Starting phenix.real_space_refine on Tue Aug 4 14:24:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11gk_75679/08_2026/11gk_75679.cif Found real_map, /net/cci-nas-00/data/ceres_data/11gk_75679/08_2026/11gk_75679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11gk_75679/08_2026/11gk_75679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11gk_75679/08_2026/11gk_75679.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11gk_75679/08_2026/11gk_75679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11gk_75679/08_2026/11gk_75679.map" } resolution = 3.0 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= 0.029 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 36 5.49 5 Mg 1 5.21 5 S 19 5.16 5 C 2331 2.51 5 N 695 2.21 5 O 796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3878 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3111 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 366} Chain breaks: 5 Chain: "B" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 393 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 373 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.98, per 1000 atoms: 0.25 Number of scatterers: 3878 At special positions: 0 Unit cell: (66.6, 82.14, 84.36, 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 19 16.00 P 36 15.00 Mg 1 11.99 O 796 8.00 N 695 7.00 C 2331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 107.1 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 4 sheets defined 40.0% alpha, 16.7% beta 15 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.857A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.379A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.507A 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 641 through 658 removed outlier: 3.543A pdb=" N SER A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 4.067A pdb=" N HIS A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS A 682 " --> pdb=" O GLN A 678 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 3.679A pdb=" N CYS A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 788 " --> pdb=" O TYR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 839 through 845 Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.957A pdb=" N ARG A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 412 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: 4.041A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 625 through 631 removed outlier: 5.024A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 664 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 705 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE A 666 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 707 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 668 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N LYS A 709 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 596 1.32 - 1.44: 1249 1.44 - 1.57: 2095 1.57 - 1.69: 70 1.69 - 1.82: 27 Bond restraints: 4037 Sorted by residual: bond pdb=" C5' G B 5 " pdb=" C4' G B 5 " ideal model delta sigma weight residual 1.508 1.537 -0.029 7.00e-03 2.04e+04 1.76e+01 bond pdb=" C2 G B 5 " pdb=" N2 G B 5 " ideal model delta sigma weight residual 1.341 1.303 0.038 1.00e-02 1.00e+04 1.45e+01 bond pdb=" C2 G C 11 " pdb=" N2 G C 11 " ideal model delta sigma weight residual 1.341 1.305 0.036 1.00e-02 1.00e+04 1.32e+01 bond pdb=" C5' A C 8 " pdb=" C4' A C 8 " ideal model delta sigma weight residual 1.508 1.533 -0.025 7.00e-03 2.04e+04 1.24e+01 bond pdb=" C5' A B 13 " pdb=" C4' A B 13 " ideal model delta sigma weight residual 1.508 1.532 -0.024 7.00e-03 2.04e+04 1.13e+01 ... (remaining 4032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 5238 2.91 - 5.82: 379 5.82 - 8.72: 20 8.72 - 11.63: 1 11.63 - 14.54: 4 Bond angle restraints: 5642 Sorted by residual: angle pdb=" C3' G B 16 " pdb=" O3' G B 16 " pdb=" P U B 17 " ideal model delta sigma weight residual 119.70 105.16 14.54 1.20e+00 6.94e-01 1.47e+02 angle pdb=" C3' C C 4 " pdb=" O3' C C 4 " pdb=" P A C 5 " ideal model delta sigma weight residual 119.70 106.72 12.98 1.20e+00 6.94e-01 1.17e+02 angle pdb=" C3' G B 15 " pdb=" O3' G B 15 " pdb=" P G B 16 " ideal model delta sigma weight residual 119.70 107.35 12.35 1.20e+00 6.94e-01 1.06e+02 angle pdb=" C3' U B 17 " pdb=" O3' U B 17 " pdb=" P G B 18 " ideal model delta sigma weight residual 119.70 107.45 12.25 1.20e+00 6.94e-01 1.04e+02 