Starting phenix.real_space_refine on Wed Sep 17 07:56:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij4_60615/09_2025/9ij4_60615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij4_60615/09_2025/9ij4_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_60615/09_2025/9ij4_60615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij4_60615/09_2025/9ij4_60615.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij4_60615/09_2025/9ij4_60615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij4_60615/09_2025/9ij4_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 1.95, per 1000 atoms: 0.27 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: 0.61 Conformation dependent library (CDL) restraints added in 444.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.03 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: 1.92 Time building geometry restraints manager: 0.86 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: 10118 3.12 - 6.25: 108 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=" N PRO A 863 " pdb=" CA PRO A 863 " pdb=" CB PRO A 863 " ideal model delta sigma weight residual 103.19 98.04 5.15 1.00e+00 1.00e+00 2.65e+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: 980 0.062 - 0.124: 191 0.124 - 0.187: 27 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: 0.330 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 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= 0.271 Angle : 0.913 15.614 10253 Z= 0.465 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 aren 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 covalent geometry : bond 0.00627 ( 7390) covalent geometry : angle 0.91347 (10253) hydrogen bonds : bond 0.12709 ( 331) hydrogen bonds : angle 7.10267 ( 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 : 0.150 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.4185 time to fit residues: 41.7857 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 : 0.273 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.210731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.172057 restraints weight = 7547.006| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.91 r_work: 0.3967 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7390 Z= 0.134 Angle : 0.585 8.199 10253 Z= 0.295 Chirality : 0.042 0.175 1202 Planarity : 0.006 0.090 1113 Dihedral : 17.559 127.185 1585 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 3.98 % Allowed : 26.95 % 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 aren not related in a simple way. whole: -1.21 (0.30), residues: 751 helix: 0.38 (0.34), residues: 229 sheet: -0.83 (0.39), residues: 177 loop : -1.56 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.020 0.002 TYR A 904 PHE 0.015 0.001 PHE A 835 TRP 0.007 0.001 TRP A 586 HIS 0.003 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7390) covalent geometry : angle 0.58508 (10253) hydrogen bonds : bond 0.03901 ( 331) hydrogen bonds : angle 5.40983 ( 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 115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5163 (OUTLIER) cc_final: 0.4893 (ptpp) REVERT: A 624 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6125 (pt0) outliers start: 27 outliers final: 10 residues processed: 109 average time/residue: 0.4136 time to fit residues: 48.5491 Evaluate side-chains 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 730 VAL Chi-restraints excluded: chain A residue 734 LEU 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: 5.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.202029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.161158 restraints weight = 7467.961| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.92 r_work: 0.3795 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7390 Z= 0.253 Angle : 0.688 9.886 10253 Z= 0.350 Chirality : 0.046 0.207 1202 Planarity : 0.006 0.073 1113 Dihedral : 17.175 84.819 1583 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 6.33 % Allowed : 25.63 % Favored : 68.04 % 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 aren not related in a simple way. whole: -1.40 (0.30), residues: 751 helix: 0.16 (0.34), residues: 234 sheet: -1.08 (0.39), residues: 177 loop : -1.56 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 652 TYR 0.018 0.002 TYR A 454 PHE 0.020 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 covalent geometry : bond 0.00571 ( 7390) covalent geometry : angle 0.68752 (10253) hydrogen bonds : bond 0.04805 ( 331) hydrogen bonds : angle 5.56863 ( 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 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.232 