Starting phenix.real_space_refine on Tue Jan 13 10:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7unt_26632/01_2026/7unt_26632.cif Found real_map, /net/cci-nas-00/data/ceres_data/7unt_26632/01_2026/7unt_26632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7unt_26632/01_2026/7unt_26632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7unt_26632/01_2026/7unt_26632.map" model { file = "/net/cci-nas-00/data/ceres_data/7unt_26632/01_2026/7unt_26632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7unt_26632/01_2026/7unt_26632.cif" } resolution = 3.6 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= -0.006 sd= 0.024 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 2 5.49 5 S 11 5.16 5 C 2059 2.51 5 N 596 2.21 5 O 602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3270 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3270 Unusual residues: {'GDP': 1} Classifications: {'peptide': 472, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 17, 'TRANS': 454, None: 1} Not linked: pdbres="GLU x 835 " pdbres="GDP x 901 " Chain breaks: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 17, 'ARG:plan': 9, 'HIS:plan': 1, 'GLU:plan': 21, 'TYR:plan': 1, 'ASN:plan1': 6, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 222 Time building chain proxies: 0.96, per 1000 atoms: 0.29 Number of scatterers: 3270 At special positions: 0 Unit cell: (79.9, 76.5, 86.7, 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 11 16.00 P 2 15.00 O 602 8.00 N 596 7.00 C 2059 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: 0.21 Conformation dependent library (CDL) restraints added in 138.0 milliseconds 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 30.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'x' and resid 354 through 366 removed outlier: 3.532A pdb=" N LYS x 366 " --> pdb=" O ILE x 362 " (cutoff:3.500A) Processing helix chain 'x' and resid 398 through 407 removed outlier: 3.787A pdb=" N MET x 405 " --> pdb=" O ALA x 401 " (cutoff:3.500A) Processing helix chain 'x' and resid 427 through 441 removed outlier: 3.877A pdb=" N ALA x 440 " --> pdb=" O HIS x 436 " (cutoff:3.500A) Processing helix chain 'x' and resid 459 through 466 removed outlier: 3.806A pdb=" N ASN x 463 " --> pdb=" O ASP x 459 " (cutoff:3.500A) Processing helix chain 'x' and resid 467 through 469 No H-bonds generated for 'chain 'x' and resid 467 through 469' Processing helix chain 'x' and resid 491 through 502 removed outlier: 3.907A pdb=" N LEU x 500 " --> pdb=" O LEU x 496 " (cutoff:3.500A) Processing helix chain 'x' and resid 597 through 623 removed outlier: 3.617A pdb=" N LEU x 617 " --> pdb=" O ARG x 613 " (cutoff:3.500A) Processing helix chain 'x' and resid 624 through 628 removed outlier: 3.530A pdb=" N ILE x 628 " --> pdb=" O LEU x 625 " (cutoff:3.500A) Processing helix chain 'x' and resid 648 through 661 removed outlier: 3.580A pdb=" N LEU x 655 " --> pdb=" O SER x 651 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY x 661 " --> pdb=" O GLY x 657 " (cutoff:3.500A) Processing helix chain 'x' and resid 680 through 691 Processing helix chain 'x' and resid 702 through 712 Processing helix chain 'x' and resid 721 through 735 removed outlier: 3.889A pdb=" N ILE x 725 " --> pdb=" O VAL x 721 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE x 726 " --> pdb=" O ILE x 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 381 through 384 removed outlier: 5.316A pdb=" N VAL x 347 " --> pdb=" O LEU x 394 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL x 416 " --> pdb=" O VAL x 445 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA x 447 " --> pdb=" O VAL x 416 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU x 418 " --> pdb=" O ALA x 447 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL x 482 " --> pdb=" O VAL x 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 554 through 556 removed outlier: 6.265A pdb=" N VAL x 519 " --> pdb=" O VAL x 537 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL x 537 " --> pdb=" O VAL x 519 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 670 through 671 removed outlier: 3.534A pdb=" N ILE x 642 " --> pdb=" O ARG x 670 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'x' and resid 670 through 671 removed outlier: 3.534A pdb=" N ILE x 642 " --> pdb=" O ARG x 670 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASN x 641 " --> pdb=" O VAL x 693 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N PHE x 695 " --> pdb=" O ASN x 641 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL x 643 " --> pdb=" O PHE x 695 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE x 697 " --> pdb=" O VAL x 643 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS x 645 " --> pdb=" O PHE x 697 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU x 694 " --> pdb=" O ARG x 717 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR x 719 " --> pdb=" O LEU x 694 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY x 696 " --> pdb=" O TYR x 719 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'x' and resid 786 through 791 removed outlier: 6.984A pdb=" N VAL x 781 " --> pdb=" O ILE x 788 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU x 790 " --> pdb=" O ILE x 779 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE x 779 " --> pdb=" O GLU x 790 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY x 747 " --> pdb=" O VAL x 830 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU x 832 " --> pdb=" O ILE x 745 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE x 745 " --> pdb=" O GLU x 832 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA x 749 " --> pdb=" O THR x 769 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR x 769 " --> pdb=" O ALA x 749 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL x 751 " --> pdb=" O MET x 767 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N MET x 767 " --> pdb=" O VAL x 751 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'x' and resid 773 through 774 removed outlier: 3.594A pdb=" N VAL x 773 " --> pdb=" O VAL x 806 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1123 1.34 - 1.46: 403 1.46 - 1.57: 1762 1.57 - 1.69: 3 1.69 - 1.81: 20 Bond restraints: 3311 Sorted by residual: bond pdb=" N TYR x 719 " pdb=" CA TYR x 719 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.27e-02 6.20e+03 4.82e+00 bond pdb=" N ASP x 424 " pdb=" CA ASP x 424 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.34e+00 bond pdb=" C5 GDP x 901 " pdb=" C4 GDP x 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" CA VAL x 550 " pdb=" CB VAL x 550 " ideal model delta sigma weight residual 1.531 1.543 -0.012 1.16e-02 7.43e+03 1.05e+00 bond pdb=" CB GLU x 614 " pdb=" CG GLU x 614 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.36e-01 ... (remaining 3306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 4237 1.11 - 2.22: 205 2.22 - 3.33: 53 3.33 - 4.44: 7 4.44 - 5.55: 6 Bond angle restraints: 4508 Sorted by residual: angle pdb=" N ILE x 451 " pdb=" CA ILE x 451 " pdb=" C ILE x 451 " ideal model delta sigma weight residual 111.77 107.72 4.05 1.04e+00 9.25e-01 1.52e+01 angle pdb=" C GLY x 425 " pdb=" N VAL x 426 " pdb=" CA VAL x 426 " ideal model delta sigma weight residual 121.97 126.13 -4.16 1.80e+00 3.09e-01 5.35e+00 angle pdb=" C ASP x 423 " pdb=" N ASP x 424 " pdb=" CA ASP x 424 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.09e+00 angle pdb=" CA TYR x 719 " pdb=" C TYR x 719 " pdb=" O TYR x 719 " ideal model delta sigma weight residual 121.33 118.99 2.34 1.08e+00 8.57e-01 4.70e+00 angle pdb=" CA VAL x 426 " pdb=" CB VAL x 426 " pdb=" CG1 VAL x 426 " ideal model delta sigma weight residual 110.40 113.80 -3.40 1.70e+00 3.46e-01 4.00e+00 ... (remaining 4503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1767 16.68 - 33.37: 160 33.37 - 50.05: 42 50.05 - 66.74: 6 66.74 - 83.42: 2 Dihedral angle restraints: 1977 sinusoidal: 657 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ARG x 742 " pdb=" C ARG x 742 " pdb=" N GLU x 743 " pdb=" CA GLU x 743 " ideal model delta harmonic sigma weight residual 180.00 164.61 15.39 0 5.00e+00 4.00e-02 9.48e+00 dihedral pdb=" CB GLU x 473 " pdb=" CG GLU x 473 " pdb=" CD GLU x 473 " pdb=" OE1 GLU x 473 " ideal model delta sinusoidal sigma weight residual 0.00 83.42 -83.42 1 3.00e+01 1.11e-03 9.44e+00 dihedral pdb=" CB LYS x 731 " pdb=" CG LYS x 731 " pdb=" CD LYS x 731 " pdb=" CE LYS x 731 " ideal model delta sinusoidal sigma weight residual 60.00 113.54 -53.54 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 1974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 322 0.030 - 0.060: 128 0.060 - 0.089: 64 0.089 - 0.119: 32 0.119 - 0.149: 7 Chirality restraints: 553 Sorted by residual: chirality pdb=" CA VAL x 442 " pdb=" N VAL x 442 " pdb=" C VAL x 442 " pdb=" CB VAL x 442 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE x 471 " pdb=" N ILE x 471 " pdb=" C ILE x 471 " pdb=" CB ILE x 471 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA TYR x 719 " pdb=" N TYR x 719 " pdb=" C TYR x 719 " pdb=" CB TYR x 719 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 550 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL x 482 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO x 483 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO x 483 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO x 483 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET x 427 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO x 428 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO x 428 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO x 428 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS x 453 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO x 454 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO x 454 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO x 454 " -0.019 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1153 2.86 - 3.37: 2992 3.37 - 3.88: 5006 3.88 - 4.39: 5180 4.39 - 4.90: 9537 Nonbonded interactions: 23868 Sorted by model distance: nonbonded pdb=" ND2 ASN x 553 " pdb=" OD1 ASP x 583 " model vdw 2.356 3.120 nonbonded pdb=" OE1 GLU x 727 " pdb=" NH2 ARG x 742 " model vdw 2.378 3.120 nonbonded pdb=" NH2 ARG x 775 " pdb=" O GLU x 794 " model vdw 2.451 3.120 nonbonded pdb=" O VAL x 420 " pdb=" N ASN x 449 " model vdw 2.451 3.120 nonbonded pdb=" O TYR x 382 " pdb=" OG1 THR x 392 " model vdw 2.474 3.040 ... (remaining 23863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 8.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 0.002 0.028 3311 Z= 0.128 Angle : 0.603 5.552 4508 Z= 0.326 Chirality : 0.045 0.149 553 Planarity : 0.004 0.047 585 Dihedral : 14.275 83.420 1131 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.05 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.58 (0.39), residues: 464 helix: 1.62 (0.47), residues: 121 sheet: -0.65 (0.51), residues: 106 loop : -2.84 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 406 TYR 0.006 0.001 TYR x 382 PHE 0.007 0.001 PHE x 393 TRP 0.004 0.001 TRP x 475 HIS 0.002 0.000 HIS x 350 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3311) covalent geometry : angle 0.60273 ( 4508) hydrogen bonds : bond 0.16174 ( 139) hydrogen bonds : angle 5.95798 ( 390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.148 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0705 time to fit residues: 6.0678 Evaluate side-chains 43 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 431 GLN x 774 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070503 restraints weight = 11337.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072402 restraints weight = 6221.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.073698 restraints weight = 4259.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074493 restraints weight = 3331.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.075059 restraints weight = 2860.127| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3311 Z= 0.158 Angle : 0.598 5.090 4508 Z= 0.314 Chirality : 0.046 0.145 553 Planarity : 0.004 0.042 585 Dihedral : 5.672 35.661 505 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.48 % Favored : 90.09 % Rotamer: Outliers : 3.85 % Allowed : 13.64 % Favored : 82.52 % 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: -1.52 (0.38), residues: 464 helix: 1.48 (0.47), residues: 126 sheet: -0.91 (0.51), residues: 102 loop : -2.59 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 752 TYR 0.016 0.002 TYR x 361 PHE 0.020 0.002 PHE x 789 TRP 0.003 0.001 TRP x 475 HIS 0.003 0.001 HIS x 399 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3311) covalent geometry : angle 0.59837 ( 4508) hydrogen bonds : bond 0.03786 ( 139) hydrogen bonds : angle 5.00137 ( 390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.151 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.0667 time to fit residues: 4.1129 Evaluate side-chains 46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 405 MET Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068506 restraints weight = 11168.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070504 restraints weight = 6081.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.071719 restraints weight = 4174.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072587 restraints weight = 3302.