Starting phenix.real_space_refine on Tue Aug 4 19:22:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11gi_75677/08_2026/11gi_75677.cif Found real_map, /net/cci-nas-00/data/ceres_data/11gi_75677/08_2026/11gi_75677.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/11gi_75677/08_2026/11gi_75677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11gi_75677/08_2026/11gi_75677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11gi_75677/08_2026/11gi_75677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11gi_75677/08_2026/11gi_75677.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= 0.034 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 40 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 3857 2.51 5 N 1134 2.21 5 O 1252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 6318 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5464 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 640} Chain breaks: 4 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 433 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 17} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 418 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 2, 'rna3p': 18} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.11, per 1000 atoms: 0.18 Number of scatterers: 6318 At special positions: 0 Unit cell: (75.48, 81.4, 111, 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 34 16.00 P 40 15.00 Mg 1 11.99 O 1252 8.00 N 1134 7.00 C 3857 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 237.4 milliseconds 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1288 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 36.8% alpha, 19.9% beta 18 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 155 through 168 removed outlier: 3.842A pdb=" N ILE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 357 through 368 Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.534A pdb=" N PHE A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.502A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 4.349A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.631A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.640A 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: 3.897A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 removed outlier: 3.503A pdb=" N MET A 645 " --> pdb=" O ASP A 641 " (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: 3.790A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 800 through 817 removed outlier: 3.856A pdb=" N TYR A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 817 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.208A 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: 3.557A pdb=" N SER A 610 " --> pdb=" O GLN A 632 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL A 598 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 706 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 767 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLN A 708 " --> pdb=" O TYR A 765 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR A 765 " --> pdb=" O GLN A 708 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 734 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 406 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 408 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.570A pdb=" N THR A 183 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 200 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.023A pdb=" N GLU A 58 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TRP A 134 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP A 60 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A 132 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.905A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 518 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL A 547 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 520 " --> pdb=" O VAL A 547 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 0.78 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: 1.21 - 1.33: 1604 1.33 - 1.45: 1387 1.45 - 1.57: 3419 1.57 - 1.69: 81 1.69 - 1.80: 53 Bond restraints: 6544 Sorted by residual: bond pdb=" CE1 HIS A 712 " pdb=" NE2 HIS A 712 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" CE1 HIS A 711 " pdb=" NE2 HIS A 711 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.11e+01 bond pdb=" CB PRO A 105 " pdb=" CG PRO A 105 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.67e+00 bond pdb=" N GLN A 708 " pdb=" CA GLN A 708 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.44e+00 bond pdb=" N VAL A 707 " pdb=" CA VAL A 707 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.24e-02 6.50e+03 5.26e+00 ... (remaining 6539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 8811 2.04 - 4.09: 224 4.09 - 6.13: 13 6.13 - 8.18: 2 8.18 - 10.22: 1 Bond angle restraints: 9051 Sorted by residual: angle pdb=" CA PRO A 105 " pdb=" N PRO A 105 " pdb=" CD PRO A 105 " ideal model delta sigma weight residual 112.00 101.78 10.22 1.40e+00 5.10e-01 5.33e+01 angle pdb=" CA PRO A 176 " pdb=" N PRO A 176 " pdb=" CD PRO A 176 