Starting phenix.real_space_refine on Wed Sep 17 04:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6r_62133/09_2025/9k6r_62133.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6r_62133/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9k6r_62133/09_2025/9k6r_62133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6r_62133/09_2025/9k6r_62133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6r_62133/09_2025/9k6r_62133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6r_62133/09_2025/9k6r_62133.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 1.27, per 1000 atoms: 0.29 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: 0.46 Conformation dependent library (CDL) restraints added in 161.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.59 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: 0.72 Time building geometry restraints manager: 0.52 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.500 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00391 ( 4565) covalent geometry : angle 0.77193 ( 6323) hydrogen bonds : bond 0.16231 ( 180) hydrogen bonds : angle 6.76507 ( 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 : 0.175 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: 0.8189 time to fit residues: 40.4304 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 : 0.165 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.184645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143760 restraints weight = 4577.023| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.74 r_work: 0.3549 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0998 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= 0.128 Angle : 0.603 6.733 6323 Z= 0.309 Chirality : 0.042 0.210 726 Planarity : 0.004 0.040 715 Dihedral : 18.468 137.435 970 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 22.38 % 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 aren not related in a simple way. whole: -0.28 (0.36), residues: 476 helix: 1.20 (0.41), residues: 158 sheet: -0.57 (0.46), residues: 111 loop : -0.99 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.010 0.001 TYR A 784 PHE 0.019 0.001 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.002 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4565) covalent geometry : angle 0.60273 ( 6323) hydrogen bonds : bond 0.06934 ( 180) hydrogen bonds : angle 5.12337 ( 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 56 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.178 Fit side-chains REVERT: A 645 MET cc_start: 0.8811 (mtp) cc_final: 0.8461 (mtp) REVERT: A 676 PHE cc_start: 0.7049 (m-10) cc_final: 0.6805 (m-10) REVERT: A 678 GLN cc_start: 0.7384 (mp10) cc_final: 0.7049 (mp10) outliers start: 10 outliers final: 1 residues processed: 54 average time/residue: 0.7531 time to fit residues: 41.9192 Evaluate side-chains 42 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.181223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140519 restraints weight = 4552.150| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.70 r_work: 0.3512 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4565 Z= 0.158 Angle : 0.622 6.623 6323 Z= 0.317 Chirality : 0.043 0.189 726 Planarity : 0.004 0.041 715 Dihedral : 18.483 136.774 968 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.43 % Allowed : 23.11 % Favored : 74.45 % 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 aren not related in a simple way. whole: -0.33 (0.37), residues: 476 helix: 1.03 (0.41), residues: 163 sheet: -0.59 (0.46), residues: 111 loop : -0.96 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.007 0.001 TYR A 784 PHE 0.021 0.002 PHE A 491 TRP 0.006 0.001 TRP A 435 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4565) covalent geometry : angle 0.62151 ( 6323) hydrogen bonds : bond 0.06895 ( 180) hydrogen bonds : angle 5.14778 ( 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 57 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.155 Fit side-chains REVERT: A 645 MET cc_start: 0.8810 (mtp) cc_final: 0.8479 (mtp) outliers start: 10 outliers final: 2 residues processed: 54 average time/residue: 0.7158 time to fit residues: 39.8698 Evaluate side-chains 50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 588 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.177857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136919 restraints weight = 4548.436| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.70 r_work: 0.3466 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.005 0.042 4565 Z= 0.218 Angle : 0.670 7.161 6323 Z= 0.344 Chirality : 0.045 0.171 726 Planarity : 0.005 0.041 715 Dihedral : 18.579 139.834 968 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.65 % Allowed : 22.63 % 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 aren not related in a simple way. whole: -0.51 (0.36), residues: 476 helix: 0.74 (0.40), residues: 163 sheet: -0.51 (0.47), residues: 109 loop : -1.05 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 761 TYR 0.033 0.002 TYR A 698 PHE 0.027 0.002 PHE A 491 TRP 0.007 0.002 TRP A 435 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 4565) covalent geometry : angle 0.66952 ( 6323) hydrogen bonds : bond 0.07283 ( 180) hydrogen bonds : angle 5.44646 ( 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 