angle pdb=" C3' A C 5 " pdb=" O3' A C 5 " pdb=" P C C 6 " ideal model delta sigma weight residual 119.70 109.93 9.77 1.20e+00 6.94e-01 6.63e+01 ... (remaining 5637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 2323 33.83 - 67.65: 123 67.65 - 101.48: 19 101.48 - 135.30: 1 135.30 - 169.13: 1 Dihedral angle restraints: 2467 sinusoidal: 1329 harmonic: 1138 Sorted by residual: dihedral pdb=" O4' C C 6 " pdb=" C1' C C 6 " pdb=" N1 C C 6 " pdb=" C2 C C 6 " ideal model delta sinusoidal sigma weight residual 200.00 30.87 169.13 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" CD ARG A 438 " pdb=" NE ARG A 438 " pdb=" CZ ARG A 438 " pdb=" NH1 ARG A 438 " ideal model delta sinusoidal sigma weight residual 0.00 71.48 -71.48 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CA ARG A 795 " pdb=" C ARG A 795 " pdb=" N SER A 796 " pdb=" CA SER A 796 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 2464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 552 0.110 - 0.220: 99 0.220 - 0.330: 5 0.330 - 0.440: 7 0.440 - 0.550: 2 Chirality restraints: 665 Sorted by residual: chirality pdb=" P C C 4 " pdb=" OP1 C C 4 " pdb=" OP2 C C 4 " pdb=" O5' C C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 2.95 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" P G B 15 " pdb=" OP1 G B 15 " pdb=" OP2 G B 15 " pdb=" O5' G B 15 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 662 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 8 " -0.175 2.00e-02 2.50e+03 7.23e-02 1.44e+02 pdb=" N9 A C 8 " 0.039 2.00e-02 2.50e+03 pdb=" C8 A C 8 " 0.060 2.00e-02 2.50e+03 pdb=" N7 A C 8 " 0.036 2.00e-02 2.50e+03 pdb=" C5 A C 8 " 0.031 2.00e-02 2.50e+03 pdb=" C6 A C 8 " -0.026 2.00e-02 2.50e+03 pdb=" N6 A C 8 " -0.102 2.00e-02 2.50e+03 pdb=" N1 A C 8 " -0.016 2.00e-02 2.50e+03 pdb=" C2 A C 8 " 0.030 2.00e-02 2.50e+03 pdb=" N3 A C 8 " 0.063 2.00e-02 2.50e+03 pdb=" C4 A C 8 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 438 " -1.045 9.50e-02 1.11e+02 4.68e-01 1.32e+02 pdb=" NE ARG A 438 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 438 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 438 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 438 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 11 " -0.110 2.00e-02 2.50e+03 6.53e-02 1.28e+02 pdb=" N9 G C 11 " 0.011 2.00e-02 2.50e+03 pdb=" C8 G C 11 " 0.116 2.00e-02 2.50e+03 pdb=" N7 G C 11 " 0.065 2.00e-02 2.50e+03 pdb=" C5 G C 11 " -0.016 2.00e-02 2.50e+03 pdb=" C6 G C 11 " -0.052 2.00e-02 2.50e+03 pdb=" O6 G C 11 " -0.053 2.00e-02 2.50e+03 pdb=" N1 G C 11 " -0.024 2.00e-02 2.50e+03 pdb=" C2 G C 11 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G C 11 " 0.117 2.00e-02 2.50e+03 pdb=" N3 G C 11 " -0.031 2.00e-02 2.50e+03 pdb=" C4 G C 11 " -0.017 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 885 2.82 - 3.34: 3444 3.34 - 3.86: 6682 3.86 - 4.38: 8017 4.38 - 4.90: 12963 Nonbonded interactions: 31991 Sorted by model distance: nonbonded pdb=" NE2 GLN A 632 " pdb=" O ILE A 638 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASP A 597 " pdb=" N VAL A 598 " model vdw 2.466 3.120 nonbonded pdb=" O4' C C 6 " pdb=" O2 C C 6 " model vdw 2.502 3.040 nonbonded pdb=" O5' A C 5 " pdb=" O4' A C 5 " model vdw 2.516 2.432 nonbonded pdb=" O5' G B 9 " pdb=" O4' G B 9 " model vdw 2.538 2.432 ... (remaining 31986 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.490 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.009 0.042 4037 Z= 0.635 Angle : 1.503 14.538 5642 Z= 1.133 Chirality : 0.087 0.550 665 Planarity : 0.023 0.468 589 Dihedral : 18.856 169.126 1729 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.30 % Allowed : 8.88 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.41), residues: 378 helix: -0.10 (0.41), residues: 146 sheet: -0.84 (0.49), residues: 93 loop : -0.90 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 688 TYR 0.104 0.016 TYR A 512 PHE 0.057 0.011 PHE A 491 TRP 0.032 0.014 TRP A 451 HIS 0.008 0.002 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.64 ( 4037) covalent geometry : angle 1.50348 / 1.13 ( 5642) hydrogen bonds : bond 0.19287 / 12.96 ( 177) hydrogen bonds : angle 7.12041 / 5.12 ( 478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.151 Fit side-chains REVERT: A 476 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7505 (ttpt) REVERT: A 509 LYS cc_start: 0.7732 (ttpt) cc_final: 0.7359 (tttp) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.5988 time to fit residues: 41.8000 Evaluate side-chains 43 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.180345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154063 restraints weight = 4077.975| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.55 r_work: 0.3604 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4037 Z= 0.168 Angle : 0.627 5.751 5642 Z= 0.338 Chirality : 0.045 0.275 665 Planarity : 0.006 0.082 589 Dihedral : 18.451 177.680 978 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.25 % Allowed : 13.31 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.42), residues: 378 helix: 0.70 (0.42), residues: 152 sheet: -0.54 (0.50), residues: 98 loop : -0.54 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 792 TYR 0.015 0.002 TYR A 698 PHE 0.023 0.002 PHE A 491 TRP 0.010 0.002 TRP A 451 HIS 0.008 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 4037) covalent geometry : angle 0.62748 / 0.34 ( 5642) hydrogen bonds : bond 0.06214 / 4.26 ( 177) hydrogen bonds : angle 4.98544 / 3.67 ( 478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 850 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6817 (mp10) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.4623 time to fit residues: 23.8712 Evaluate side-chains 47 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN A 652 GLN A 772 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.153776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125269 restraints weight = 4024.652| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.61 r_work: 0.3236 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4037 Z= 0.191 Angle : 0.642 5.900 5642 Z= 0.344 Chirality : 0.048 0.303 665 Planarity : 0.005 0.049 589 Dihedral : 18.479 179.347 978 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.14 % Allowed : 15.38 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.42), residues: 378 helix: 0.82 (0.42), residues: 150 sheet: -0.47 (0.50), residues: 98 loop : -0.39 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 668 TYR 0.017 0.003 TYR A 790 PHE 0.020 0.003 PHE A 491 TRP 0.015 0.003 TRP A 451 HIS 0.005 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 4037) covalent geometry : angle 0.64201 / 0.34 ( 5642) hydrogen bonds : bond 0.06527 / 4.48 ( 177) hydrogen bonds : angle 4.54330 / 3.32 ( 478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7679 (tttp) REVERT: A 850 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6900 (mm-40) outliers start: 14 outliers final: 5 residues processed: 51 average time/residue: 0.5295 time to fit residues: 27.7950 Evaluate side-chains 47 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123582 restraints weight = 4068.889| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.59 r_work: 0.3250 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4037 Z= 0.149 Angle : 0.530 6.333 5642 Z= 0.281 Chirality : 0.042 0.263 665 Planarity : 0.005 0.051 589 Dihedral : 18.510 179.000 978 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.14 % Allowed : 18.05 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.43), residues: 378 helix: 1.09 (0.42), residues: 151 sheet: -0.43 (0.52), residues: 99 loop : -0.42 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 438 TYR 0.012 0.001 TYR A 790 PHE 0.020 0.002 PHE A 491 TRP 0.011 0.001 TRP A 451 HIS 0.004 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 4037) covalent geometry : angle 0.53021 / 0.28 ( 5642) hydrogen bonds : bond 0.05112 / 3.49 ( 177) hydrogen bonds : angle 4.36332 / 3.21 ( 478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.096 Fit side-chains REVERT: A 509 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7674 (tttp) REVERT: A 746 PHE cc_start: 0.7059 (t80) cc_final: 0.6723 (t80) REVERT: A 850 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6988 (mp10) outliers start: 14 outliers final: 5 residues processed: 52 average time/residue: 0.5177 time to fit residues: 27.8059 Evaluate side-chains 44 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122818 restraints weight = 4051.099| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.56 r_work: 0.3227 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4037 Z= 0.137 Angle : 0.528 6.319 5642 Z= 0.278 Chirality : 0.042 0.252 665 Planarity : 0.005 0.050 589 Dihedral : 18.499 178.171 978 