Starting phenix.real_space_refine on Thu Jul 2 03:40:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e29_27829/07_2026/8e29_27829.map" } resolution = 3.1 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= 0.018 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 33 5.49 5 S 31 5.16 5 C 3821 2.51 5 N 1053 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 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: 6197 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5511 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 41, 'TRANS': 650} Chain breaks: 2 Chain: "B" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 686 Classifications: {'RNA': 33} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 18} Link IDs: {'rna2p': 5, 'rna3p': 27} Time building chain proxies: 1.42, per 1000 atoms: 0.23 Number of scatterers: 6197 At special positions: 0 Unit cell: (77.05, 87.1, 105.19, 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 33 15.00 O 1259 8.00 N 1053 7.00 C 3821 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 320.2 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 30.8% alpha, 23.6% beta 8 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.734A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.538A pdb=" N ARG A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.645A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.795A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.759A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.709A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.166A pdb=" N PHE A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 765 removed outlier: 3.586A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.096A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 114 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL A 235 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP A 97 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL A 235 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 252 removed outlier: 6.791A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.822A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.365A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.459A pdb=" N ALA A 557 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N CYS A 570 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 559 " --> pdb=" O GLN A 568 " (cutoff:3.500A) 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 792 through 796 removed outlier: 7.095A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.666A 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 810 235 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1300 1.33 - 1.45: 1510 1.45 - 1.57: 3468 1.57 - 1.69: 65 1.69 - 1.81: 47 Bond restraints: 6390 Sorted by residual: bond pdb=" CG LEU A 691 " pdb=" CD1 LEU A 691 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.91e+00 bond pdb=" CG LEU A 691 " pdb=" CD2 LEU A 691 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.77e+00 bond pdb=" CB TRP A 468 " pdb=" CG TRP A 468 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.69e+00 bond pdb=" CA SER A 465 " pdb=" CB SER A 465 " ideal model delta sigma weight residual 1.536 1.476 0.060 2.53e-02 1.56e+03 5.60e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 ... (remaining 6385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8116 1.87 - 3.75: 546 3.75 - 5.62: 105 5.62 - 7.50: 21 7.50 - 9.37: 10 Bond angle restraints: 8798 Sorted by residual: angle pdb=" N ARG A 104 " pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " ideal model delta sigma weight residual 111.84 106.31 5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" N HIS A 688 " pdb=" CA HIS A 688 " pdb=" C HIS A 688 " ideal model delta sigma weight residual 109.46 103.34 6.12 1.66e+00 3.63e-01 1.36e+01 angle pdb=" CA GLU A 512 " pdb=" CB GLU A 512 " pdb=" CG GLU A 512 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" C CYS A 449 " pdb=" N GLU A 450 " pdb=" CA GLU A 450 " ideal model delta sigma weight residual 122.60 117.02 5.58 1.56e+00 4.11e-01 1.28e+01 angle pdb=" N SER A 701 " pdb=" CA SER A 701 " pdb=" C SER A 701 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 ... (remaining 8793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 3507 21.48 - 42.96: 285 42.96 - 64.43: 52 64.43 - 85.91: 7 85.91 - 107.39: 2 Dihedral angle restraints: 3853 sinusoidal: 1823 harmonic: 2030 Sorted by residual: dihedral pdb=" O4' U B 30 " pdb=" C1' U B 30 " pdb=" N1 U B 30 " pdb=" C2 U B 30 " ideal model delta sinusoidal sigma weight residual -160.00 -105.96 -54.04 1 1.50e+01 4.44e-03 1.76e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 3850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 672 0.060 - 0.119: 248 0.119 - 0.179: 86 0.179 - 0.238: 11 0.238 - 0.298: 3 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CB VAL A 113 " pdb=" CA VAL A 113 " pdb=" CG1 VAL A 113 " pdb=" CG2 VAL A 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU A 560 " pdb=" CB LEU A 560 " pdb=" CD1 LEU A 560 " pdb=" CD2 LEU A 560 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1017 not shown) Planarity restraints: 1019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 708 " 0.025 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" CG ASP A 708 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASP A 708 " 0.030 2.00e-02 2.50e+03 pdb=" OD2 ASP A 708 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 743 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ARG A 743 " -0.059 2.00e-02 2.50e+03 pdb=" O ARG A 743 " 0.022 2.00e-02 2.50e+03 pdb=" N MET A 744 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 583 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLU A 583 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 583 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 584 " -0.019 2.00e-02 2.50e+03 ... (remaining 1016 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1796 2.82 - 3.34: 4911 3.34 - 3.86: 9644 3.86 - 4.38: 10585 4.38 - 4.90: 19143 Nonbonded interactions: 46079 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.305 3.040 nonbonded pdb=" O THR A 835 " pdb=" OG SER A 838 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR A 653 " pdb=" O PHE A 837 " model vdw 2.311 3.040 nonbonded pdb=" O THR A 386 " pdb=" OG1 THR A 386 " model vdw 2.329 3.040 nonbonded pdb=" NH1 ARG A 388 " pdb=" OE2 GLU A 450 " model vdw 2.372 3.120 ... (remaining 46074 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: 2.740 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.520 Find NCS groups from input model: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.012 0.101 6390 Z= 0.501 Angle : 1.137 9.374 8798 Z= 0.630 Chirality : 0.069 0.298 1020 Planarity : 0.008 0.058 1019 Dihedral : 15.448 107.388 2531 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.66 % Allowed : 6.90 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.29), residues: 686 helix: -1.02 (0.32), residues: 205 sheet: 0.18 (0.41), residues: 155 loop : -1.61 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 104 TYR 0.028 0.005 TYR A 853 PHE 0.049 0.004 PHE A 699 TRP 0.024 0.005 TRP A 468 HIS 0.017 0.002 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.01231 / 0.50 ( 6390) covalent geometry : angle 1.13719 / 0.63 ( 8798) hydrogen bonds : bond 0.16817 / 11.17 ( 258) hydrogen bonds : angle 6.09197 / 4.09 ( 715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.240 Fit side-chains REVERT: A 424 ASP cc_start: 0.8112 (t70) cc_final: 0.7877 (t0) REVERT: A 726 ASP cc_start: 0.7801 (p0) cc_final: 0.7515 (t0) REVERT: A 851 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7078 (mp) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.0807 time to fit residues: 7.8143 Evaluate side-chains 57 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126496 restraints weight = 6509.998| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.75 r_work: 0.3429 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6390 Z= 0.115 Angle : 0.576 7.834 8798 Z= 0.294 Chirality : 0.040 0.137 1020 Planarity : 0.005 0.040 1019 Dihedral : 11.646 108.245 1151 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.82 % Allowed : 11.66 % Favored : 87.52 % 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: -0.52 (0.31), residues: 686 helix: 0.65 (0.36), residues: 214 sheet: 0.35 (0.40), residues: 168 loop : -1.47 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 803 TYR 0.011 0.001 TYR A 653 PHE 0.015 0.001 PHE A 699 TRP 0.016 0.001 TRP A 468 HIS 0.002 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6390) covalent geometry : angle 0.57577 / 0.29 ( 8798) hydrogen bonds : bond 0.05246 / 3.40 ( 258) hydrogen bonds : angle 4.56754 / 3.17 ( 715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.133 Fit side-chains REVERT: A 58 ASP cc_start: 0.8003 (t70) cc_final: 0.7746 (t0) REVERT: A 726 ASP cc_start: 0.8249 (p0) cc_final: 0.7828 (t0) REVERT: A 803 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7479 (ttp-110) REVERT: A 851 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6856 (mp) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 0.0646 time to