61 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.159 Fit side-chains REVERT: A 645 MET cc_start: 0.8815 (mtp) cc_final: 0.8446 (mtp) REVERT: A 648 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6810 (tt0) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 0.7546 time to fit residues: 43.5273 Evaluate side-chains 50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 702 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 34 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.182349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142096 restraints weight = 4542.075| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.68 r_work: 0.3534 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1636 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= 0.124 Angle : 0.573 6.496 6323 Z= 0.291 Chirality : 0.041 0.145 726 Planarity : 0.004 0.040 715 Dihedral : 18.543 135.610 968 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.43 % Allowed : 22.87 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.36), residues: 476 helix: 0.99 (0.40), residues: 164 sheet: -0.36 (0.48), residues: 103 loop : -0.94 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 761 TYR 0.017 0.001 TYR A 698 PHE 0.019 0.001 PHE A 491 TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4565) covalent geometry : angle 0.57290 ( 6323) hydrogen bonds : bond 0.06420 ( 180) hydrogen bonds : angle 4.99457 ( 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 57 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.174 Fit side-chains REVERT: A 645 MET cc_start: 0.8842 (mtp) cc_final: 0.8476 (mtp) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.7477 time to fit residues: 40.8668 Evaluate side-chains 48 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.182554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141774 restraints weight = 4584.869| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.70 r_work: 0.3531 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1700 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 : 0.562 6.361 6323 Z= 0.285 Chirality : 0.040 0.131 726 Planarity : 0.004 0.042 715 Dihedral : 18.626 134.845 968 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.68 % Allowed : 24.57 % 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 aren not related in a simple way. whole: -0.18 (0.37), residues: 476 helix: 1.08 (0.40), residues: 164 sheet: -0.39 (0.49), residues: 103 loop : -0.88 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.016 0.001 TYR A 784 PHE 0.019 0.001 PHE A 491 TRP 0.007 0.001 TRP A 435 HIS 0.002 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4565) covalent geometry : angle 0.56248 ( 6323) hydrogen bonds : bond 0.06414 ( 180) hydrogen bonds : angle 4.89726 ( 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 60 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.174 Fit side-chains REVERT: A 468 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7960 (mmmt) REVERT: A 504 MET cc_start: 0.6751 (ttp) cc_final: 0.6474 (ttm) REVERT: A 645 MET cc_start: 0.8863 (mtp) cc_final: 0.8510 (mtp) REVERT: A 648 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6592 (tt0) REVERT: A 678 GLN cc_start: 0.7441 (mp10) cc_final: 0.7075 (mp10) outliers start: 11 outliers final: 3 residues processed: 57 average time/residue: 0.7865 time to fit residues: 46.0657 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 : 0.090 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 0.0170 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.181500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140802 restraints weight = 4508.304| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.68 r_work: 0.3518 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1813 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= 0.139 Angle : 0.579 6.386 6323 Z= 0.294 Chirality : 0.041 0.149 726 Planarity : 0.004 0.040 715 Dihedral : 18.647 134.968 968 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.16 % Allowed : 23.84 % Favored : 72.99 % 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 aren not related in a simple way. whole: -0.18 (0.37), residues: 476 helix: 1.09 (0.41), residues: 164 sheet: -0.52 (0.47), residues: 109 loop : -0.80 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.013 0.001 TYR A 698 PHE 0.021 0.001 PHE A 491 TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4565) covalent geometry : angle 0.57892 ( 6323) hydrogen bonds : bond 0.06503 ( 180) hydrogen bonds : angle 4.97744 ( 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 57 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.133 Fit side-chains REVERT: A 468 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7951 (mmmt) REVERT: A 504 MET cc_start: 0.6852 (ttp) cc_final: 0.6556 (ttm) REVERT: A 645 MET cc_start: 0.8820 (mtp) cc_final: 0.8489 (mtp) REVERT: A 648 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6647 (tt0) outliers start: 13 outliers final: 5 residues processed: 53 average time/residue: 0.7620 time to fit residues: 41.5396 Evaluate side-chains 52 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 A 623 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139051 restraints weight = 4514.905| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.66 