Fit side-chains REVERT: A 294 LYS cc_start: 0.5175 (OUTLIER) cc_final: 0.4867 (ptpp) REVERT: A 329 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.6479 (mpp) REVERT: A 333 ASP cc_start: 0.7722 (m-30) cc_final: 0.6817 (t0) REVERT: A 369 ASP cc_start: 0.6637 (t0) cc_final: 0.6398 (t0) REVERT: A 392 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5450 (mpt) REVERT: A 436 PRO cc_start: 0.6043 (Cg_exo) cc_final: 0.5754 (Cg_endo) REVERT: A 498 MET cc_start: 0.7184 (mtt) cc_final: 0.6924 (mtt) REVERT: A 530 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6038 (mp) REVERT: A 531 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6528 (mm-30) REVERT: A 794 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5637 (mm) REVERT: A 918 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5772 (ttp) outliers start: 43 outliers final: 16 residues processed: 125 average time/residue: 0.4326 time to fit residues: 57.9728 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 : 0.245 ------------------------------------------------------------------------------- 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 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 328 VAL 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 495 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 538 SER 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.206638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167050 restraints weight = 7539.747| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.91 r_work: 0.3853 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7390 Z= 0.130 Angle : 0.570 8.488 10253 Z= 0.289 Chirality : 0.042 0.182 1202 Planarity : 0.005 0.065 1113 Dihedral : 17.269 87.321 1583 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % 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 aren not related in a simple way. whole: -1.02 (0.31), residues: 751 helix: 0.62 (0.35), residues: 236 sheet: -1.06 (0.39), residues: 177 loop : -1.34 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.010 0.001 TYR A 342 PHE 0.014 0.002 PHE A 835 TRP 0.007 0.001 TRP A 604 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7390) covalent geometry : angle 0.56973 (10253) hydrogen bonds : bond 0.03613 ( 331) hydrogen bonds : angle 5.24076 ( 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 132 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6505 (mtt) REVERT: A 294 LYS cc_start: 0.5166 (OUTLIER) cc_final: 0.4859 (ptpp) REVERT: A 333 ASP cc_start: 0.7460 (m-30) cc_final: 0.6602 (t0) REVERT: A 369 ASP cc_start: 0.6477 (t0) cc_final: 0.6262 (t0) REVERT: A 392 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.5331 (mpt) REVERT: A 436 PRO cc_start: 0.6154 (Cg_exo) cc_final: 0.5913 (Cg_endo) REVERT: A 498 MET cc_start: 0.7027 (mtt) cc_final: 0.6796 (mtt) REVERT: A 515 LEU cc_start: 0.6658 (tp) cc_final: 0.6342 (tp) REVERT: A 624 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6022 (pt0) REVERT: A 782 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5404 (mp) REVERT: A 794 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5659 (mm) outliers start: 39 outliers final: 19 residues processed: 119 average time/residue: 0.4240 time to fit residues: 54.0175 Evaluate side-chains 112 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU 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 392 MET Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 499 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 755 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 777 MET 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 907 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 71 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 5 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 0.0870 overall best weight: 0.8738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.208343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168920 restraints weight = 7505.545| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.92 r_work: 0.3880 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7390 Z= 0.125 Angle : 0.569 10.324 10253 Z= 0.286 Chirality : 0.042 0.182 1202 Planarity : 0.005 0.055 1113 Dihedral : 17.245 86.852 1583 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 5.45 % Allowed : 27.69 % 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 aren not related in a simple way. whole: -0.76 (0.31), residues: 751 helix: 0.98 (0.36), residues: 229 sheet: -1.03 (0.38), residues: 178 loop : -1.17 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.014 0.001 TYR A 425 PHE 