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073090 restraints weight = 2826.711| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3311 Z= 0.198 Angle : 0.619 8.068 4508 Z= 0.322 Chirality : 0.045 0.143 553 Planarity : 0.004 0.041 585 Dihedral : 6.044 40.340 505 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.91 % Favored : 89.66 % Rotamer: Outliers : 4.20 % Allowed : 18.88 % Favored : 76.92 % 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: -1.72 (0.38), residues: 464 helix: 1.30 (0.46), residues: 128 sheet: -0.97 (0.49), residues: 103 loop : -2.77 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 524 TYR 0.014 0.002 TYR x 361 PHE 0.012 0.001 PHE x 393 TRP 0.002 0.001 TRP x 475 HIS 0.003 0.001 HIS x 621 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3311) covalent geometry : angle 0.61852 ( 4508) hydrogen bonds : bond 0.03779 ( 139) hydrogen bonds : angle 5.00748 ( 390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.122 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.0727 time to fit residues: 4.0230 Evaluate side-chains 46 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 405 MET Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 679 ILE Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 760 PHE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 691 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.070262 restraints weight = 11123.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072216 restraints weight = 6065.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073525 restraints weight = 4144.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074318 restraints weight = 3258.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074884 restraints weight = 2806.911| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3311 Z= 0.123 Angle : 0.577 8.008 4508 Z= 0.300 Chirality : 0.045 0.136 553 Planarity : 0.004 0.038 585 Dihedral : 5.714 38.114 505 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.41 % Favored : 91.16 % Rotamer: Outliers : 4.20 % Allowed : 21.33 % Favored : 74.48 % 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: -1.58 (0.38), residues: 464 helix: 1.32 (0.46), residues: 132 sheet: -1.06 (0.49), residues: 101 loop : -2.58 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG x 524 TYR 0.012 0.001 TYR x 361 PHE 0.010 0.001 PHE x 393 TRP 0.002 0.001 TRP x 475 HIS 0.001 0.000 HIS x 621 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3311) covalent geometry : angle 0.57707 ( 4508) hydrogen bonds : bond 0.03115 ( 139) hydrogen bonds : angle 4.78102 ( 390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.122 Fit side-chains REVERT: x 774 HIS cc_start: 0.8144 (t-90) cc_final: 0.7937 (t-90) outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 0.0659 time to fit residues: 3.9656 Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 405 MET Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 760 PHE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 691 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.070329 restraints weight = 11114.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072346 restraints weight = 5966.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073679 restraints weight = 4041.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074503 restraints weight = 3141.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.075094 restraints weight = 2695.104| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3311 Z= 0.117 Angle : 0.580 8.390 4508 Z= 0.299 Chirality : 0.045 0.147 553 Planarity : 0.004 0.039 585 Dihedral : 5.600 37.013 505 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.84 % Favored : 90.73 % Rotamer: Outliers : 3.50 % Allowed : 24.13 % Favored : 72.38 % 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: -1.43 (0.39), residues: 464 helix: 1.58 (0.46), residues: 129 sheet: -1.00 (0.49), residues: 104 loop : -2.53 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG x 613 TYR 0.010 0.001 TYR x 361 PHE 0.009 0.001 PHE x 393 TRP 0.002 0.001 TRP x 475 HIS 0.004 0.001 HIS x 621 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3311) covalent geometry : angle 0.58010 ( 4508) hydrogen bonds : bond 0.02983 ( 139) hydrogen bonds : angle 4.67052 ( 390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.152 Fit side-chains REVERT: x 612 PHE cc_start: 0.8897 (m-10) cc_final: 0.8451 (m-10) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.0539 time to fit residues: 3.6800 Evaluate side-chains 51 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 760 PHE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 691 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069684 restraints weight = 11376.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071737 restraints weight = 6110.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.073061 restraints weight = 4127.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073864 restraints weight = 3216.