Starting phenix.real_space_refine on Tue Aug 4 18:19:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e2a_27830/08_2026/8e2a_27830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2a_27830/08_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_27830/08_2026/8e2a_27830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2a_27830/08_2026/8e2a_27830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e2a_27830/08_2026/8e2a_27830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2a_27830/08_2026/8e2a_27830.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e2a_27830/08_2026/8e2a_27830.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e2a_27830/08_2026/8e2a_27830.cif" } 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-2.2rc3-6140/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: {'RNAv2': 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: 1.28, per 1000 atoms: 0.22 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: 0.50 Conformation dependent library (CDL) restraints added in 269.9 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: 1.23 Time building geometry restraints manager: 0.58 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: 7744 1.62 - 3.24: 265 3.24 - 4.86: 53 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: 3296 17.71 - 35.42: 240 35.42 - 53.13: 38 53.13 - 70.83: 13 70.83 - 88.54: 8 Dihedral angle restraints: 3595 sinusoidal: 1583 harmonic: 2012 Sorted by residual: dihedral pdb=" C4' U B 17 " pdb=" C3' U B 17 " pdb=" C2' U B 17 " pdb=" C1' U B 17 " ideal model delta sinusoidal sigma weight residual 36.34 -36.02 72.36 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" O4' U B 17 " pdb=" C4' U B 17 " pdb=" C3' U B 17 " pdb=" C2' U B 17 " ideal model delta sinusoidal sigma weight residual -35.15 24.79 -59.94 1 4.00e+00 6.25e-02 2.99e+02 dihedral pdb=" O4' U B 17 " pdb=" C2' U B 17 " pdb=" C1' U B 17 " pdb=" C3' U B 17 " ideal model delta sinusoidal sigma weight residual -94.41 -35.75 -58.66 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 747 0.062 - 0.124: 145 0.124 - 0.186: 14 0.186 - 0.248: 14 0.248 - 0.310: 3 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=" C2' U B 17 " pdb=" C3' U B 17 " pdb=" O2' U B 17 " pdb=" C1' U B 17 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' U B 17 " pdb=" C4' U B 17 " pdb=" O3' U B 17 " pdb=" C2' U B 17 " both_signs ideal model delta sigma weight residual False -2.50 -2.75 0.25 2.00e-01 2.50e+01 1.61e+00 ... (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: 1.890 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- 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= 0.186 Angle : 0.737 8.103 8074 Z= 0.384 Chirality : 0.057 0.310 923 Planarity : 0.005 0.048 990 Dihedral : 13.357 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 0.00431 / 0.19 ( 5918) covalent geometry : angle 0.73680 / 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 : 0.211 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: 0.6410 time to fit residues: 61.7233 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 : 0.168 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.155758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113572 restraints weight = 6313.752| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.33 r_work: 0.3266 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1124 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= 0.134 Angle : 0.651 14.146 8074 Z= 0.304 Chirality : 0.053 0.695 923 Planarity : 0.004 0.039 990 Dihedral : 7.544 60.404 917 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.49 % Allowed : 8.62 % Favored : 89.88 % 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: 1.68 (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 0.000 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 0.003 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5918) covalent geometry : angle 0.65100 / 0.30 ( 8074) hydrogen bonds : bond 0.04318 / 3.07 ( 250) hydrogen bonds : angle 4.25124 / 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 : 0.138 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.7491 (tt0) cc_final: 0.7145 (mt0) REVERT: A 681 GLN cc_start: 0.7453 (mm110) cc_final: 0.7209 (mm110) REVERT: A 841 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6900 (mt-10) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.5383 time to fit residues: 36.0201 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 : 0.211 ------------------------------------------------------------------------------- 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: 0.5980 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.156831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114632 