 average time/residue: 1.3953 time to fit residues: 79.3347 Evaluate side-chains 50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER 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 672 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4090 r_free = 0.4090 target = 0.181569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140621 restraints weight = 4549.077| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.72 r_work: 0.3511 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1492 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= 0.142 Angle : 0.598 6.657 6323 Z= 0.304 Chirality : 0.042 0.157 726 Planarity : 0.004 0.041 715 Dihedral : 18.467 136.503 968 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.92 % Allowed : 23.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.37), residues: 476 helix: 1.12 (0.41), residues: 163 sheet: -0.57 (0.47), residues: 109 loop : -0.88 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS A 682 PHE 0.021 0.001 PHE A 491 TYR 0.016 0.001 TYR A 698 ARG 0.004 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06618 ( 180) hydrogen bonds : angle 5.04625 ( 482) covalent geometry : bond 0.00315 ( 4565) covalent geometry : angle 0.59764 ( 6323) *********************** 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 59 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.435 Fit side-chains REVERT: A 504 MET cc_start: 0.6792 (ttp) cc_final: 0.6498 (ttm) REVERT: A 645 MET cc_start: 0.8836 (mtp) cc_final: 0.8482 (mtp) REVERT: A 648 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6653 (tt0) outliers start: 12 outliers final: 5 residues processed: 54 average time/residue: 1.4733 time to fit residues: 82.2418 Evaluate side-chains 50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER 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 676 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.0030 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4119 r_free = 0.4119 target = 0.184007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143250 restraints weight = 4582.287| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.71 r_work: 0.3543 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4565 Z= 0.121 Angle : 0.567 6.349 6323 Z= 0.287 Chirality : 0.040 0.140 726 Planarity : 0.004 0.040 715 Dihedral : 18.493 134.634 968 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.95 % Allowed : 23.84 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.37), residues: 476 helix: 1.14 (0.40), residues: 164 sheet: -0.40 (0.48), residues: 103 loop : -0.85 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.002 0.001 HIS A 634 PHE 0.019 0.001 PHE A 491 TYR 0.011 0.001 TYR A 698 ARG 0.003 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06343 ( 180) hydrogen bonds : angle 4.86670 ( 482) covalent geometry : bond 0.00268 ( 4565) covalent geometry : angle 0.56663 ( 6323) *********************** 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 57 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.432 Fit side-chains REVERT: A 504 MET cc_start: 0.6774 (ttp) cc_final: 0.6510 (ttm) REVERT: A 645 MET cc_start: 0.8868 (mtp) cc_final: 0.8494 (mtp) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 1.6001 time to fit residues: 87.4495 Evaluate side-chains 51 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 676 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.183374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142768 restraints weight = 4486.451| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.68 r_work: 0.3540 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1658 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= 0.123 Angle : 0.560 6.377 6323 Z= 0.284 Chirality : 0.040 0.132 726 Planarity : 0.004 0.040 715 Dihedral : 18.561 134.707 968 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 23.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.37), residues: 476 helix: 1.19 (0.40), residues: 164 sheet: -0.39 (0.48), residues: 103 loop : -0.82 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.002 0.001 HIS A 634 PHE 0.019 0.001 PHE A 491 TYR 0.015 0.001 TYR A 784 ARG 0.003 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06356 ( 180) hydrogen bonds : angle 4.82922 ( 482) covalent geometry : bond 0.00271 ( 4565) covalent geometry : angle 0.56009 ( 6323) *********************** 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 61 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.435 Fit side-chains REVERT: A 468 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7931 (mmmt) REVERT: A 504 MET cc_start: 0.6757 (ttp) cc_final: 0.6524 (ttm) REVERT: A 645 MET cc_start: 0.8860 (mtp) cc_final: 0.8504 (mtp) REVERT: A 648 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6597 (tt0) REVERT: A 678 GLN cc_start: 0.7520 (mp10) cc_final: 0.7277 (mp10) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 1.6214 time to fit residues: 95.2296 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 : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 483 MET 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 34 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4102 r_free = 0.4102 target = 0.181980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141634 restraints weight = 4465.050| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.65 r_work: 0.3525 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4565 Z= 0.133 Angle : 0.570 6.412 6323 Z= 0.289 Chirality : 0.040 0.133 726 Planarity : 0.004 0.039 715 Dihedral : 18.614 134.798 968 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 23.