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.81e+01 angle pdb=" O5' C B 11 " pdb=" C5' C B 11 " pdb=" C4' C B 11 " ideal model delta sigma weight residual 109.40 112.62 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" N GLY A 670 " pdb=" CA GLY A 670 " pdb=" C GLY A 670 " ideal model delta sigma weight residual 111.36 115.73 -4.37 1.17e+00 7.31e-01 1.40e+01 angle pdb=" O5' A C 21 " pdb=" C5' A C 21 " pdb=" C4' A C 21 " ideal model delta sigma weight residual 109.40 112.30 -2.90 8.00e-01 1.56e+00 1.31e+01 ... (remaining 9046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 3437 16.06 - 32.12: 341 32.12 - 48.18: 130 48.18 - 64.24: 79 64.24 - 80.30: 14 Dihedral angle restraints: 4001 sinusoidal: 2012 harmonic: 1989 Sorted by residual: dihedral pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" N PRO A 63 " pdb=" CA PRO A 63 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CG ARG A 475 " pdb=" CD ARG A 475 " pdb=" NE ARG A 475 " pdb=" CZ ARG A 475 " ideal model delta sinusoidal sigma weight residual -180.00 -138.10 -41.90 2 1.50e+01 4.44e-03 9.51e+00 dihedral pdb=" CB MET A 364 " pdb=" CG MET A 364 " pdb=" SD MET A 364 " pdb=" CE MET A 364 " ideal model delta sinusoidal sigma weight residual -60.00 -0.03 -59.97 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 705 0.038 - 0.077: 189 0.077 - 0.115: 86 0.115 - 0.154: 51 0.154 - 0.192: 3 Chirality restraints: 1034 Sorted by residual: chirality pdb=" C1' G B 5 " pdb=" O4' G B 5 " pdb=" C2' G B 5 " pdb=" N9 G B 5 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA LYS A 709 " pdb=" N LYS A 709 " pdb=" C LYS A 709 " pdb=" CB LYS A 709 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA VAL A 707 " pdb=" N VAL A 707 " pdb=" C VAL A 707 " pdb=" CB VAL A 707 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1031 not shown) Planarity restraints: 1021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 104 " 0.093 5.00e-02 4.00e+02 1.34e-01 2.85e+01 pdb=" N PRO A 105 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " 0.333 9.50e-02 1.11e+02 1.49e-01 1.37e+01 pdb=" NE ARG A 710 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 62 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 63 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " 0.039 5.00e-02 4.00e+02 ... (remaining 1018 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 14 2.45 - 3.07: 3796 3.07 - 3.68: 9322 3.68 - 4.29: 14772 4.29 - 4.90: 24185 Nonbonded interactions: 52089 Sorted by model distance: nonbonded pdb=" OD2 ASP A 597 " pdb="MG MG A 901 " model vdw 1.843 2.170 nonbonded pdb=" OP1 U C 12 " pdb="MG MG A 901 " model vdw 2.062 2.170 nonbonded pdb=" ND1 HIS A 807 " pdb="MG MG A 901 " model vdw 2.075 2.250 nonbonded pdb=" O PRO A 661 " pdb=" OH TYR A 698 " model vdw 2.167 3.040 nonbonded pdb=" NH1 ARG A 90 " pdb=" O PRO A 105 " model vdw 2.289 3.120 ... (remaining 52084 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: 1.530 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.330 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.420 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: 0.8958 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 0.119 6544 Z= 0.231 Angle : 0.679 10.225 9051 Z= 0.450 Chirality : 0.051 0.192 1034 Planarity : 0.008 0.149 1021 Dihedral : 17.097 80.305 2713 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.32), residues: 674 helix: 1.40 (0.36), residues: 220 sheet: -0.43 (0.38), residues: 165 loop : -0.80 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 395 TYR 0.012 0.001 TYR A 790 PHE 0.009 0.001 PHE A 704 TRP 0.010 0.001 TRP A 435 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.23 ( 6544) covalent geometry : angle 0.67895 / 0.45 ( 9051) hydrogen bonds : bond 0.16299 / 11.45 ( 288) hydrogen bonds : angle 6.38890 / 4.63 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.142 Fit side-chains REVERT: A 133 LYS cc_start: 0.7957 (tttt) cc_final: 0.7208 (tttp) REVERT: A 395 ARG cc_start: 0.7689 (mmp80) cc_final: 0.7266 (mtm-85) REVERT: A 554 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7360 (ttm110) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.5193 time to fit residues: 47.1229 Evaluate side-chains 75 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.131191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102608 restraints weight = 7058.054| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.70 r_work: 0.2997 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6544 Z= 0.156 Angle : 0.539 4.985 9051 Z= 0.294 Chirality : 0.043 0.161 1034 Planarity : 0.006 0.076 1021 Dihedral : 15.222 74.070 1359 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 13.90 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.32), residues: 674 helix: 1.51 (0.35), residues: 222 sheet: -0.47 (0.37), residues: 172 loop : -0.79 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.013 0.001 TYR A 55 PHE 0.016 0.001 PHE A 704 TRP 0.010 0.001 TRP A 435 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6544) covalent geometry : angle 0.53855 / 0.29 ( 9051) hydrogen bonds : bond 0.05099 / 3.42 ( 