Starting phenix.real_space_refine on Thu Jul 2 05:19:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij4_60615/07_2026/9ij4_60615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij4_60615/07_2026/9ij4_60615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij4_60615/07_2026/9ij4_60615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij4_60615/07_2026/9ij4_60615.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij4_60615/07_2026/9ij4_60615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij4_60615/07_2026/9ij4_60615.cif" } resolution = 2.7 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= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 42 5.16 5 C 4357 2.51 5 N 1237 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 7129 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6047 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 37, 'TRANS': 717} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 531 Classifications: {'RNA': 25} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 23} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.25 Number of scatterers: 7129 At special positions: 0 Unit cell: (76.38, 85.5, 103.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 51 15.00 Mg 1 11.99 O 1441 8.00 N 1237 7.00 C 4357 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: 0.62 Conformation dependent library (CDL) restraints added in 544.8 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 11 sheets defined 33.2% alpha, 23.4% beta 23 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.834A pdb=" N HIS A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.709A pdb=" N GLU A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 502 through 507 removed outlier: 4.302A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.964A pdb=" N TRP A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 631 removed outlier: 4.539A pdb=" N GLY A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 646 through 661 removed outlier: 3.512A pdb=" N VAL A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.601A pdb=" N VAL A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 781 through 802 removed outlier: 4.354A pdb=" N SER A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.512A pdb=" N GLN A 830 " --> pdb=" O TYR A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 838 removed outlier: 3.581A pdb=" N PHE A 838 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 838' Processing helix chain 'A' and resid 914 through 926 Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 225 removed outlier: 4.312A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 909 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET A 845 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL A 744 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 743 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 757 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337 removed outlier: 4.660A pdb=" N LEU A 372 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 279 Processing sheet with id=AA5, first strand: chain 'A' and resid 287 through 292 removed outlier: 3.643A pdb=" N VAL A 287 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 423 through 426 Processing sheet with id=AA7, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 442 Processing sheet with id=AA9, first strand: chain 'A' and resid 570 through 572 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 641 removed outlier: 6.088A pdb=" N ALA A 605 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE A 670 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE A 607 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 667 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE A 697 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS A 669 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 860 through 861 281 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1026 1.29 - 1.42: 2177 1.42 - 1.55: 4015 1.55 - 1.68: 107 1.68 - 1.82: 65 Bond restraints: 7390 Sorted by residual: bond pdb=" CA ILE A 318 " pdb=" CB ILE A 318 " ideal model delta sigma weight residual 1.539 1.506 0.033 5.40e-03 3.43e+04 3.77e+01 bond pdb=" CA PRO A 636 " pdb=" C PRO A 636 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.59e+01 bond pdb=" CG ASN A 763 " pdb=" OD1 ASN A 763 " ideal model delta sigma weight residual 1.231 1.156 0.075 1.90e-02 2.77e+03 1.54e+01 bond pdb=" CB ILE A 651 " pdb=" CG2 ILE A 651 " ideal model delta