restraints weight = 6280.539| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.32 r_work: 0.3282 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1502 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= 0.106 Angle : 0.560 8.390 8074 Z= 0.266 Chirality : 0.045 0.178 923 Planarity : 0.004 0.037 990 Dihedral : 7.217 60.795 917 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.33 % Allowed : 9.95 % 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: 0.40 (0.32), residues: 680 helix: 1.92 (0.37), residues: 211 sheet: 0.32 (0.38), residues: 170 loop : -0.99 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 803 TYR 0.009 0.001 TYR A 674 PHE 0.011 0.001 PHE A 757 TRP 0.012 0.001 TRP A 468 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 5918) covalent geometry : angle 0.55963 / 0.27 ( 8074) hydrogen bonds : bond 0.03831 / 2.73 ( 250) hydrogen bonds : angle 3.94205 / 2.83 ( 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 64 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.6758 (tpp) cc_final: 0.6426 (tpt) REVERT: A 318 GLN cc_start: 0.7463 (tt0) cc_final: 0.7113 (mt0) REVERT: A 523 GLU cc_start: 0.7387 (mp0) cc_final: 0.6563 (mm-30) REVERT: A 841 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6868 (mt-10) outliers start: 8 outliers final: 3 residues processed: 60 average time/residue: 0.6014 time to fit residues: 37.6412 Evaluate side-chains 53 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 9.9990 chunk 15 optimal weight: 0.0980 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 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 = 0.3840 r_free = 0.3840 target = 0.156649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114208 restraints weight = 6256.944| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.32 r_work: 0.3278 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1684 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= 0.107 Angle : 0.549 7.354 8074 Z= 0.262 Chirality : 0.045 0.189 923 Planarity : 0.004 0.034 990 Dihedral : 7.143 58.984 917 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.16 % Allowed : 11.44 % Favored : 87.40 % 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: 0.44 (0.32), residues: 680 helix: 1.89 (0.37), residues: 217 sheet: 0.36 (0.38), residues: 170 loop : -0.98 (0.35), 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 0.001 PHE A 757 TRP 0.012 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 5918) covalent geometry : angle 0.54862 / 0.26 ( 8074) hydrogen bonds : bond 0.03793 / 2.71 ( 250) hydrogen bonds : angle 3.85226 / 2.78 ( 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 62 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.208 Fit side-chains REVERT: A 54 MET cc_start: 0.6738 (tpp) cc_final: 0.6402 (tpt) REVERT: A 523 GLU cc_start: 0.7396 (mp0) cc_final: 0.6555 (mm-30) REVERT: A 681 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7575 (mm110) REVERT: A 780 GLN cc_start: 0.7592 (mt0) cc_final: 0.7360 (mt0) REVERT: A 841 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6882 (mt-10) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.5032 time to fit residues: 31.0576 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 : 0.128 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.154945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112196 restraints weight = 6382.580| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.34 r_work: 0.3250 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1739 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= 0.123 Angle : 0.562 6.851 8074 Z= 0.269 Chirality : 0.045 0.183 923 Planarity : 0.004 0.036 990 Dihedral : 7.148 58.697 917 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.33 % Allowed : 11.94 % Favored : 86.73 % 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: 0.54 (0.32), residues: 680 helix: 2.07 (0.37), residues: 211 sheet: 0.47 (0.38), residues: 168 loop : -0.97 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.012 0.001 PHE A 757 TRP 0.012 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 5918) covalent geometry : angle 0.56159 / 0.27 ( 8074) hydrogen bonds : bond 0.04107 / 2.92 ( 250) hydrogen bonds : angle 3.92018 / 2.83 ( 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 63 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.6764 (tpp) cc_final: 0.6400 (tpt) REVERT: A 523 GLU cc_start: 0.7419 (mp0) cc_final: 0.6587 (mm-30) REVERT: A 681 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7691 (mm110) REVERT: A 764 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7303 (tt0) REVERT: A 841 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6872 (mt-10) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.5805 