0.015 0.001 PHE A 835 TRP 0.005 0.001 TRP A 604 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7390) covalent geometry : angle 0.56932 (10253) hydrogen bonds : bond 0.03401 ( 331) hydrogen bonds : angle 5.10300 ( 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 129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5256 (OUTLIER) cc_final: 0.4955 (ptpp) REVERT: A 333 ASP cc_start: 0.7567 (m-30) cc_final: 0.6713 (t0) REVERT: A 392 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.5311 (mpt) REVERT: A 436 PRO cc_start: 0.6112 (Cg_exo) cc_final: 0.5860 (Cg_endo) REVERT: A 498 MET cc_start: 0.7155 (mtt) cc_final: 0.6869 (mtt) REVERT: A 624 GLU cc_start: 0.6637 (mt-10) cc_final: 0.5921 (pt0) REVERT: A 647 ILE cc_start: 0.7057 (mt) cc_final: 0.6792 (mt) REVERT: A 782 ILE cc_start: 0.5905 (OUTLIER) cc_final: 0.5434 (mp) REVERT: A 794 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5742 (mm) outliers start: 37 outliers final: 18 residues processed: 117 average time/residue: 0.3993 time to fit residues: 50.3883 Evaluate side-chains 108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 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 266 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 530 LEU 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 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 935 THR 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: 10.0000 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.205955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165919 restraints weight = 7489.010| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.92 r_work: 0.3847 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7390 Z= 0.155 Angle : 0.588 8.676 10253 Z= 0.295 Chirality : 0.043 0.179 1202 Planarity : 0.005 0.069 1113 Dihedral : 17.184 85.609 1582 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 5.15 % Allowed : 28.28 % Favored : 66.57 % 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 aren not related in a simple way. whole: -0.78 (0.31), residues: 751 helix: 0.94 (0.35), residues: 232 sheet: -0.97 (0.39), residues: 176 loop : -1.23 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 652 TYR 0.013 0.002 TYR A 425 PHE 0.015 0.002 PHE A 835 TRP 0.006 0.001 TRP A 586 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7390) covalent geometry : angle 0.58750 (10253) hydrogen bonds : bond 0.03628 ( 331) hydrogen bonds : angle 5.11622 ( 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 125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5249 (OUTLIER) cc_final: 0.4951 (ptpp) REVERT: A 329 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.6105 (mpp) REVERT: A 333 ASP cc_start: 0.7531 (m-30) cc_final: 0.6697 (t0) REVERT: A 392 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5236 (mpt) REVERT: A 431 ASP cc_start: 0.6287 (t70) cc_final: 0.6010 (t70) REVERT: A 498 MET cc_start: 0.7348 (mtt) cc_final: 0.7026 (mtt) REVERT: A 562 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: A 624 GLU cc_start: 0.6634 (mt-10) cc_final: 0.5927 (pt0) REVERT: A 647 ILE cc_start: 0.7118 (mt) cc_final: 0.6829 (mt) REVERT: A 666 MET cc_start: 0.7354 (mmt) cc_final: 0.7146 (mmm) REVERT: A 782 ILE cc_start: 0.5864 (OUTLIER) cc_final: 0.5396 (mp) REVERT: A 794 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5584 (mm) outliers start: 35 outliers final: 21 residues processed: 115 average time/residue: 0.4135 time to fit residues: 51.3506 Evaluate side-chains 114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 329 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 392 MET 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 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 755 VAL 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 935 THR 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: 7.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4299 r_free = 0.4299 target = 0.197220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.158156 restraints weight = 7515.176| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.99 r_work: 0.3734 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 7390 Z= 0.345 Angle : 0.793 10.777 10253 Z= 0.403 Chirality : 0.051 0.217 1202 Planarity : 0.006 0.066 1113 Dihedral : 17.253 83.375 1582 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 6.77 % Allowed : 26.51 % 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 aren not related in a simple way. whole: -1.44 (0.30), residues: 751 helix: 0.12 (0.34), residues: 233 sheet: -1.23 (0.39), residues: 177 loop : -1.50 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 