sigma weight residual 1.521 1.396 0.125 3.30e-02 9.18e+02 1.44e+01 bond pdb=" CG PRO A 863 " pdb=" CD PRO A 863 " ideal model delta sigma weight residual 1.503 1.377 0.126 3.40e-02 8.65e+02 1.38e+01 ... (remaining 7385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 10117 3.12 - 6.25: 109 6.25 - 9.37: 16 9.37 - 12.49: 6 12.49 - 15.61: 5 Bond angle restraints: 10253 Sorted by residual: angle pdb=" CA PRO A 468 " pdb=" N PRO A 468 " pdb=" CD PRO A 468 " ideal model delta sigma weight residual 112.00 97.93 14.07 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N PRO A 863 " pdb=" CD PRO A 863 " pdb=" CG PRO A 863 " ideal model delta sigma weight residual 103.20 89.14 14.06 1.50e+00 4.44e-01 8.78e+01 angle pdb=" CA PRO A 863 " pdb=" CB PRO A 863 " pdb=" CG PRO A 863 " ideal model delta sigma weight residual 104.50 88.89 15.61 1.90e+00 2.77e-01 6.75e+01 angle pdb=" CA PRO A 863 " pdb=" N PRO A 863 " pdb=" CD PRO A 863 " ideal model delta sigma weight residual 112.00 104.20 7.80 1.40e+00 5.10e-01 3.10e+01 angle pdb=" C1' C B 24 " pdb=" N1 C B 24 " pdb=" C2 C B 24 " ideal model delta sigma weight residual 118.80 124.82 -6.02 1.10e+00 8.26e-01 2.99e+01 ... (remaining 10248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3696 17.90 - 35.80: 525 35.80 - 53.70: 195 53.70 - 71.60: 71 71.60 - 89.50: 24 Dihedral angle restraints: 4511 sinusoidal: 2301 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ASP A 296 " pdb=" C ASP A 296 " pdb=" N ASP A 297 " pdb=" CA ASP A 297 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PRO A 637 " pdb=" C PRO A 637 " pdb=" N ALA A 638 " pdb=" CA ALA A 638 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA MET A 442 " pdb=" C MET A 442 " pdb=" N SER A 443 " pdb=" CA SER A 443 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 4508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 979 0.062 - 0.124: 191 0.124 - 0.187: 28 0.187 - 0.249: 3 0.249 - 0.311: 1 Chirality restraints: 1202 Sorted by residual: chirality pdb=" CG LEU A 490 " pdb=" CB LEU A 490 " pdb=" CD1 LEU A 490 " pdb=" CD2 LEU A 490 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA MET A 348 " pdb=" N MET A 348 " pdb=" C MET A 348 " pdb=" CB MET A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE A 501 " pdb=" CA ILE A 501 " pdb=" CG1 ILE A 501 " pdb=" CG2 ILE A 501 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1199 not shown) Planarity restraints: 1113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 690 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO A 691 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 691 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 691 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 467 " -0.075 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A 468 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 652 " 0.312 9.50e-02 1.11e+02 1.41e-01 1.62e+01 pdb=" NE ARG A 652 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 652 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 652 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 652 " 0.023 2.00e-02 2.50e+03 ... (remaining 1110 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 13 2.36 - 3.00: 3326 3.00 - 3.63: 11213 3.63 - 4.27: 18181 4.27 - 4.90: 28276 Nonbonded interactions: 61009 Sorted by model distance: nonbonded pdb=" OD2 ASP A 813 " pdb="MG MG A1001 " model vdw 1.731 2.170 nonbonded pdb=" OD1 ASP A 743 " pdb="MG MG A1001 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP A 743 " pdb=" OD2 ASP A 813 " model vdw 2.238 3.040 nonbonded pdb=" O THR A 649 " pdb=" OG1 THR A 653 " model vdw 2.241 3.040 nonbonded pdb=" O SER A 544 " pdb=" OG1 THR A 548 " model vdw 2.290 3.040 ... (remaining 61004 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 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 : 0.006 0.126 7390 Z= 0.302 Angle : 0.914 15.614 10253 Z= 0.573 Chirality : 0.051 0.311 1202 Planarity : 0.009 0.141 1113 Dihedral : 19.915 89.501 3081 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 0.88 % Allowed : 28.42 % Favored : 70.69 % 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: -1.89 (0.29), residues: 751 helix: -0.70 (0.31), residues: 225 sheet: -0.79 (0.40), residues: 171 loop : -1.81 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG A 652 TYR 0.034 0.003 TYR A 904 PHE 0.028 0.003 PHE A 835 TRP 0.011 0.002 TRP A 586 HIS 0.006 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.30 ( 7390) covalent geometry : angle 