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074467 restraints weight = 2766.309| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3311 Z= 0.137 Angle : 0.605 8.254 4508 Z= 0.313 Chirality : 0.045 0.148 553 Planarity : 0.004 0.039 585 Dihedral : 5.707 37.769 505 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.48 % Favored : 90.09 % Rotamer: Outliers : 3.85 % Allowed : 26.22 % Favored : 69.93 % 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: -1.43 (0.39), residues: 464 helix: 1.61 (0.46), residues: 129 sheet: -1.08 (0.49), residues: 104 loop : -2.50 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 670 TYR 0.009 0.001 TYR x 361 PHE 0.024 0.001 PHE x 789 TRP 0.002 0.001 TRP x 475 HIS 0.003 0.001 HIS x 621 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3311) covalent geometry : angle 0.60468 ( 4508) hydrogen bonds : bond 0.02998 ( 139) hydrogen bonds : angle 4.68783 ( 390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: x 774 HIS cc_start: 0.8360 (t-90) cc_final: 0.8097 (p90) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.0517 time to fit residues: 3.4090 Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 760 PHE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 691 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068676 restraints weight = 11492.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.070719 restraints weight = 6149.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072049 restraints weight = 4167.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.072915 restraints weight = 3253.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073360 restraints weight = 2781.245| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3311 Z= 0.157 Angle : 0.624 8.832 4508 Z= 0.320 Chirality : 0.045 0.149 553 Planarity : 0.004 0.038 585 Dihedral : 5.813 39.598 505 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.48 % Favored : 90.09 % Rotamer: Outliers : 3.50 % Allowed : 26.57 % Favored : 69.93 % 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: -1.42 (0.39), residues: 464 helix: 1.65 (0.46), residues: 129 sheet: -1.15 (0.49), residues: 104 loop : -2.48 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG x 613 TYR 0.009 0.001 TYR x 719 PHE 0.024 0.002 PHE x 789 TRP 0.001 0.001 TRP x 475 HIS 0.002 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3311) covalent geometry : angle 0.62416 ( 4508) hydrogen bonds : bond 0.03102 ( 139) hydrogen bonds : angle 4.64713 ( 390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: x 774 HIS cc_start: 0.8461 (t-90) cc_final: 0.8218 (p90) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.0603 time to fit residues: 3.7438 Evaluate side-chains 51 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 760 PHE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 691 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.086544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068500 restraints weight = 11729.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070505 restraints weight = 6211.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071847 restraints weight = 4208.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.072723 restraints weight = 3268.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073132 restraints weight = 2789.810| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3311 Z= 0.156 Angle : 0.618 9.150 4508 Z= 0.317 Chirality : 0.045 0.149 553 Planarity : 0.004 0.038 585 Dihedral : 5.861 40.683 505 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.48 % Favored : 90.09 % Rotamer: Outliers : 3.15 % Allowed : 28.67 % Favored : 68.18 % 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: -1.43 (0.39), residues: 464 helix: 1.63 (0.46), residues: 129 sheet: -1.16 (0.49), residues: 104 loop : -2.46 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 613 TYR 0.009 0.001 TYR x 719 PHE 0.031 0.002 PHE x 789 TRP 0.001 0.001 TRP x 475 HIS 0.003 0.001 HIS x 621 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3311) covalent geometry : angle 0.61797 ( 4508) hydrogen bonds : bond 0.03107 ( 139) hydrogen bonds : angle 4.62102 ( 390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: x 772 MET cc_start: 0.8025 (tmm) cc_final: 0.7543 (tmm) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.0538 time to fit residues: 3.3064 Evaluate side-chains 48 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 691 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.069266 restraints weight = 11443.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.071293 restraints weight = 6073.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072639 restraints weight = 4095.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073510 restraints weight = 3187.