r_work: 0.3496 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4565 Z= 0.165 Angle : 0.601 6.594 6323 Z= 0.306 Chirality : 0.041 0.163 726 Planarity : 0.004 0.040 715 Dihedral : 18.499 136.283 968 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.68 % Allowed : 25.06 % Favored : 72.26 % 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 aren not related in a simple way. whole: -0.33 (0.37), residues: 476 helix: 0.89 (0.40), residues: 168 sheet: -0.58 (0.46), residues: 110 loop : -0.88 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.011 0.001 TYR A 698 PHE 0.023 0.002 PHE A 491 TRP 0.008 0.002 TRP A 435 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4565) covalent geometry : angle 0.60072 ( 6323) hydrogen bonds : bond 0.06697 ( 180) hydrogen bonds : angle 5.14260 ( 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: 11 poor density : 44 time to evaluate : 0.162 Fit side-chains REVERT: A 468 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7955 (mmmt) REVERT: A 504 MET cc_start: 0.6916 (ttp) cc_final: 0.6616 (ttm) REVERT: A 645 MET cc_start: 0.8823 (mtp) cc_final: 0.8489 (mtp) REVERT: A 648 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6700 (tt0) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.7597 time to fit residues: 40.6939 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 : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 468 LYS 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 27 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.176285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134726 restraints weight = 4489.582| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.69 r_work: 0.3438 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4565 Z= 0.241 Angle : 0.684 7.215 6323 Z= 0.352 Chirality : 0.045 0.236 726 Planarity : 0.005 0.040 715 Dihedral : 18.506 140.046 968 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.43 % Allowed : 24.33 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.36), residues: 476 helix: 0.53 (0.40), residues: 168 sheet: -0.44 (0.48), residues: 107 loop : -1.02 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 761 TYR 0.014 0.002 TYR A 815 PHE 0.030 0.002 PHE A 491 TRP 0.010 0.002 TRP A 435 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 4565) covalent geometry : angle 0.68436 ( 6323) hydrogen bonds : bond 0.07399 ( 180) hydrogen bonds : angle 5.53082 ( 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 54 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.204 Fit side-chains REVERT: A 468 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7985 (mmmt) REVERT: A 645 MET cc_start: 0.8807 (mtp) cc_final: 0.8464 (mtp) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 0.8326 time to fit residues: 42.8719 Evaluate side-chains 49 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.0270 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141454 restraints weight = 4436.480| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.68 r_work: 0.3532 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4565 Z= 0.117 Angle : 0.573 6.978 6323 Z= 0.293 Chirality : 0.040 0.131 726 Planarity : 0.004 0.040 715 Dihedral : 18.113 134.718 968 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.22 % Allowed : 26.03 % 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 aren not related in a simple way. whole: -0.30 (0.37), residues: 476 helix: 0.88 (0.40), residues: 169 sheet: -0.43 (0.48), residues: 103 loop : -0.92 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 761 TYR 0.013 0.001 TYR A 698 PHE 0.018 0.001 PHE A 491 TRP 0.007 0.001 TRP A 435 HIS 0.002 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4565) covalent geometry : angle 0.57334 ( 6323) hydrogen bonds : bond 0.06362 ( 180) hydrogen bonds : angle 4.95110 ( 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 52 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.172 Fit side-chains REVERT: A 645 MET cc_start: 0.8860 (mtp) cc_final: 0.8419 (mtp) REVERT: A 678 GLN cc_start: 0.7458 (mp10) cc_final: 0.7100 (mp10) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.7604 time to fit residues: 39.9985 Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.180760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139323 restraints weight = 4487.830| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.71 r_work: 0.3506 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4565 Z= 0.143 Angle : 0.604 7.923 6323 Z= 0.307 Chirality : 0.042 0.233 726 Planarity : 0.004 0.042 715 Dihedral : 17.987 134.851 968 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.97 % Allowed : 26.28 % 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 aren not related in a simple way. whole: -0.26 (0.37), residues: 476 helix: 0.93 (0.40), residues: 168 sheet: -0.51 (0.47), residues: 109 loop : -0.84 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 761 TYR 0.022 0.002 TYR A 784 PHE 0.020 0.001 PHE A 491 TRP 0.010 0.001 TRP A 435 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4565) covalent geometry : angle 0.60382 ( 6323) hydrogen bonds : bond 0.06632 ( 180) hydrogen bonds : angle 4.98004 ( 482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.95 seconds wall clock time: 32 minutes 58.30 seconds (1978.30 seconds total)