0.91446 / 0.57 (10253) hydrogen bonds : bond 0.12709 / 8.17 ( 331) hydrogen bonds : angle 7.10267 / 4.87 ( 889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.243 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.4224 time to fit residues: 42.2030 Evaluate side-chains 81 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.211382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174107 restraints weight = 7779.844| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.06 r_work: 0.4080 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7390 Z= 0.139 Angle : 0.581 7.597 10253 Z= 0.304 Chirality : 0.042 0.168 1202 Planarity : 0.007 0.087 1113 Dihedral : 17.606 122.284 1585 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 3.68 % Allowed : 27.25 % Favored : 69.07 % 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: -1.30 (0.30), residues: 751 helix: 0.24 (0.33), residues: 228 sheet: -0.82 (0.39), residues: 177 loop : -1.60 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.025 0.002 TYR A 904 PHE 0.014 0.001 PHE A 835 TRP 0.009 0.001 TRP A 586 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7390) covalent geometry : angle 0.58120 / 0.30 (10253) hydrogen bonds : bond 0.04633 / 3.12 ( 331) hydrogen bonds : angle 5.59632 / 3.83 ( 889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5070 (OUTLIER) cc_final: 0.4798 (ptpp) REVERT: A 624 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6104 (pt0) outliers start: 25 outliers final: 10 residues processed: 105 average time/residue: 0.4110 time to fit residues: 46.4527 Evaluate side-chains 91 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.205423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166288 restraints weight = 7456.690| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.07 r_work: 0.3886 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7390 Z= 0.188 Angle : 0.612 9.091 10253 Z= 0.317 Chirality : 0.044 0.171 1202 Planarity : 0.006 0.072 1113 Dihedral : 17.188 81.748 1583 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 5.89 % Allowed : 25.18 % Favored : 68.92 % 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: -1.24 (0.30), residues: 751 helix: 0.33 (0.34), residues: 234 sheet: -0.93 (0.39), residues: 177 loop : -1.53 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 652 TYR 0.016 0.002 TYR A 454 PHE 0.018 0.002 PHE A 835 TRP 0.010 0.002 TRP A 769 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 7390) covalent geometry : angle 0.61200 / 0.32 (10253) hydrogen bonds : bond 0.04547 / 3.14 ( 331) hydrogen bonds : angle 5.41554 / 3.72 ( 889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5193 (OUTLIER) cc_final: 0.4893 (ptpp) REVERT: A 329 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.6823 (mpp) REVERT: A 333 ASP cc_start: 0.7622 (m-30) cc_final: 0.6744 (t0) REVERT: A 369 ASP cc_start: 0.6677 (t0) cc_final: 0.6408 (t0) REVERT: A 392 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.5504 (mpt) REVERT: A 510 ARG cc_start: 0.6116 (mmp80) cc_final: 0.5732 (tpm170) REVERT: A 531 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6645 (mm-30) REVERT: A 624 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6001 (pt0) REVERT: A 651 ILE cc_start: 0.7435 (mt) cc_final: 0.7223 (mt) REVERT: A 794 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5544 (mm) outliers start: 40 outliers final: 14 residues processed: 121 average time/residue: 0.4303 time to fit residues: 55.9409 Evaluate side-chains 104 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.203921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163529 restraints weight = 7533.145| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.93 r_work: 0.3810 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7390 Z= 0.195 Angle : 0.611 9.352 10253 Z= 0.318 Chirality : 0.045 0.189 1202 Planarity : 0.005 0.063 1113 Dihedral : 17.209 84.607 1583 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.19 % Favored : 92.68 % Rotamer: Outliers : 5.74 % Allowed : 25.77 % Favored : 68.48 % 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: -1.26 (0.30), residues: 751 helix: 0.39 (0.35), residues: 234 sheet: -1.09 (0.38), residues: 177 loop : -1.52 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.013 0.002 TYR A 342 PHE 0.017 0.002 PHE A 835 TRP 0.008 0.002 TRP A 769 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 7390) covalent geometry : angle 0.61132 / 0.32 (10253) hydrogen bonds : bond 0.04412 / 3.06 ( 331) hydrogen bonds : angle 5.41295 / 3.72 ( 889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6135 (ttm) REVERT: A 294 LYS cc_start: 0.5165 (OUTLIER) cc_final: 0.4879 (ptpp) REVERT: A 329 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.6553 (mpp) REVERT: A 333 ASP cc_start: 0.7683 (m-30) cc_final: 0.6803 (t0) REVERT: A 369 ASP cc_start: 0.6694 (t0) cc_final: 0.6454 (t0) REVERT: A 531 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: A 794 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5640 (mm) outliers start: 39 outliers final: 18 residues processed: 112 average time/residue: 0.4087 time to fit residues: 49.3138 Evaluate side-chains 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 5 optimal weight: 0.0040 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.204766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165781 restraints weight = 7475.009| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.03 r_work: 0.3822 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7390 Z= 0.163 Angle : 0.588 9.012 10253 Z= 0.304 Chirality : 0.043 0.178 1202 Planarity : 0.005 0.054 1113 Dihedral : 17.239 85.763 1583 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 5.45 % Allowed : 26.36 % Favored : 68.19 % 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: -1.12 (0.31), residues: 751 helix: 0.57 (0.35), residues: 233 sheet: -1.07 (0.38), residues: 177 loop : -1.44 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.012 0.002 TYR A 342 PHE 0.018 0.002 PHE A 835 TRP 0.007 0.001 TRP A 769 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 7390) covalent geometry : angle 0.58757 / 0.30 (10253) hydrogen bonds : bond 0.04099 / 2.84 ( 331) hydrogen bonds : angle 5.34648 / 3.66 ( 889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6773 (mtt) REVERT: A 294 LYS cc_start: 0.5183 (OUTLIER) cc_final: 0.4878 (ptpp) REVERT: A 329 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.6528 (mpp) REVERT: A 333 ASP cc_start: 0.7723 (m-30) cc_final: 0.6857 (t0) REVERT: A 369 ASP cc_start: 0.6724 (t0) cc_final: 0.6507 (t0) REVERT: A 436 PRO cc_start: 0.6086 (Cg_exo) cc_final: 0.5813 (Cg_endo) REVERT: A 515 LEU cc_start: 0.6782 (tp) cc_final: 0.6426 (tp) REVERT: A 531 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6676 (mm-30) REVERT: A 562 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: A 647 ILE cc_start: 0.7055 (mt) cc_final: 0.6775 (mt) REVERT: A 794 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5675 (mm) outliers start: 37 outliers final: 21 residues processed: 116 average time/residue: 0.4124 time to fit residues: 51.3935 Evaluate side-chains 115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 918 MET Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.203989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165139 restraints weight = 7699.674| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.05 r_work: 0.3908 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7390 Z= 0.168 Angle : 0.593 8.906 10253 Z= 0.308 Chirality : 0.044 0.178 1202 Planarity : 0.005 0.050 1113 Dihedral : 17.226 85.615 1583 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 5.15 % Allowed : 27.84 % Favored : 67.01 % 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: -1.09 (0.31), residues: 751 helix: 0.59 (0.35), residues: 234 sheet: -1.06 (0.39), residues: 177 loop : -1.41 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.012 0.002 TYR A 342 PHE 0.017 0.002 PHE A 835 TRP 0.006 0.001 TRP A 769 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 7390) covalent geometry : angle 0.59272 / 0.31 (10253) hydrogen bonds : bond 0.04076 / 2.82 ( 331) hydrogen bonds : angle 5.32958 / 3.65 ( 889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5153 (OUTLIER) cc_final: 0.4838 (ptpp) REVERT: A 329 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.6457 (mpp) REVERT: A 333 ASP cc_start: 0.7593 (m-30) cc_final: 0.6723 (t0) REVERT: A 369 ASP cc_start: 0.6539 (t0) cc_final: 0.6324 (t0) REVERT: A 436 PRO cc_start: 0.6106 (Cg_exo) cc_final: 0.5841 (Cg_endo) REVERT: A 531 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6362 (mm-30) REVERT: A 562 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: A 647 ILE cc_start: 0.7147 (mt) cc_final: 0.6823 (mt) REVERT: A 794 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5522 (mm) outliers start: 35 outliers final: 23 residues processed: 116 average time/residue: 0.3733 time to fit residues: 46.7346 Evaluate