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074019 restraints weight = 2711.124| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3311 Z= 0.130 Angle : 0.613 8.828 4508 Z= 0.315 Chirality : 0.046 0.147 553 Planarity : 0.004 0.038 585 Dihedral : 5.782 39.927 505 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.27 % Favored : 90.30 % Rotamer: Outliers : 3.15 % Allowed : 29.02 % Favored : 67.83 % 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: -1.42 (0.39), residues: 464 helix: 1.56 (0.46), residues: 130 sheet: -1.16 (0.49), residues: 104 loop : -2.42 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG x 613 TYR 0.008 0.001 TYR x 361 PHE 0.025 0.001 PHE x 789 TRP 0.002 0.001 TRP x 475 HIS 0.003 0.001 HIS x 621 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3311) covalent geometry : angle 0.61310 ( 4508) hydrogen bonds : bond 0.02949 ( 139) hydrogen bonds : angle 4.53242 ( 390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: x 772 MET cc_start: 0.8130 (tmm) cc_final: 0.7616 (tmm) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.0577 time to fit residues: 3.4568 Evaluate side-chains 48 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 39 optimal weight: 8.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 436 HIS x 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.087570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070630 restraints weight = 11404.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072520 restraints weight = 6232.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.073809 restraints weight = 4279.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074618 restraints weight = 3359.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075102 restraints weight = 2872.173| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3311 Z= 0.125 Angle : 0.618 8.711 4508 Z= 0.317 Chirality : 0.046 0.146 553 Planarity : 0.004 0.038 585 Dihedral : 5.728 39.120 505 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.27 % Favored : 90.30 % Rotamer: Outliers : 3.15 % Allowed : 29.02 % Favored : 67.83 % 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: -1.42 (0.39), residues: 464 helix: 1.55 (0.46), residues: 129 sheet: -1.11 (0.49), residues: 104 loop : -2.43 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG x 613 TYR 0.007 0.001 TYR x 361 PHE 0.022 0.001 PHE x 789 TRP 0.002 0.001 TRP x 475 HIS 0.002 0.001 HIS x 621 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3311) covalent geometry : angle 0.61839 ( 4508) hydrogen bonds : bond 0.02893 ( 139) hydrogen bonds : angle 4.50951 ( 390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: x 772 MET cc_start: 0.8162 (tmm) cc_final: 0.7662 (tmm) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.0526 time to fit residues: 3.1607 Evaluate side-chains 49 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 470 VAL Chi-restraints excluded: chain x residue 549 LEU Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 714 LEU Chi-restraints excluded: chain x residue 745 ILE Chi-restraints excluded: chain x residue 773 VAL Chi-restraints excluded: chain x residue 824 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 436 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.085582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067659 restraints weight = 11612.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.069599 restraints weight = 6258.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070907 restraints weight = 4255.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071713 restraints weight = 3329.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072266 restraints weight = 2844.120| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3311 Z= 0.195 Angle : 0.646 8.824 4508 Z= 0.332 Chirality : 0.046 0.155 553 Planarity : 0.004 0.038 585 Dihedral : 6.161 45.287 505 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.34 % Favored : 89.22 % Rotamer: Outliers : 3.50 % Allowed : 29.02 % Favored : 67.48 % 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: -1.59 (0.39), residues: 464 helix: 1.28 (0.46), residues: 133 sheet: -1.37 (0.52), residues: 95 loop : -2.40 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG x 706 TYR 0.011 0.002 TYR x 719 PHE 0.019 0.002 PHE x 789 TRP 0.002 0.001 TRP x 475 HIS 0.004 0.001 HIS x 383 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3311) covalent geometry : angle 0.64635 ( 4508) hydrogen bonds : bond 0.03310 ( 139) hydrogen bonds : angle 4.69662 ( 390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 922.86 seconds wall clock time: 16 minutes 39.03 seconds (999.03 seconds total)