646 TYR 0.018 0.003 TYR A 454 PHE 0.025 0.003 PHE A 835 TRP 0.012 0.002 TRP A 550 HIS 0.008 0.002 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00779 ( 7390) covalent geometry : angle 0.79284 (10253) hydrogen bonds : bond 0.05551 ( 331) hydrogen bonds : angle 5.72083 ( 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 143 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.296 Fit side-chains REVERT: A 294 LYS cc_start: 0.5288 (OUTLIER) cc_final: 0.4966 (ptpp) REVERT: A 329 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.6670 (mpp) REVERT: A 333 ASP cc_start: 0.7636 (m-30) cc_final: 0.6883 (t0) REVERT: A 431 ASP cc_start: 0.6451 (t70) cc_final: 0.6150 (t70) REVERT: A 531 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: A 555 HIS cc_start: 0.7217 (t-90) cc_final: 0.6983 (t-90) REVERT: A 647 ILE cc_start: 0.7308 (mt) cc_final: 0.6919 (mt) REVERT: A 776 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.5089 (mm110) REVERT: A 794 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5473 (mm) REVERT: A 918 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6133 (ttp) outliers start: 46 outliers final: 24 residues processed: 130 average time/residue: 0.4827 time to fit residues: 67.0857 Evaluate side-chains 118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 294 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 369 ASP 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 580 THR 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 752 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 776 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 421 ASN 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 = 0.4374 r_free = 0.4374 target = 0.205868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166398 restraints weight = 7550.546| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.92 r_work: 0.3852 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7390 Z= 0.136 Angle : 0.629 11.594 10253 Z= 0.311 Chirality : 0.044 0.189 1202 Planarity : 0.005 0.058 1113 Dihedral : 17.332 87.438 1582 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 4.12 % Allowed : 29.31 % Favored : 66.57 % 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 aren not related in a simple way. whole: -0.98 (0.31), residues: 751 helix: 0.79 (0.35), residues: 232 sheet: -1.14 (0.38), residues: 176 loop : -1.34 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 366 TYR 0.026 0.002 TYR A 904 PHE 0.017 0.002 PHE A 775 TRP 0.009 0.001 TRP A 604 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7390) covalent geometry : angle 0.62889 (10253) hydrogen bonds : bond 0.03630 ( 331) hydrogen bonds : angle 5.29609 ( 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 121 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.271 Fit side-chains REVERT: A 294 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.4896 (ptpp) REVERT: A 333 ASP cc_start: 0.7589 (m-30) cc_final: 0.6802 (t0) REVERT: A 431 ASP cc_start: 0.6291 (t70) cc_final: 0.5999 (t70) REVERT: A 515 LEU cc_start: 0.6664 (tp) cc_final: 0.6259 (tp) REVERT: A 647 ILE cc_start: 0.7179 (mt) cc_final: 0.6895 (mt) REVERT: A 782 ILE cc_start: 0.5883 (OUTLIER) cc_final: 0.5472 (mp) REVERT: A 794 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5590 (mm) REVERT: A 918 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5713 (ttp) outliers start: 28 outliers final: 14 residues processed: 112 average time/residue: 0.4227 time to fit residues: 51.0675 Evaluate side-chains 107 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 495 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.207827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168789 restraints weight = 7496.263| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.92 r_work: 0.3877 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7390 Z= 0.129 Angle : 0.617 12.274 10253 Z= 0.304 Chirality : 0.044 0.187 1202 Planarity : 0.005 0.052 1113 Dihedral : 17.302 86.405 1582 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 3.39 % Allowed : 31.08 % 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 aren not related in a simple way. whole: -0.87 (0.31), residues: 751 helix: 0.96 (0.35), residues: 232 sheet: -1.16 (0.37), residues: 176 loop : -1.28 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 419 TYR 0.033 0.002 TYR A 420 PHE 0.014 0.001 PHE A 835 TRP 0.007 0.001 TRP A 604 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7390) covalent geometry : angle 0.61719 (10253) hydrogen bonds : bond 0.03436 ( 331) hydrogen bonds : angle 5.14833 ( 