side-chains 115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 918 MET Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN A 954 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.199258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159807 restraints weight = 7710.023| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.05 r_work: 0.3878 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7390 Z= 0.264 Angle : 0.695 9.544 10253 Z= 0.362 Chirality : 0.048 0.199 1202 Planarity : 0.006 0.058 1113 Dihedral : 17.182 84.577 1583 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 7.22 % Allowed : 25.92 % Favored : 66.86 % 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: -1.32 (0.30), residues: 751 helix: 0.35 (0.35), residues: 231 sheet: -1.22 (0.38), residues: 177 loop : -1.48 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.032 0.003 TYR A 904 PHE 0.023 0.002 PHE A 835 TRP 0.009 0.002 TRP A 550 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.26 ( 7390) covalent geometry : angle 0.69465 / 0.36 (10253) hydrogen bonds : bond 0.05190 / 3.54 ( 331) hydrogen bonds : angle 5.56777 / 3.81 ( 889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.156 Fit side-chains REVERT: A 294 LYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4953 (ptpp) REVERT: A 329 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.6727 (mpp) REVERT: A 333 ASP cc_start: 0.7647 (m-30) cc_final: 0.6771 (t0) REVERT: A 369 ASP cc_start: 0.6560 (t0) cc_final: 0.6356 (t0) REVERT: A 436 PRO cc_start: 0.6191 (Cg_exo) cc_final: 0.5920 (Cg_endo) REVERT: A 531 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6205 (mm-30) REVERT: A 562 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: A 647 ILE cc_start: 0.7207 (mt) cc_final: 0.6901 (mt) REVERT: A 794 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5358 (mm) REVERT: A 918 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5816 (ttp) outliers start: 49 outliers final: 28 residues processed: 129 average time/residue: 0.3812 time to fit residues: 52.7292 Evaluate side-chains 121 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 918 MET Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN A 954 GLN A 963 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.205703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.166217 restraints weight = 7529.402| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.96 r_work: 0.3857 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7390 Z= 0.133 Angle : 0.596 11.711 10253 Z= 0.307 Chirality : 0.043 0.181 1202 Planarity : 0.005 0.075 1113 Dihedral : 17.359 87.824 1583 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 4.42 % Allowed : 28.87 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.31), residues: 751 helix: 0.85 (0.36), residues: 229 sheet: -1.09 (0.38), residues: 176 loop : -1.28 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 937 TYR 0.016 0.002 TYR A 904 PHE 0.015 0.002 PHE A 758 TRP 0.010 0.001 TRP A 604 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7390) covalent geometry : angle 0.59552 / 0.31 (10253) hydrogen bonds : bond 0.03877 / 2.68 ( 331) hydrogen bonds : angle 5.31448 / 3.66 ( 889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.4915 (ptpp) REVERT: A 333 ASP cc_start: 0.7670 (m-30) cc_final: 0.6778 (t0) REVERT: A 369 ASP cc_start: 0.6531 (t0) cc_final: 0.6300 (t0) REVERT: A 436 PRO cc_start: 0.6199 (Cg_exo) cc_final: 0.5952 (Cg_endo) REVERT: A 647 ILE cc_start: 0.7183 (mt) cc_final: 0.6894 (mt) REVERT: A 719 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.5542 (mmt) REVERT: A 763 ASN cc_start: 0.7634 (p0) cc_final: 0.7255 (p0) REVERT: A 794 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5616 (mm) REVERT: A 918 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5864 (ttp) outliers start: 30 outliers final: 18 residues processed: 111 average time/residue: 0.3639 time to fit residues: 43.5898 Evaluate side-chains 110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 918 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 31 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.206416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167156 restraints weight = 7471.295| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.91 r_work: 0.3861 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7390 Z= 0.134 Angle : 0.585 10.942 10253 Z= 0.301 Chirality : 0.044 0.178 1202 Planarity : 0.005 0.083 1113 Dihedral : 17.286 86.438 