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.37), residues: 476 helix: 1.15 (0.40), residues: 164 sheet: -0.56 (0.47), residues: 109 loop : -0.77 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.002 0.001 HIS A 682 PHE 0.020 0.001 PHE A 491 TYR 0.014 0.001 TYR A 784 ARG 0.003 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06392 ( 180) hydrogen bonds : angle 4.88773 ( 482) covalent geometry : bond 0.00295 ( 4565) covalent geometry : angle 0.57031 ( 6323) *********************** 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 58 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.469 Fit side-chains REVERT: A 468 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7977 (mmmt) REVERT: A 504 MET cc_start: 0.6883 (ttp) cc_final: 0.6641 (ttm) REVERT: A 645 MET cc_start: 0.8853 (mtp) cc_final: 0.8517 (mtp) REVERT: A 648 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6616 (tt0) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 1.7356 time to fit residues: 96.4134 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 : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 483 MET 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 5 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.180590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139537 restraints weight = 4398.642| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.67 r_work: 0.3499 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1932 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= 0.160 Angle : 0.596 6.512 6323 Z= 0.303 Chirality : 0.041 0.160 726 Planarity : 0.004 0.039 715 Dihedral : 18.502 135.916 968 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 23.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.37), residues: 476 helix: 1.13 (0.40), residues: 163 sheet: -0.59 (0.46), residues: 110 loop : -0.80 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.003 0.001 HIS A 600 PHE 0.023 0.001 PHE A 491 TYR 0.008 0.001 TYR A 815 ARG 0.003 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06624 ( 180) hydrogen bonds : angle 5.07836 ( 482) covalent geometry : bond 0.00359 ( 4565) covalent geometry : angle 0.59597 ( 6323) *********************** 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 56 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.496 Fit side-chains REVERT: A 468 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (mmmt) REVERT: A 504 MET cc_start: 0.6908 (ttp) cc_final: 0.6662 (ttm) REVERT: A 645 MET cc_start: 0.8855 (mtp) cc_final: 0.8526 (mtp) REVERT: A 648 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6686 (tt0) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 2.0559 time to fit residues: 110.1352 Evaluate side-chains 53 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 468 LYS 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 676 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4064 r_free = 0.4064 target = 0.178561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137578 restraints weight = 4476.633| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.68 r_work: 0.3474 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4565 Z= 0.185 Angle : 0.631 6.821 6323 Z= 0.322 Chirality : 0.043 0.182 726 Planarity : 0.004 0.039 715 Dihedral : 18.379 137.434 968 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 24.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.37), residues: 476 helix: 0.96 (0.40), residues: 163 sheet: -0.65 (0.46), residues: 110 loop : -0.91 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 435 HIS 0.004 0.001 HIS A 600 PHE 0.026 0.002 PHE A 491 TYR 0.009 0.002 TYR A 815 ARG 0.004 0.001 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06894 ( 180) hydrogen bonds : angle 5.28044 ( 482) covalent geometry : bond 0.00414 ( 4565) covalent geometry : angle 0.63062 ( 6323) *********************** 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 53 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.438 Fit side-chains REVERT: A 504 MET cc_start: 0.6913 (ttp) cc_final: 0.6622 (ttm) REVERT: A 645 MET cc_start: 0.8828 (mtp) cc_final: 0.8436 (mtp) REVERT: A 648 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6756 (tt0) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.5834 time to fit residues: 80.0023 Evaluate side-chains 48 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 538 THR 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 22 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4108 r_free = 0.4108 target = 0.182864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142575 restraints weight = 4438.154| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.68 r_work: 0.3540 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4565 Z= 0.112 Angle : 0.559 6.204 6323 Z= 0.285 Chirality : 0.040 0.130 726 Planarity : 0.004 0.039 715 Dihedral : 18.192 133.819 968 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.37), residues: 476 helix: 1.14 (0.40), residues: 164 sheet: -0.56 (0.48), residues: 109 loop : -0.77 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.002 0.001 HIS A 682 PHE 0.018 0.001 PHE A 491 TYR 0.020 0.001 TYR A 698 ARG 0.005 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06293 ( 180) hydrogen bonds : angle 4.86487 ( 482) covalent geometry : bond 0.00242 ( 4565) covalent geometry : angle 0.55909 ( 6323) ********************** 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 58 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.456 Fit side-chains REVERT: A 504 MET cc_start: 0.6902 (ttp) cc_final: 0.6634 (ttm) REVERT: A 645 MET cc_start: 0.8872 (mtp) cc_final: 0.8408 (mtp) REVERT: A 648 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6602 (tt0) REVERT: A 678 GLN cc_start: 0.7416 (mp10) cc_final: 0.7167 (mp10) REVERT: A 784 TYR cc_start: 0.7904 (t80) cc_final: 0.7592 (t80) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 1.9318 time to fit residues: 107.9706 Evaluate side-chains 53 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.181971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141096 restraints weight = 4423.878| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.69 r_work: 0.3522 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4565 Z= 0.128 Angle : 0.579 6.677 6323 Z= 0.294 Chirality : 0.040 0.135 726 Planarity : 0.004 0.041 715 Dihedral : 18.199 133.557 968 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.22 % Allowed : 25.30 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.37), residues: 476 helix: 1.19 (0.40), residues: 164 sheet: -0.53 (0.48), residues: 109 loop : -0.79 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.002 0.001 HIS A 634 PHE 0.020 0.001 PHE A 491 TYR 0.020 0.001 TYR A 698 ARG 0.004 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.06388 ( 180) hydrogen bonds : angle 4.85871 ( 482) covalent geometry : bond 0.00282 ( 4565) covalent geometry : angle 0.57907 ( 6323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4311.89 seconds wall clock time: 77 minutes 51.13 seconds (4671.13 seconds total)