fit residues: 5.8635 Evaluate side-chains 59 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.173969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118062 restraints weight = 6392.086| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.97 r_work: 0.3297 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6390 Z= 0.156 Angle : 0.564 6.996 8798 Z= 0.288 Chirality : 0.040 0.145 1020 Planarity : 0.005 0.040 1019 Dihedral : 11.590 108.722 1146 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.15 % Allowed : 13.30 % Favored : 85.55 % 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: -0.26 (0.32), residues: 686 helix: 1.00 (0.37), residues: 213 sheet: 0.48 (0.40), residues: 172 loop : -1.44 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.012 0.002 TYR A 674 PHE 0.016 0.002 PHE A 699 TRP 0.015 0.002 TRP A 468 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6390) covalent geometry : angle 0.56441 / 0.29 ( 8798) hydrogen bonds : bond 0.05572 / 3.60 ( 258) hydrogen bonds : angle 4.43218 / 3.09 ( 715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.126 Fit side-chains REVERT: A 726 ASP cc_start: 0.8331 (p0) cc_final: 0.7906 (t0) REVERT: A 794 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8436 (ttm110) REVERT: A 803 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7381 (ttp-110) REVERT: A 851 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6630 (mp) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.0652 time to fit residues: 5.5565 Evaluate side-chains 59 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.175626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119912 restraints weight = 6471.174| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.98 r_work: 0.3307 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6390 Z= 0.120 Angle : 0.512 6.716 8798 Z= 0.261 Chirality : 0.039 0.142 1020 Planarity : 0.004 0.037 1019 Dihedral : 11.426 106.909 1146 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.48 % Allowed : 14.45 % Favored : 84.07 % 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: 0.03 (0.32), residues: 686 helix: 1.40 (0.38), residues: 209 sheet: 0.58 (0.40), residues: 172 loop : -1.33 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.011 0.001 TYR A 674 PHE 0.012 0.001 PHE A 699 TRP 0.014 0.001 TRP A 468 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6390) covalent geometry : angle 0.51186 / 0.26 ( 8798) hydrogen bonds : bond 0.04720 / 3.06 ( 258) hydrogen bonds : angle 4.21488 / 2.95 ( 715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.209 Fit side-chains REVERT: A 58 ASP cc_start: 0.8007 (t70) cc_final: 0.7752 (t0) REVERT: A 726 ASP cc_start: 0.8318 (p0) cc_final: 0.7904 (t0) REVERT: A 794 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8427 (ttm110) REVERT: A 803 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7102 (ttp-110) REVERT: A 851 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6536 (mp) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.0532 time to fit residues: 5.0267 Evaluate side-chains 63 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 0.0060 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115786 restraints weight = 6593.108| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.99 r_work: 0.3254 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6390 Z= 0.189 Angle : 0.569 6.688 8798 Z= 0.290 Chirality : 0.041 0.150 1020 Planarity : 0.004 0.040 1019 Dihedral : 11.422 105.273 1146 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.13 % Allowed : 15.76 % Favored : 82.10 % 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: -0.12 (0.33), residues: 686 helix: 1.21 (0.37), residues: 212 sheet: 0.59 (0.41), residues: 172 loop : -1.46 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.012 0.002 TYR A 340 PHE 0.016 0.002 PHE A 699 TRP 0.014 0.002 TRP A 468 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 ( 6390) covalent geometry : angle 0.56856 / 0.29 ( 8798) hydrogen bonds : bond 0.05742 / 3.69 ( 258) hydrogen bonds : angle 4.34690 / 3.04 ( 715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.270 Fit side-chains REVERT: A 58 ASP cc_start: 0.8015 (t70) cc_final: 0.7779 (t0) REVERT: A 726 ASP cc_start: 0.8265 (p0) cc_final: 0.7857 (t0) REVERT: A 794 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8409 (ttm110) REVERT: A 803 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7231 (ttp-110) REVERT: A 851 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6681 (mp) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.0576 time to fit