Starting phenix.real_space_refine on Thu Jul 2 02:30:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2a_27830/07_2026/8e2a_27830.map" } resolution = 2.8 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= 0.021 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 31 5.16 5 C 3621 2.51 5 N 985 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5768 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5456 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 40, 'TRANS': 645} Chain breaks: 2 Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain breaks: 1 Time building chain proxies: 1.35, per 1000 atoms: 0.23 Number of scatterers: 5768 At special positions: 0 Unit cell: (70.35, 84.42, 109.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 15 15.00 O 1116 8.00 N 985 7.00 C 3621 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: 0.49 Conformation dependent library (CDL) restraints added in 201.4 milliseconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 9 sheets defined 32.9% alpha, 22.9% beta 4 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.730A pdb=" N ALA A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.664A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix removed outlier: 3.712A pdb=" N TYR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.587A pdb=" N GLN A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 500 " --> pdb=" O HIS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.666A pdb=" N ALA A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 601 removed outlier: 3.671A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 3.775A pdb=" N LEU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 651 through 666 removed outlier: 3.800A pdb=" N LEU A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.519A pdb=" N PHE A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.817A pdb=" N VAL A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 766 removed outlier: 3.646A pdb=" N THR A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.335A pdb=" N LEU A 110 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE A 238 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 112 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.954A pdb=" N GLY A 569 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLN A 568 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 302 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 4.012A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 383 removed outlier: 6.157A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA8, first strand: chain 'A' and resid 791 through 796 removed outlier: 3.636A pdb=" N VAL A 791 " --> pdb=" O VAL A 786 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP A 783 " --> pdb=" O MET A 775 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 802 through 810 238 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1662 1.33 - 1.45: 928 1.45 - 1.57: 3253 1.57 - 1.69: 28 1.69 - 1.81: 47 Bond restraints: 5918 Sorted by residual: bond pdb=" C ARG A 616 " pdb=" O ARG A 616 " ideal model delta sigma weight residual 1.235 1.217 0.019 1.26e-02 6.30e+03 2.16e+00 bond pdb=" C LEU A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.40e+00 bond pdb=" CA GLY A 811 " pdb=" C GLY A 811 " ideal model delta sigma weight residual 1.514 1.530 -0.015 1.41e-02 5.03e+03 1.21e+00 bond pdb=" CG LEU A 423 " pdb=" CD1 LEU A 423 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" C ARG A 616 " pdb=" N MET A 617 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.35e-02 5.49e+03 1.10e+00 ... (remaining 5913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 7782 1.62 - 3.24: 234 3.24 - 4.86: 46 4.86 - 6.48: 8 6.48 - 8.10: 4 Bond angle restraints: 8074 Sorted by residual: angle pdb=" C LYS A 812 " pdb=" N LYS A 813 " pdb=" CA LYS A 813 " ideal model delta sigma weight residual 121.61 126.86 -5.25 1.39e+00 5.18e-01 1.43e+01 angle pdb=" N MET A 617 " pdb=" CA MET A 617 " pdb=" C MET A 617 " ideal model delta sigma weight residual 112.38 116.17 -3.79 1.22e+00 6.72e-01 9.65e+00 angle pdb=" C ARG A 616 " pdb=" CA ARG A 616 " pdb=" CB ARG A 616 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.59e+00 angle pdb=" C THR A 615 " pdb=" N ARG A 616 " pdb=" CA ARG A 616 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" N SER A 848 " pdb=" CA SER A 848 " pdb=" C SER A 848 " ideal model delta sigma weight residual 111.02 114.01 -2.99 1.22e+00 6.72e-01 5.99e+00 ... (remaining 8069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3314 17.71 - 35.42: 234 35.42 - 53.13: 32 53.13 - 70.83: 8 70.83 - 88.54: 7 Dihedral angle restraints: 3595 sinusoidal: 