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.55 % Allowed : 20.12 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.43), residues: 378 helix: 1.28 (0.42), residues: 150 sheet: -0.59 (0.51), residues: 100 loop : -0.43 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 506 TYR 0.017 0.001 TYR A 654 PHE 0.011 0.002 PHE A 491 TRP 0.011 0.001 TRP A 451 HIS 0.003 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4037) covalent geometry : angle 0.52824 / 0.28 ( 5642) hydrogen bonds : bond 0.04932 / 3.38 ( 177) hydrogen bonds : angle 4.30280 / 3.18 ( 478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.077 Fit side-chains REVERT: A 473 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: A 509 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7693 (ttmp) REVERT: A 804 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: A 850 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7007 (mp10) outliers start: 12 outliers final: 5 residues processed: 44 average time/residue: 0.6078 time to fit residues: 27.4901 Evaluate side-chains 46 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.150316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122689 restraints weight = 4102.918| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.58 r_work: 0.3255 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4037 Z= 0.119 Angle : 0.506 6.044 5642 Z= 0.265 Chirality : 0.041 0.222 665 Planarity : 0.004 0.049 589 Dihedral : 18.470 177.330 978 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.55 % Allowed : 21.01 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.43), residues: 378 helix: 1.47 (0.42), residues: 150 sheet: -0.56 (0.52), residues: 96 loop : -0.33 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 688 TYR 0.010 0.001 TYR A 790 PHE 0.012 0.001 PHE A 491 TRP 0.009 0.001 TRP A 451 HIS 0.002 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4037) covalent geometry : angle 0.50555 / 0.26 ( 5642) hydrogen bonds : bond 0.04339 / 2.98 ( 177) hydrogen bonds : angle 4.22268 / 3.12 ( 478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 509 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7707 (tttp) REVERT: A 804 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: A 850 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7036 (mp10) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.6015 time to fit residues: 26.6473 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.0030 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123900 restraints weight = 4089.785| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.60 r_work: 0.3268 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4037 Z= 0.105 Angle : 0.497 7.108 5642 Z= 0.259 Chirality : 0.039 0.204 665 Planarity : 0.004 0.047 589 Dihedral : 18.441 176.690 978 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.66 % Allowed : 21.89 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.43), residues: 378 helix: 1.62 (0.42), residues: 150 sheet: -0.48 (0.52), residues: 96 loop : -0.45 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 688 TYR 0.010 0.001 TYR A 790 PHE 0.012 0.001 PHE A 491 TRP 0.008 0.001 TRP A 451 HIS 0.002 0.000 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 4037) covalent geometry : angle 0.49730 / 0.26 ( 5642) hydrogen bonds : bond 0.04023 / 2.78 ( 177) hydrogen bonds : angle 4.09060 / 3.03 ( 478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 804 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: A 850 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7066 (mp10) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.5257 time to fit residues: 23.9047 Evaluate side-chains 48 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 850 GLN Chi-restraints excluded: chain A residue 853 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124225 restraints weight = 4060.394| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.57 r_work: 0.3243 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4037 Z= 0.101 Angle : 0.479 5.781 5642 Z= 0.251 Chirality : 0.039 0.188 665 Planarity : 0.004 0.046 589 Dihedral : 18.375 175.807 978 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.25 % Allowed : 21.89 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.43), residues: 378 helix: 1.70 (0.42), residues: 150 sheet: -0.44 (0.52), residues: 96 loop : -0.41 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 