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 112 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4911 (ptpp) REVERT: A 333 ASP cc_start: 0.7554 (m-30) cc_final: 0.6763 (t0) REVERT: A 431 ASP cc_start: 0.6406 (t70) cc_final: 0.6113 (t70) REVERT: A 515 LEU cc_start: 0.6659 (tp) cc_final: 0.6242 (tp) REVERT: A 624 GLU cc_start: 0.6625 (mt-10) cc_final: 0.5936 (pt0) REVERT: A 647 ILE cc_start: 0.7132 (mt) cc_final: 0.6861 (mt) REVERT: A 763 ASN cc_start: 0.7642 (p0) cc_final: 0.7269 (p0) REVERT: A 782 ILE cc_start: 0.5541 (OUTLIER) cc_final: 0.5307 (mp) REVERT: A 794 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5678 (mm) REVERT: A 918 MET cc_start: 0.6190 (ttp) cc_final: 0.5719 (ttp) outliers start: 23 outliers final: 15 residues processed: 104 average time/residue: 0.4219 time to fit residues: 47.2037 Evaluate side-chains 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 294 LYS Chi-restraints excluded: chain A residue 302 ILE 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 538 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN A 963 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.204999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.165297 restraints weight = 7552.745| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.94 r_work: 0.3840 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7390 Z= 0.161 Angle : 0.643 12.591 10253 Z= 0.317 Chirality : 0.044 0.181 1202 Planarity : 0.005 0.061 1113 Dihedral : 17.254 85.155 1582 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 3.09 % Allowed : 31.37 % 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 aren not related in a simple way. whole: -0.90 (0.31), residues: 751 helix: 0.90 (0.35), residues: 232 sheet: -1.09 (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 0.034 0.002 TYR A 420 PHE 0.017 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 covalent geometry : bond 0.00366 ( 7390) covalent geometry : angle 0.64325 (10253) hydrogen bonds : bond 0.03683 ( 331) hydrogen bonds : angle 5.18133 ( 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 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5259 (OUTLIER) cc_final: 0.4971 (ptpp) REVERT: A 333 ASP cc_start: 0.7642 (m-30) cc_final: 0.6846 (t0) REVERT: A 431 ASP cc_start: 0.6337 (t70) cc_final: 0.5991 (t70) REVERT: A 515 LEU cc_start: 0.6701 (tp) cc_final: 0.6322 (tp) REVERT: A 647 ILE cc_start: 0.7169 (mt) cc_final: 0.6886 (mt) REVERT: A 763 ASN cc_start: 0.7697 (p0) cc_final: 0.7325 (p0) REVERT: A 776 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.4547 (mm110) REVERT: A 782 ILE cc_start: 0.5698 (OUTLIER) cc_final: 0.5338 (mp) REVERT: A 794 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5571 (mm) REVERT: A 918 MET cc_start: 0.6220 (ttp) cc_final: 0.5757 (ttp) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.4235 time to fit residues: 46.5814 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 : 0.257 ------------------------------------------------------------------------------- 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 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 495 LEU 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 742 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 776 GLN 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 928 MET 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: 1.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN ** A 421 ASN ** 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 = 0.4365 r_free = 0.4365 target = 0.205124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165540 restraints weight = 7509.991| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.92 r_work: 0.3843 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 7390 Z= 0.210 Angle : 0.984 59.200 10253 Z= 0.572 Chirality : 0.044 0.180 1202 Planarity : 0.005 0.059 1113 Dihedral : 17.253 85.172 1582 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 3.09 % Allowed : 31.22 % Favored : 65.68 % 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 aren not related in a simple way. whole: -0.91 (0.31), residues: 751 helix: 0.89 (0.35), residues: 232 sheet: -1.08 (0.38), residues: 176 loop : -1.34 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.029 0.002 TYR A 420 PHE 0.017 0.002 PHE A 835 TRP 0.006 0.001 TRP A 884 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7390) covalent geometry : angle 0.98407 (10253) hydrogen bonds : bond 0.03834 ( 331) hydrogen bonds : angle 5.17986 ( 889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.95 seconds wall clock time: 46 minutes 20.90 seconds (2780.90 seconds total)