1583 harmonic: 2012 Sorted by residual: dihedral pdb=" CA ASP A 824 " pdb=" C ASP A 824 " pdb=" N MET A 825 " pdb=" CA MET A 825 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU A 673 " pdb=" C LEU A 673 " pdb=" N TYR A 674 " pdb=" CA TYR A 674 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE A 699 " pdb=" C PHE A 699 " pdb=" N THR A 700 " pdb=" CA THR A 700 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 764 0.062 - 0.124: 145 0.124 - 0.186: 13 0.186 - 0.248: 0 0.248 - 0.310: 1 Chirality restraints: 923 Sorted by residual: chirality pdb=" CG LEU A 618 " pdb=" CB LEU A 618 " pdb=" CD1 LEU A 618 " pdb=" CD2 LEU A 618 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ARG A 616 " pdb=" N ARG A 616 " pdb=" C ARG A 616 " pdb=" CB ARG A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA HIS A 409 " pdb=" N HIS A 409 " pdb=" C HIS A 409 " pdb=" CB HIS A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 920 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 610 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 611 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 634 " 0.013 2.00e-02 2.50e+03 1.09e-02 2.09e+00 pdb=" CG PHE A 634 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 634 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 634 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 634 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 634 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 634 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 648 " 0.007 2.00e-02 2.50e+03 1.07e-02 2.00e+00 pdb=" CG PHE A 648 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 648 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 648 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 648 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 648 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 648 " -0.000 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 226 2.72 - 3.26: 5283 3.26 - 3.81: 8564 3.81 - 4.35: 11167 4.35 - 4.90: 19247 Nonbonded interactions: 44487 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.173 3.040 nonbonded pdb=" OD1 ASP A 651 " pdb=" N LYS A 652 " model vdw 2.182 3.120 nonbonded pdb=" ND1 HIS A 409 " pdb=" OG SER A 465 " model vdw 2.249 3.120 nonbonded pdb=" OD2 ASP A 307 " pdb=" NZ LYS A 309 " model vdw 2.283 3.120 nonbonded pdb=" OD2 ASP A 412 " pdb=" NH1 ARG A 483 " model vdw 2.314 3.120 ... (remaining 44482 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: 1.740 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.000 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:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5918 Z= 0.185 Angle : 0.709 8.103 8074 Z= 0.379 Chirality : 0.047 0.310 923 Planarity : 0.005 0.048 990 Dihedral : 12.664 88.543 2285 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.31), residues: 680 helix: 1.18 (0.36), residues: 208 sheet: 0.34 (0.38), residues: 161 loop : -1.32 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 74 TYR 0.018 0.002 TYR A 853 PHE 0.025 0.002 PHE A 634 TRP 0.016 0.002 TRP A 468 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 5918) covalent geometry : angle 0.70874 / 0.38 ( 8074) hydrogen bonds : bond 0.10103 / 6.84 ( 250) hydrogen bonds : angle 5.39520 / 3.84 ( 687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.201 Fit side-chains REVERT: A 54 MET cc_start: 0.6703 (tpt) cc_final: 0.6386 (tpp) REVERT: A 74 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6557 (ttp-110) REVERT: A 242 LYS cc_start: 0.7942 (mttt) cc_final: 0.7730 (mmtm) REVERT: A 318 GLN cc_start: 0.7127 (tt0) cc_final: 0.6890 (mt0) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.6789 time to fit residues: 65.3535 Evaluate side-chains 55 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN A 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112886 restraints weight = 6304.300| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.37 r_work: 0.3234 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5918 Z= 0.123 Angle : 0.575 9.916 8074 Z= 0.288 Chirality : 0.042 0.140 923 Planarity : 0.004 0.040 990 Dihedral : 5.780 45.935 917 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.49 % Allowed : 8.46 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.32), residues: 680 helix: 1.66 (0.37), residues: 209 sheet: 0.25 (0.38), residues: 170 loop : -1.11 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 803 TYR 0.010 0.001 TYR A 674 PHE 0.014 0.002 PHE A 648 TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 5918) covalent geometry : angle 0.57527 / 0.29 ( 8074) hydrogen bonds : bond 0.04307 / 3.06 ( 250) hydrogen bonds : angle 4.25610 / 3.04 ( 687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.7416 (tt0) cc_final: 0.7068 (mt0) REVERT: A 681 GLN cc_start: 0.7390 (mm110) cc_final: 0.7142 (mm110) REVERT: A 841 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6894 (mt-10) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.5820 time to fit residues: 38.9358 Evaluate side-chains 58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112185 restraints weight = 6253.335| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.37 r_work: 0.3223 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5918 Z= 0.118 Angle : 0.540 8.451 8074 Z= 0.269 Chirality : 0.042 0.137 923 Planarity : 0.004 0.040 990 Dihedral : 5.659 45.491 917 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.16 % Allowed : 10.12 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.32), residues: 680 helix: 1.99 (0.37), residues: 205 sheet: 0.34 (0.38), residues: 170 loop : -1.02 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 803 TYR 0.009 0.001 TYR A 674 PHE 0.012 0.001 PHE A 757 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5918) covalent geometry : angle 0.53965 / 0.27 ( 8074) hydrogen bonds : bond 0.04090 / 2.91 ( 250) hydrogen bonds : angle 4.02702 / 2.89 ( 687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.6784 (tpp) cc_final: 0.6455 (tpt) REVERT: A 318 GLN cc_start: 0.7427 (tt0) cc_final: 0.7061 (mt0) REVERT: A 523 GLU cc_start: 0.7345 (mp0) cc_final: 0.6539 (mm-30) REVERT: A 841 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6868 (mt-10) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.6577 time to fit residues: 41.0120 Evaluate side-chains 56 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 20.0000 chunk 15 optimal weight: 0.0170 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.156000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113164 restraints weight = 6228.858| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.37 r_work: 0.3241 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5918 Z= 0.101 Angle : 0.503 7.548 8074 Z= 0.253 Chirality : 0.041 0.135 923 Planarity : 0.004 0.035 990 Dihedral : 5.601 45.770 917 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.33 % Allowed : 11.11 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.32), residues: 680 helix: 2.22 (0.37), residues: 205 sheet: 0.36 (0.38), residues: 170 loop : -0.91 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.010 0.001 PHE A 757 TRP 0.012 0.001 TRP A 468 HIS 0.002 0.000 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 5918) covalent geometry : angle 0.50346 / 0.25 ( 8074) hydrogen bonds : bond 0.03736 / 2.68 ( 250) hydrogen bonds : angle 3.85605 / 2.77 ( 687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.6735 (tpp) cc_final: 0.6407 (tpt) REVERT: A 318 GLN cc_start: 0.7405 (tt0) cc_final: 0.7056 (mt0) REVERT: A 523 GLU cc_start: 0.7332 (mp0) cc_final: 0.6491 (mm-30) REVERT: A 681 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7560 (mm110) REVERT: A 780 GLN cc_start: 0.7567 (mt0) cc_final: 0.7349 (mt0) REVERT: A 841 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6859 (mt-10) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.5996 time to fit residues: 38.7415 Evaluate side-chains 57 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.157371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114312 restraints weight = 6341.168| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.41 r_work: 0.3266 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5918 Z= 0.091 Angle : 0.474 6.784 8074 Z= 0.240 Chirality : 0.040 0.133 923 Planarity : 0.004 0.031 990 Dihedral : 5.603 46.363 917 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.33 % Allowed : 11.61 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.32), residues: 680 helix: 2.40 (0.37), residues: 205 sheet: 0.43 (0.38), residues: 170 loop : -0.77 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 608 TYR 0.008 0.001 TYR A 674 PHE 0.009 0.001 PHE A 757 TRP 0.012 0.001 TRP A 468 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 5918) covalent geometry : angle 0.47434 / 0.24 ( 8074) hydrogen bonds : bond 0.03445 / 2.47 ( 250) hydrogen bonds : angle 3.70820 / 2.68 ( 687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.6724 (tpp) cc_final: 0.6356 (tpt) REVERT: A 318 GLN cc_start: 0.7362 (tt0) cc_final: 0.6997 (mt0) REVERT: A 523 GLU cc_start: 0.7344 (mp0) cc_final: 0.6479 (mm-30) REVERT: A 780 GLN cc_start: 0.7560 (mt0) cc_final: 0.7341 (mt0) REVERT: A 841 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6830 (mt-10) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.6062 time to fit residues: 39.9936 Evaluate side-chains 59 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN A 614 GLN A 681 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108722 restraints weight = 6352.620| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.38 r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5918 Z= 0.191 Angle : 0.605 9.615 8074 Z= 0.300 Chirality : 0.044 0.144 923 Planarity : 0.005 0.041 990 Dihedral : 5.828 46.369 917 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.82 % Allowed : 11.77 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.32), residues: 680 helix: 1.97 (0.37), residues: 205 sheet: 0.41 (0.39), residues: 170 loop : -0.99 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 803 TYR 0.009 0.001 TYR A 575 PHE 0.013 0.002 PHE A 782 TRP 0.012 0.002 TRP A 468 HIS 0.003 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 ( 5918) covalent geometry : angle 0.60462 / 0.30 ( 8074) hydrogen bonds : bond 0.04859 / 3.43 ( 250) hydrogen bonds : angle 4.08850 / 2.95 ( 687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.236 Fit side-chains REVERT: A 54 MET cc_start: 0.6796 (tpp) cc_final: 0.6414 (tpt) REVERT: A 80 PHE cc_start: 0.7930 (m-80) cc_final: 0.7712 (m-80) REVERT: A 318 GLN cc_start: 0.7462 (tt0) cc_final: 0.7111 (mt0) REVERT: A 523 GLU cc_start: 0.7407 (mp0) cc_final: 0.6620 (mm-30) REVERT: A 681 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7623 (mm110) REVERT: A 764 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7343 (tt0) REVERT: A 780 GLN cc_start: 0.7540 (mt0) cc_final: 0.7318 (mt0) REVERT: A 841 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6865 (mt-10) outliers start: 11 outliers final: 6 residues processed: 58 average time/residue: 0.6670 time to fit residues: 40.3196 Evaluate side-chains 59 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.0070 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.155532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112177 restraints weight = 6289.960| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.38 r_work: 0.3223 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5918 Z= 0.100 Angle : 0.508 9.251 8074 Z= 0.255 Chirality : 0.040 0.136 923 Planarity : 0.004 0.034 990 Dihedral : 5.709 45.777 917 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.00 % Allowed : 12.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.33), residues: 680 helix: 2.16 (0.37), residues: 211 sheet: 0.46 (0.39), residues: 170 loop : -0.89 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.010 0.001 PHE A 757 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 5918) covalent geometry : angle 0.50803 / 0.26 ( 8074) hydrogen bonds : bond 0.03721 / 2.67 ( 250) hydrogen bonds : angle 3.81842 / 2.77 ( 687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.231 Fit side-chains REVERT: A 54 MET cc_start: 0.6766 (tpp) cc_final: 0.6363 (tpt) REVERT: A 523 GLU cc_start: 0.7357 (mp0) cc_final: 0.6509 (mm-30) REVERT: A 681 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7608 (mm110) REVERT: A 764 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7247 (tt0) REVERT: A 780 GLN cc_start: 0.7558 (mt0) cc_final: 0.7311 (mt0) REVERT: A 841 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6855 (mt-10) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.6398 time to fit residues: 38.7300 Evaluate side-chains 57 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.155688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112345 restraints weight = 6257.059| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.38 r_work: 0.3229 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5918 Z= 0.103 Angle : 0.505 9.901 8074 Z= 0.253 Chirality : 0.040 0.135 923 Planarity : 0.004 0.033 990 Dihedral : 5.654 46.218 917 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.33 % Allowed : 13.43 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.33), residues: 680 helix: 2.02 (0.37), residues: 217 sheet: 0.48 (0.39), residues: 170 loop : -0.89 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.010 0.001 PHE A 757 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 5918) covalent geometry : angle 0.50519 / 0.25 ( 8074) hydrogen bonds : bond 0.03716 / 2.66 ( 250) hydrogen bonds : angle 3.77308 / 2.74 ( 687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.213 Fit side-chains REVERT: A 54 MET cc_start: 0.6759 (tpp) cc_final: 0.6362 (tpt) REVERT: A 523 GLU cc_start: 0.7351 (mp0) cc_final: 0.6515 (mm-30) REVERT: A 681 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7629 (mm110) REVERT: A 780 GLN