288) hydrogen bonds : angle 5.08690 / 3.69 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.237 Fit side-chains REVERT: A 395 ARG cc_start: 0.7777 (mmp80) cc_final: 0.7577 (mmm-85) REVERT: A 554 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6991 (ttm110) REVERT: A 677 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8215 (mm110) outliers start: 13 outliers final: 5 residues processed: 85 average time/residue: 0.4901 time to fit residues: 43.6958 Evaluate side-chains 78 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.125085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.096178 restraints weight = 7122.353| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.75 r_work: 0.2791 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6544 Z= 0.182 Angle : 0.547 5.003 9051 Z= 0.296 Chirality : 0.044 0.166 1034 Planarity : 0.005 0.061 1021 Dihedral : 15.116 74.263 1359 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.35 % Allowed : 15.24 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.33), residues: 674 helix: 1.52 (0.35), residues: 223 sheet: -0.45 (0.38), residues: 172 loop : -0.83 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.013 0.001 TYR A 55 PHE 0.017 0.002 PHE A 704 TRP 0.010 0.001 TRP A 435 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 6544) covalent geometry : angle 0.54663 / 0.30 ( 9051) hydrogen bonds : bond 0.05036 / 3.33 ( 288) hydrogen bonds : angle 4.79557 / 3.47 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.224 Fit side-chains REVERT: A 133 LYS cc_start: 0.7879 (tttt) cc_final: 0.6972 (tttp) REVERT: A 395 ARG cc_start: 0.7774 (mmp80) cc_final: 0.7434 (mmm-85) REVERT: A 396 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: A 400 MET cc_start: 0.8513 (mmm) cc_final: 0.8132 (tpt) REVERT: A 447 GLU cc_start: 0.8518 (tt0) cc_final: 0.8147 (tm-30) REVERT: A 554 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7049 (ttm110) REVERT: A 677 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8193 (mm110) outliers start: 14 outliers final: 5 residues processed: 82 average time/residue: 0.5407 time to fit residues: 46.3727 Evaluate side-chains 78 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.0370 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097186 restraints weight = 7163.987| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.77 r_work: 0.2972 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6544 Z= 0.116 Angle : 0.478 4.912 9051 Z= 0.260 Chirality : 0.041 0.156 1034 Planarity : 0.005 0.050 1021 Dihedral : 15.121 73.925 1359 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.01 % Allowed : 16.08 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.33), residues: 674 helix: 1.71 (0.36), residues: 222 sheet: -0.48 (0.38), residues: 172 loop : -0.75 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.009 0.001 TYR A 749 PHE 0.011 0.001 PHE A 704 TRP 0.010 0.001 TRP A 435 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6544) covalent geometry : angle 0.47813 / 0.26 ( 9051) hydrogen bonds : bond 0.04099 / 2.71 ( 288) hydrogen bonds : angle 4.56057 / 3.33 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.270 Fit side-chains REVERT: A 51 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7194 (mmmt) REVERT: A 400 MET cc_start: 0.8478 (mmm) cc_final: 0.8199 (tpt) REVERT: A 464 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6762 (mp0) REVERT: A 554 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6904 (ttm110) REVERT: A 658 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7456 (mtp85) REVERT: A 677 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8159 (mm110) outliers start: 12 outliers final: 3 residues processed: 82 average time/residue: 0.5348 time to fit residues: 45.8387 Evaluate side-chains 75 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108385 restraints weight = 6954.079| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.63 r_work: 0.2939 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6544 Z= 0.127 Angle : 0.482 4.942 9051 Z= 0.261 Chirality : 0.041 0.155 1034 Planarity : 0.005 0.043 1021 Dihedral : 15.082 74.007 1359 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 17.09 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.17 (0.33), residues: 674 helix: 1.73 (0.35), residues: 222 sheet: -0.52 (0.38), residues: 172 loop : -0.72 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 630 TYR 0.008 0.001 TYR A 749 PHE 0.013 0.001 PHE A 704 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6544) covalent geometry : angle 0.48178 / 0.26 ( 9051) hydrogen bonds : bond 0.04099 / 2.71 ( 288) hydrogen bonds : angle 4.49784 / 3.28 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.138 Fit side-chains REVERT: A 396 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7733 (tp30) REVERT: A 400 MET cc_start: 0.8468 (mmm) cc_final: 0.8190 (tpt) REVERT: A 464 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6866 (mp0) REVERT: A 554 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7035 (ttm110) REVERT: A 658 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7594 (mtp85) REVERT: A 677 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8122 (mm110) outliers start: 10 outliers final: 5 residues processed: 81 average time/residue: 0.4860 time to fit residues: 41.1809 Evaluate side-chains 75 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8304 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.125135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095750 restraints weight = 7154.236| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.73 r_work: 0.2754 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6544 Z= 0.189 Angle : 0.538 4.995 9051 Z= 0.288 Chirality : 0.044 0.162 1034 Planarity : 0.005 0.038 1021 Dihedral : 15.030 74.280 1359 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.51 % Allowed : 16.75 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.08 (0.33), residues: 674 helix: 1.61 (0.35), residues: 223 sheet: -0.52 (0.38), residues: 172 loop : -0.78 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 534 TYR 0.009 0.001 TYR A 749 PHE 0.017 0.002 PHE A 704 TRP 0.010 0.001 TRP A 435 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 6544) covalent geometry : angle 0.53759 / 0.29 ( 9051) hydrogen bonds : bond 0.04731 / 3.10 ( 288) hydrogen bonds : angle 4.58388 / 3.33 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.131 Fit side-chains REVERT: A 51 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7126 (mmmt) REVERT: A 355 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8069 (ttpt) REVERT: A 396 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: A 400 MET cc_start: 0.8441 (mmm) cc_final: 0.8206 (tpt) REVERT: A 554 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7023 (ttm110) REVERT: A 658 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7585 (mtp85) REVERT: A 677 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8126 (mm110) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.4693 time to fit residues: 42.6865 Evaluate side-chains 81 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.129116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099874 restraints weight = 7060.096| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.71 r_work: 0.2800 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6544 Z= 0.124 Angle : 0.482 4.949 9051 Z= 0.262 Chirality : 0.041 0.157 1034 Planarity : 0.005 0.039 1021 Dihedral : 15.053 73.966 1359 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.68 % Allowed : 18.09 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.20 (0.33), residues: 674 helix: 1.78 (0.36), residues: 222 sheet: -0.54 (0.38), residues: 172 loop : -0.69 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.008 0.001 TYR A 749 PHE 0.012 0.001 PHE A 704 TRP 0.011 0.001 TRP A 435 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 6544) covalent geometry : angle 0.48247 / 0.26 ( 9051) hydrogen bonds : bond 0.04086 / 2.69 ( 288) hydrogen bonds : angle 4.48951 / 3.28 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.132 Fit side-chains REVERT: A 51 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7137 (mmmt) REVERT: A 396 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: A 400 MET cc_start: 0.8407 (mmm) cc_final: 0.8137 (tpt) REVERT: A 464 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6790 (mp0) REVERT: A 554 ARG cc_start: 0.7898 (mtm110) cc_final: 0.6987 (ttm110) REVERT: A 658 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7545 (mtp85) REVERT: A 677 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8100 (mm110) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.5424 time to fit residues: 45.8427 Evaluate side-chains 79 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 679 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.124882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.096298 restraints weight = 7171.980| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.74 r_work: 0.2894 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6544 Z= 0.249 Angle : 0.597 5.174 9051 Z= 0.318 Chirality : 0.048 0.165 1034 Planarity : 0.006 0.039 1021 Dihedral : 15.008 74.505 1359 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.35 % Allowed : 17.92 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.01 (0.33), residues: 674 helix: 1.45 (0.35), residues: 224 sheet: -0.42 (0.38), residues: 166 loop : -0.85 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.011 0.002 TYR A 512 PHE 0.018 0.002 PHE A 704 TRP 0.009 0.001 TRP A 435 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.25 ( 6544) covalent geometry : angle 0.59717 / 0.32 ( 9051) hydrogen bonds : bond 0.05348 / 3.50 ( 288) hydrogen bonds : angle 4.68792 / 3.39 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.209 Fit side-chains REVERT: A 51 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7183 (mmmt) REVERT: A 355 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8093 (ttpt) REVERT: A 396 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: A 400 MET cc_start: 0.8404 (mmm) cc_final: 0.8149 (tpt) REVERT: A 542 MET cc_start: 0.8744 (ptt) cc_final: 0.8317 (ptm) REVERT: A 658 