residues: 5.2959 Evaluate side-chains 65 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116748 restraints weight = 6456.829| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.97 r_work: 0.3266 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6390 Z= 0.154 Angle : 0.534 6.255 8798 Z= 0.273 Chirality : 0.039 0.147 1020 Planarity : 0.004 0.038 1019 Dihedral : 11.345 103.298 1146 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.28 % Allowed : 16.26 % Favored : 80.46 % 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: -0.03 (0.33), residues: 686 helix: 1.35 (0.38), residues: 212 sheet: 0.65 (0.41), residues: 170 loop : -1.44 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.010 0.001 TYR A 674 PHE 0.013 0.001 PHE A 699 TRP 0.015 0.002 TRP A 468 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 ( 6390) covalent geometry : angle 0.53429 / 0.27 ( 8798) hydrogen bonds : bond 0.05262 / 3.40 ( 258) hydrogen bonds : angle 4.26873 / 2.99 ( 715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.229 Fit side-chains REVERT: A 58 ASP cc_start: 0.8040 (t70) cc_final: 0.7813 (t0) REVERT: A 657 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6813 (mtt90) REVERT: A 726 ASP cc_start: 0.8257 (p0) cc_final: 0.7863 (t0) REVERT: A 794 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8348 (ttm110) REVERT: A 851 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6621 (mp) outliers start: 20 outliers final: 11 residues processed: 71 average time/residue: 0.0707 time to fit residues: 6.8317 Evaluate side-chains 69 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 0.0570 chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120440 restraints weight = 6456.511| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.99 r_work: 0.3317 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6390 Z= 0.096 Angle : 0.480 6.268 8798 Z= 0.246 Chirality : 0.038 0.139 1020 Planarity : 0.004 0.036 1019 Dihedral : 11.183 101.102 1146 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.97 % Allowed : 17.41 % Favored : 80.62 % 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: 0.27 (0.33), residues: 686 helix: 1.75 (0.38), residues: 209 sheet: 0.73 (0.41), residues: 170 loop : -1.30 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.008 0.001 TYR A 674 PHE 0.008 0.001 PHE A 782 TRP 0.016 0.001 TRP A 468 HIS 0.002 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6390) covalent geometry : angle 0.48014 / 0.25 ( 8798) hydrogen bonds : bond 0.04186 / 2.72 ( 258) hydrogen bonds : angle 4.07039 / 2.87 ( 715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.127 Fit side-chains REVERT: A 58 ASP cc_start: 0.8020 (t70) cc_final: 0.7805 (t0) REVERT: A 319 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7907 (mp) REVERT: A 657 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6794 (mtt90) REVERT: A 726 ASP cc_start: 0.8245 (p0) cc_final: 0.7848 (t0) REVERT: A 794 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8309 (ttm110) REVERT: A 803 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6961 (ttp-110) REVERT: A 851 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6424 (mp) outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.0673 time to fit residues: 6.0980 Evaluate side-chains 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.174863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118783 restraints weight = 6516.357| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.00 r_work: 0.3293 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6390 Z= 0.125 Angle : 0.512 6.281 8798 Z= 0.259 Chirality : 0.039 0.145 1020 Planarity : 0.004 0.037 1019 Dihedral : 11.146 99.507 1146 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 17.90 % Favored : 80.13 % 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 (0.33), residues: 686 helix: 1.72 (0.38), residues: 209 sheet: 0.83 (0.42), residues: 170 loop : -1.31 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.009 0.001 TYR A 340 PHE 0.011 0.001 PHE A 481 TRP 0.013 0.001 TRP A 468 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 6390) covalent geometry : angle 0.51163 / 0.26 ( 8798) hydrogen bonds : bond 0.04596 / 2.96 ( 258) hydrogen bonds : angle 4.10246 / 2.88 ( 715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.216 Fit side-chains REVERT: A 657 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6745 (mtt90) REVERT: A 726 ASP cc_start: 0.8256 (p0) cc_final: 0.7846 (t0) REVERT: A 794 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8352 (ttm110) REVERT: A 803 ARG cc_start: 0.7199 (ttp-110) cc_final: 0.6910 (ttp-110) REVERT: A 851 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6463 (mp) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.0639 time to fit residues: 5.9477 Evaluate side-chains 69 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.0040 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115651 restraints weight = 6541.608| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.99 r_work: 0.3250 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6390 Z= 0.175 Angle : 0.572 6.921 8798 Z= 0.290 Chirality : 0.040 0.153 1020 Planarity : 0.004 0.039 1019 Dihedral : 11.153 97.049 1146 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.81 % Allowed : 18.23 % Favored : 79.97 % 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: 0.07 (0.33), residues: 686 helix: 1.42 (0.38), residues: 213 sheet: 0.80 (0.42), residues: 170 loop : -1.45 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.011 0.002 TYR A 340 PHE 0.014 0.002 PHE A 782 TRP 0.012 0.002 TRP A 468 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.17 ( 6390) covalent geometry : angle 0.57241 / 0.29 ( 8798) hydrogen bonds : bond 0.05573 / 3.58 ( 258) hydrogen bonds : angle 4.30212 / 3.00 ( 715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.193 Fit side-chains REVERT: A 657 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6380 (mmt90) REVERT: A 726 ASP cc_start: 0.8251 (p0) cc_final: 0.7832 (t0) REVERT: A 794 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8385 (ttm110) REVERT: A 803 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6905 (ttp-110) REVERT: A 851 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6654 (mp) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.0660 time to fit residues: 5.3123 Evaluate side-chains 60 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.175303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119293 restraints weight = 6454.337| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.98 r_work: 0.3302 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6390 Z= 0.111 Angle : 0.510 7.238 8798 Z= 0.259 Chirality : 0.038 0.143 1020 Planarity : 0.004 0.037 1019 Dihedral : 10.999 94.760 1146 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.81 % Allowed : 18.06 % Favored : 80.13 % 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: 0.31 (0.33), residues: 686 helix: 1.75 (0.38), residues: 209 sheet: 0.89 (0.42), residues: 170 loop : -1.35 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.009 0.001 TYR A 674 PHE 0.009 0.001 PHE A 481 TRP 0.015 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 6390) covalent geometry : angle 0.50991 / 0.26 ( 8798) hydrogen bonds : bond 0.04448 / 2.88 ( 258) hydrogen bonds : angle 4.12172 / 2.89 ( 715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.224 Fit side-chains REVERT: A 319 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 657 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6308 (mmt90) REVERT: A 726 ASP cc_start: 0.8259 (p0) cc_final: 0.7847 (t0) REVERT: A 794 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8321 (ttm110) REVERT: A 803 ARG cc_start: 0.7124 (ttp-110) cc_final: 0.6818 (ttp-110) REVERT: A 851 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6434 (mp) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.0685 time to fit residues: 5.9200 Evaluate side-chains 66 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 65 optimal weight: 0.0070 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.2510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123258 restraints weight = 6517.499| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.09 r_work: 0.3366 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6390 Z= 0.088 Angle : 0.477 7.302 8798 Z= 0.243 Chirality : 0.037 0.137 1020 Planarity : 0.004 0.039 1019 Dihedral : 10.705 90.097 1146 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.15 % Allowed : 18.72 % Favored : 80.13 % 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 (0.34), residues: 686 helix: 2.04 (0.39), residues: 209 sheet: 0.93 (0.42), residues: 171 loop : -1.18 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.008 0.001 TYR A 674 PHE 0.008 0.001 PHE A 481 TRP 0.015 0.001 TRP A 468 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 6390) covalent geometry : angle 0.47740 / 0.24 ( 8798) hydrogen bonds : bond 0.03114 / 2.02 ( 258) hydrogen bonds : angle 3.86938 / 2.72 ( 715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.77 seconds wall clock time: 23 minutes 42.62 seconds (1422.62 seconds total)