688 TYR 0.009 0.001 TYR A 790 PHE 0.011 0.001 PHE A 491 TRP 0.008 0.001 TRP A 451 HIS 0.002 0.000 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 4037) covalent geometry : angle 0.47855 / 0.25 ( 5642) hydrogen bonds : bond 0.03784 / 2.62 ( 177) hydrogen bonds : angle 4.00978 / 2.98 ( 478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 804 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: A 850 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7109 (mp10) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.5140 time to fit residues: 23.3919 Evaluate side-chains 48 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 17 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119796 restraints weight = 4107.052| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.42 r_work: 0.3238 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4037 Z= 0.115 Angle : 0.498 5.906 5642 Z= 0.261 Chirality : 0.040 0.170 665 Planarity : 0.004 0.046 589 Dihedral : 18.329 175.596 978 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.66 % Allowed : 22.19 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.43), residues: 378 helix: 1.69 (0.42), residues: 150 sheet: -0.25 (0.53), residues: 91 loop : -0.62 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 668 TYR 0.022 0.001 TYR A 857 PHE 0.012 0.001 PHE A 491 TRP 0.009 0.001 TRP A 451 HIS 0.002 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 4037) covalent geometry : angle 0.49777 / 0.26 ( 5642) hydrogen bonds : bond 0.04030 / 2.80 ( 177) hydrogen bonds : angle 4.01557 / 2.98 ( 478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 804 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: A 850 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7122 (mp10) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.5029 time to fit residues: 21.2333 Evaluate side-chains 41 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116984 restraints weight = 4125.004| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.41 r_work: 0.3181 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4037 Z= 0.137 Angle : 0.519 6.096 5642 Z= 0.273 Chirality : 0.041 0.136 665 Planarity : 0.004 0.047 589 Dihedral : 18.299 175.752 978 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.85 % Allowed : 21.30 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.43), residues: 378 helix: 1.60 (0.41), residues: 150 sheet: -0.29 (0.53), residues: 91 loop : -0.60 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 668 TYR 0.021 0.001 TYR A 857 PHE 0.014 0.001 PHE A 491 TRP 0.010 0.001 TRP A 451 HIS 0.002 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4037) covalent geometry : angle 0.51864 / 0.27 ( 5642) hydrogen bonds : bond 0.04535 / 3.14 ( 177) hydrogen bonds : angle 4.07124 / 3.03 ( 478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.129 Fit side-chains REVERT: A 473 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: A 804 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: A 850 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7131 (mp10) outliers start: 13 outliers final: 6 residues processed: 40 average time/residue: 0.5928 time to fit residues: 24.4363 Evaluate side-chains 43 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.0030 chunk 35 optimal weight: 0.6980 overall best weight: 0.3308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120214 restraints weight = 4114.593| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.41 r_work: 0.3267 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4037 Z= 0.099 Angle : 0.480 5.635 5642 Z= 0.253 Chirality : 0.038 0.133 665 Planarity : 0.004 0.046 589 Dihedral : 18.278 174.754 978 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.37 % Allowed : 22.49 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.43), residues: 378 helix: 1.78 (0.42), residues: 150 sheet: -0.35 (0.53), residues: 91 loop : -0.54 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 814 TYR 0.019 0.001 TYR A 857 PHE 0.011 0.001 PHE A 491 TRP 0.007 0.001 TRP A 451 HIS 0.002 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 4037) covalent geometry : angle 0.48031 / 0.25 ( 5642) hydrogen bonds : bond 0.03865 / 2.70 ( 177) hydrogen bonds : angle 3.98151 / 2.95 ( 478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1264.47 seconds wall clock time: 22 minutes 15.41 seconds (1335.41 seconds total)