cc_start: 0.7538 (mt0) cc_final: 0.7320 (mm110) REVERT: A 841 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6845 (mt-10) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.5378 time to fit residues: 34.2844 Evaluate side-chains 58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.0000 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.5804 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.156647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113490 restraints weight = 6283.210| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.38 r_work: 0.3247 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5918 Z= 0.097 Angle : 0.501 10.991 8074 Z= 0.251 Chirality : 0.040 0.134 923 Planarity : 0.004 0.032 990 Dihedral : 5.629 46.406 917 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.00 % Allowed : 13.76 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.33), residues: 680 helix: 2.11 (0.37), residues: 217 sheet: 0.47 (0.39), residues: 170 loop : -0.83 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.010 0.001 PHE A 782 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 5918) covalent geometry : angle 0.50082 / 0.25 ( 8074) hydrogen bonds : bond 0.03554 / 2.54 ( 250) hydrogen bonds : angle 3.73914 / 2.71 ( 687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.224 Fit side-chains REVERT: A 54 MET cc_start: 0.6700 (tpp) cc_final: 0.6286 (tpt) REVERT: A 80 PHE cc_start: 0.7856 (m-80) cc_final: 0.7641 (m-80) REVERT: A 318 GLN cc_start: 0.7374 (tt0) cc_final: 0.7012 (mt0) REVERT: A 507 LYS cc_start: 0.7381 (mppt) cc_final: 0.6738 (tttt) REVERT: A 523 GLU cc_start: 0.7356 (mp0) cc_final: 0.6521 (mm-30) REVERT: A 681 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7651 (mm110) REVERT: A 780 GLN cc_start: 0.7535 (mt0) cc_final: 0.7330 (mm110) REVERT: A 841 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6839 (mt-10) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.6949 time to fit residues: 42.7440 Evaluate side-chains 59 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109809 restraints weight = 6374.559| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.41 r_work: 0.3201 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5918 Z= 0.144 Angle : 0.552 11.619 8074 Z= 0.273 Chirality : 0.042 0.139 923 Planarity : 0.004 0.038 990 Dihedral : 5.764 46.429 917 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.00 % Allowed : 14.10 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.33), residues: 680 helix: 1.90 (0.37), residues: 217 sheet: 0.44 (0.39), residues: 170 loop : -0.94 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.011 0.002 PHE A 757 TRP 0.012 0.001 TRP A 468 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 5918) covalent geometry : angle 0.55213 / 0.27 ( 8074) hydrogen bonds : bond 0.04347 / 3.08 ( 250) hydrogen bonds : angle 3.94316 / 2.86 ( 687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.225 Fit side-chains REVERT: A 54 MET cc_start: 0.6804 (tpp) cc_final: 0.6392 (tpt) REVERT: A 80 PHE cc_start: 0.7891 (m-80) cc_final: 0.7667 (m-80) REVERT: A 507 LYS cc_start: 0.7429 (mppt) cc_final: 0.6784 (tttt) REVERT: A 523 GLU cc_start: 0.7390 (mp0) cc_final: 0.6614 (mm-30) REVERT: A 681 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7658 (mm110) REVERT: A 780 GLN cc_start: 0.7529 (mt0) cc_final: 0.7322 (mm110) REVERT: A 841 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6843 (mt-10) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.6571 time to fit residues: 40.4134 Evaluate side-chains 59 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 841 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.155485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112371 restraints weight = 6224.418| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.36 r_work: 0.3230 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5918 Z= 0.105 Angle : 0.531 11.714 8074 Z= 0.265 Chirality : 0.040 0.135 923 Planarity : 0.004 0.035 990 Dihedral : 5.708 46.134 917 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.83 % Allowed : 14.43 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.33), residues: 680 helix: 2.03 (0.37), residues: 217 sheet: 0.49 (0.39), residues: 170 loop : -0.84 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.010 0.001 PHE A 757 TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 5918) covalent geometry : angle 0.53104 / 0.27 ( 8074) hydrogen bonds : bond 0.03753 / 2.68 ( 250) hydrogen bonds : angle 3.82858 / 2.78 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.88 seconds wall clock time: 43 minutes 31.66 seconds (2611.66 seconds total)