time to fit residues: 35.6514 Evaluate side-chains 58 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 835 THR 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: 3.9990 chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.156304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113554 restraints weight = 6320.911| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.32 r_work: 0.3268 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5918 Z= 0.104 Angle : 0.554 10.274 8074 Z= 0.265 Chirality : 0.045 0.179 923 Planarity : 0.004 0.032 990 Dihedral : 7.133 58.673 917 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.53 (0.33), residues: 680 helix: 1.97 (0.37), residues: 217 sheet: 0.40 (0.38), residues: 170 loop : -0.93 (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 0.012 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 5918) covalent geometry : angle 0.55351 / 0.27 ( 8074) hydrogen bonds : bond 0.03745 / 2.67 ( 250) hydrogen bonds : angle 3.83389 / 2.78 ( 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 65 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.6743 (tpp) cc_final: 0.6368 (tpt) REVERT: A 318 GLN cc_start: 0.7458 (tt0) cc_final: 0.7102 (mt0) REVERT: A 523 GLU cc_start: 0.7406 (mp0) cc_final: 0.6577 (mm-30) REVERT: A 681 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7737 (mm110) REVERT: A 841 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6849 (mt-10) outliers start: 8 outliers final: 3 residues processed: 62 average time/residue: 0.4825 time to fit residues: 31.2595 Evaluate side-chains 57 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 0.0070 chunk 45 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN A 614 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113448 restraints weight = 6321.953| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.32 r_work: 0.3268 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5918 Z= 0.110 Angle : 0.552 9.307 8074 Z= 0.265 Chirality : 0.044 0.181 923 Planarity : 0.004 0.033 990 Dihedral : 7.092 58.291 917 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.16 % Allowed : 12.77 % 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: 0.56 (0.33), residues: 680 helix: 2.00 (0.37), residues: 217 sheet: 0.43 (0.39), residues: 170 loop : -0.91 (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 0.012 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 5918) covalent geometry : angle 0.55241 / 0.26 ( 8074) hydrogen bonds : bond 0.03755 / 2.68 ( 250) hydrogen bonds : angle 3.81283 / 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 64 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.134 Fit side-chains REVERT: A 54 MET cc_start: 0.6772 (tpp) cc_final: 0.6381 (tpt) REVERT: A 318 GLN cc_start: 0.7463 (tt0) cc_final: 0.7112 (mt0) REVERT: A 523 GLU cc_start: 0.7395 (mp0) cc_final: 0.6565 (mm-30) REVERT: A 681 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7734 (mm110) REVERT: A 841 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6857 (mt-10) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.5578 time to fit residues: 36.0758 Evaluate side-chains 55 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.0040 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.157088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114382 restraints weight = 6272.309| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.32 r_work: 0.3278 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2027 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= 0.102 Angle : 0.543 10.219 8074 Z= 0.260 Chirality : 0.044 0.184 923 Planarity : 0.004 0.032 990 Dihedral : 7.070 58.211 917 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.00 % Allowed : 13.60 % Favored : 85.41 % 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: 2.09 (0.37), residues: 217 sheet: 0.42 (0.39), residues: 170 loop : -0.86 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 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 0.002 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 5918) covalent geometry : angle 0.54313 / 0.26 ( 8074) hydrogen bonds : bond 0.03604 / 2.57 ( 250) hydrogen bonds : angle 3.77407 / 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 59 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.172 Fit side-chains REVERT: A 54 MET cc_start: 0.6778 (tpp) cc_final: 0.6378 (tpt) REVERT: A 80 PHE cc_start: 0.7918 (m-80) cc_final: 0.7715 (m-80) REVERT: A 318 GLN cc_start: 0.7460 (tt0) cc_final: 0.7121 (mt0) REVERT: A 523 GLU cc_start: 0.7380 (mp0) cc_final: 0.6541 (mm-30) REVERT: A 681 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7751 (mm110) REVERT: A 841 