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7493 (mtp85) REVERT: A 677 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8182 (mm110) REVERT: A 697 ASP cc_start: 0.8626 (p0) cc_final: 0.8151 (m-30) outliers start: 14 outliers final: 7 residues processed: 83 average time/residue: 0.5252 time to fit residues: 45.5655 Evaluate side-chains 79 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.128410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098888 restraints weight = 7171.608| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.79 r_work: 0.2986 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6544 Z= 0.116 Angle : 0.484 4.954 9051 Z= 0.262 Chirality : 0.041 0.153 1034 Planarity : 0.004 0.038 1021 Dihedral : 15.015 73.922 1359 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.68 % Allowed : 18.26 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.20 (0.33), residues: 674 helix: 1.75 (0.36), residues: 223 sheet: -0.52 (0.38), residues: 172 loop : -0.70 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.008 0.001 TYR A 749 PHE 0.012 0.001 PHE A 704 TRP 0.012 0.001 TRP A 435 HIS 0.003 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6544) covalent geometry : angle 0.48360 / 0.26 ( 9051) hydrogen bonds : bond 0.04001 / 2.64 ( 288) hydrogen bonds : angle 4.50724 / 3.29 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.215 Fit side-chains REVERT: A 51 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7152 (mmmt) REVERT: A 355 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: A 396 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: A 400 MET cc_start: 0.8407 (mmm) cc_final: 0.8164 (tpt) REVERT: A 464 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6776 (mp0) REVERT: A 554 ARG cc_start: 0.7859 (mtm110) cc_final: 0.6923 (ttm110) REVERT: A 658 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7513 (mtp85) REVERT: A 677 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8138 (mm110) REVERT: A 697 ASP cc_start: 0.8604 (p0) cc_final: 0.8205 (m-30) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.5532 time to fit residues: 48.7092 Evaluate side-chains 81 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.128147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.098678 restraints weight = 7046.085| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.77 r_work: 0.2956 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6544 Z= 0.128 Angle : 0.489 5.032 9051 Z= 0.262 Chirality : 0.041 0.156 1034 Planarity : 0.005 0.037 1021 Dihedral : 14.782 74.016 1359 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.51 % Allowed : 18.93 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.33), residues: 674 helix: 1.73 (0.36), residues: 223 sheet: -0.49 (0.38), residues: 172 loop : -0.67 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 72 TYR 0.008 0.001 TYR A 749 PHE 0.012 0.001 PHE A 704 TRP 0.011 0.001 TRP A 435 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6544) covalent geometry : angle 0.48929 / 0.26 ( 9051) hydrogen bonds : bond 0.04047 / 2.67 ( 288) hydrogen bonds : angle 4.47731 / 3.26 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.180 Fit side-chains REVERT: A 51 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7137 (mmmt) REVERT: A 133 LYS cc_start: 0.7769 (ptmm) cc_final: 0.7563 (ptmt) REVERT: A 355 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8094 (ttpt) REVERT: A 396 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: A 400 MET cc_start: 0.8387 (mmm) cc_final: 0.8151 (tpt) REVERT: A 554 ARG cc_start: 0.7772 (mtm110) cc_final: 0.6854 (ttm110) REVERT: A 658 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7520 (mtp85) REVERT: A 677 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8128 (mm110) REVERT: A 697 ASP cc_start: 0.8595 (p0) cc_final: 0.8219 (m-30) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.6198 time to fit residues: 51.0922 Evaluate side-chains 80 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 8 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.127934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098284 restraints weight = 7135.681| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.78 r_work: 0.2983 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6544 Z= 0.107 Angle : 0.469 4.944 9051 Z= 0.252 Chirality : 0.040 0.151 1034 Planarity : 0.004 0.036 1021 Dihedral : 14.708 73.897 1359 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.68 % Allowed : 18.59 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.31 (0.33), residues: 674 helix: 1.86 (0.36), residues: 222 sheet: -0.49 (0.38), residues: 172 loop : -0.61 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.008 0.001 TYR A 749 PHE 0.011 0.001 PHE A 704 TRP 0.010 0.001 TRP A 435 HIS 0.003 0.000 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6544) covalent geometry : angle 0.46866 / 0.25 ( 9051) hydrogen bonds : bond 0.03691 / 2.46 ( 288) hydrogen bonds : angle 4.40553 / 3.23 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.90 seconds wall clock time: 29 minutes 19.36 seconds (1759.36 seconds total)