1582 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 3.68 % Allowed : 30.19 % Favored : 66.13 % 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: -0.85 (0.31), residues: 751 helix: 0.88 (0.36), residues: 230 sheet: -1.06 (0.38), residues: 176 loop : -1.24 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 937 TYR 0.013 0.002 TYR A 904 PHE 0.015 0.002 PHE A 835 TRP 0.007 0.001 TRP A 604 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7390) covalent geometry : angle 0.58476 / 0.30 (10253) hydrogen bonds : bond 0.03766 / 2.60 ( 331) hydrogen bonds : angle 5.24040 / 3.59 ( 889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5215 (OUTLIER) cc_final: 0.4905 (ptpp) REVERT: A 333 ASP cc_start: 0.7669 (m-30) cc_final: 0.6766 (t0) REVERT: A 436 PRO cc_start: 0.6173 (Cg_exo) cc_final: 0.5897 (Cg_endo) REVERT: A 647 ILE cc_start: 0.7174 (mt) cc_final: 0.6889 (mt) REVERT: A 763 ASN cc_start: 0.7462 (p0) cc_final: 0.6885 (p0) REVERT: A 782 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5224 (mp) REVERT: A 794 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5596 (mm) REVERT: A 918 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5822 (ttp) outliers start: 25 outliers final: 17 residues processed: 107 average time/residue: 0.3772 time to fit residues: 43.6204 Evaluate side-chains 110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 918 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** 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 = 0.4356 r_free = 0.4356 target = 0.203769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.164667 restraints weight = 7526.420| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.10 r_work: 0.3815 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7390 Z= 0.173 Angle : 0.619 11.310 10253 Z= 0.318 Chirality : 0.045 0.181 1202 Planarity : 0.006 0.086 1113 Dihedral : 17.230 85.113 1581 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 3.83 % Allowed : 30.34 % Favored : 65.83 % 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: -0.93 (0.31), residues: 751 helix: 0.79 (0.35), residues: 232 sheet: -1.03 (0.38), residues: 176 loop : -1.33 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 937 TYR 0.013 0.002 TYR A 342 PHE 0.019 0.002 PHE A 835 TRP 0.006 0.001 TRP A 884 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 7390) covalent geometry : angle 0.61935 / 0.32 (10253) hydrogen bonds : bond 0.04021 / 2.76 ( 331) hydrogen bonds : angle 5.30134 / 3.62 ( 889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5225 (OUTLIER) cc_final: 0.4925 (ptpp) REVERT: A 333 ASP cc_start: 0.7780 (m-30) cc_final: 0.6874 (t0) REVERT: A 369 ASP cc_start: 0.6512 (t0) cc_final: 0.6239 (t0) REVERT: A 436 PRO cc_start: 0.6184 (Cg_exo) cc_final: 0.5932 (Cg_endo) REVERT: A 647 ILE cc_start: 0.7193 (mt) cc_final: 0.6912 (mt) REVERT: A 763 ASN cc_start: 0.7561 (p0) cc_final: 0.7187 (p0) REVERT: A 782 ILE cc_start: 0.5685 (OUTLIER) cc_final: 0.5355 (mp) REVERT: A 794 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5634 (mm) outliers start: 26 outliers final: 19 residues processed: 108 average time/residue: 0.4117 time to fit residues: 47.8964 Evaluate side-chains 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 918 MET Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** 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 = 0.4373 r_free = 0.4373 target = 0.205646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167060 restraints weight = 7514.531| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.05 r_work: 0.3840 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7390 Z= 0.144 Angle : 0.606 11.852 10253 Z= 0.309 Chirality : 0.044 0.177 1202 Planarity : 0.005 0.084 1113 Dihedral : 17.263 85.799 1581 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 3.68 % Allowed : 30.78 % Favored : 65.54 % 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: -0.89 (0.31), residues: 751 helix: 0.79 (0.35), residues: 233 sheet: -1.05 (0.38), residues: 176 loop : -1.26 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 937 TYR 0.013 0.002 TYR A 904 PHE 0.017 0.002 PHE A 835 TRP 0.006 0.001 TRP A 884 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7390) covalent geometry : angle 0.60615 / 0.31 (10253) hydrogen bonds : bond 0.03807 / 2.62 ( 331) hydrogen bonds : angle 5.25435 / 3.60 ( 889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.16 seconds wall clock time: 44 minutes 29.41 seconds (2669.41 seconds total)