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6877 (mt-10) outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 0.5572 time to fit residues: 33.2303 Evaluate side-chains 54 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.157195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114223 restraints weight = 6287.334| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.33 r_work: 0.3284 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2079 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 : 0.547 10.895 8074 Z= 0.262 Chirality : 0.044 0.182 923 Planarity : 0.004 0.032 990 Dihedral : 7.042 57.681 917 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.00 % Allowed : 13.60 % Favored : 85.41 % 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: 0.67 (0.33), residues: 680 helix: 2.10 (0.37), residues: 217 sheet: 0.42 (0.39), residues: 170 loop : -0.81 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 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 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 5918) covalent geometry : angle 0.54718 / 0.26 ( 8074) hydrogen bonds : bond 0.03624 / 2.58 ( 250) hydrogen bonds : angle 3.77957 / 2.75 ( 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 60 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.221 Fit side-chains REVERT: A 54 MET cc_start: 0.6709 (tpp) cc_final: 0.6296 (tpt) REVERT: A 318 GLN cc_start: 0.7465 (tt0) cc_final: 0.7119 (mt0) REVERT: A 507 LYS cc_start: 0.7389 (mppt) cc_final: 0.6745 (tttt) REVERT: A 523 GLU cc_start: 0.7353 (mp0) cc_final: 0.6549 (mm-30) REVERT: A 681 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7746 (mm110) REVERT: A 841 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6896 (mt-10) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.5380 time to fit residues: 32.6391 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 : 0.184 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.4980 chunk 68 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.152010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108854 restraints weight = 6400.622| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.34 r_work: 0.3205 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5918 Z= 0.205 Angle : 0.658 11.318 8074 Z= 0.313 Chirality : 0.048 0.208 923 Planarity : 0.005 0.042 990 Dihedral : 7.149 55.613 917 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.16 % Allowed : 13.43 % Favored : 85.41 % 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: 0.29 (0.32), residues: 680 helix: 1.64 (0.36), residues: 217 sheet: 0.38 (0.38), residues: 170 loop : -1.03 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 543 TYR 0.010 0.001 TYR A 575 PHE 0.014 0.002 PHE A 544 TRP 0.010 0.002 TRP A 468 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.20 ( 5918) covalent geometry : angle 0.65829 / 0.31 ( 8074) hydrogen bonds : bond 0.05002 / 3.52 ( 250) hydrogen bonds : angle 4.14025 / 3.00 ( 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 59 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.225 Fit side-chains REVERT: A 80 PHE cc_start: 0.7944 (m-80) cc_final: 0.7715 (m-80) REVERT: A 318 GLN cc_start: 0.7534 (tt0) cc_final: 0.7179 (mt0) REVERT: A 507 LYS cc_start: 0.7472 (mppt) cc_final: 0.6819 (tttt) REVERT: A 523 GLU cc_start: 0.7418 (mp0) cc_final: 0.6715 (mm-30) REVERT: A 681 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7736 (mm110) REVERT: A 841 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6891 (mt-10) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.6085 time to fit residues: 35.4698 Evaluate side-chains 55 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.156052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113323 restraints weight = 6216.449| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.31 r_work: 0.3268 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5918 Z= 0.104 Angle : 0.574 12.621 8074 Z= 0.269 Chirality : 0.045 0.180 923 Planarity : 0.004 0.034 990 Dihedral : 7.065 57.048 917 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.66 % Allowed : 14.26 % Favored : 85.07 % 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: 0.53 (0.33), residues: 680 helix: 1.96 (0.37), residues: 217 sheet: 0.38 (0.38), residues: 170 loop : -0.90 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 803 TYR 0.008 0.001 TYR A 674 PHE 0.009 0.001 PHE A 80 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 0.00235 / 0.10 ( 5918) covalent geometry : angle 0.57359 / 0.27 ( 8074) hydrogen bonds : bond 0.03751 / 2.67 ( 250) hydrogen bonds : angle 3.88184 / 2.82 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.96 seconds wall clock time: 37 minutes 1.57 seconds (2221.57 seconds total)