Starting phenix.real_space_refine on Wed Feb 12 00:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij4_60615/02_2025/9ij4_60615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij4_60615/02_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_60615/02_2025/9ij4_60615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij4_60615/02_2025/9ij4_60615.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij4_60615/02_2025/9ij4_60615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij4_60615/02_2025/9ij4_60615.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.51, per 1000 atoms: 0.63 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: 1.97 Conformation dependent library (CDL) restraints added in 676.4 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: 2.80 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: 3.01 Time building geometry restraints manager: 2.26 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.650 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:16.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- 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= 0.383 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP A 586 HIS 0.006 0.001 HIS A 865 PHE 0.028 0.003 PHE A 835 TYR 0.034 0.003 TYR A 904 ARG 0.035 0.001 ARG A 652 *********************** 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 : 0.755 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.9047 time to fit residues: 90.6318 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 : 0.718 ------------------------------------------------------------------------------- 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 66 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.211062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172596 restraints weight = 7445.082| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.90 r_work: 0.3981 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7390 Z= 0.190 Angle : 0.586 7.775 10253 Z= 0.296 Chirality : 0.042 0.173 1202 Planarity : 0.006 0.090 1113 Dihedral : 17.567 126.099 1585 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 3.83 % Allowed : 27.54 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.30), residues: 751 helix: 0.32 (0.33), residues: 229 sheet: -0.80 (0.39), residues: 177 loop : -1.58 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.003 0.001 HIS A 242 PHE 0.014 0.001 PHE A 835 TYR 0.020 0.002 TYR A 904 ARG 0.004 0.000 ARG A 652 *********************** 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 113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5129 (OUTLIER) cc_final: 0.4852 (ptpp) REVERT: A 624 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6082 (pt0) outliers start: 26 outliers final: 10 residues processed: 107 average time/residue: 0.8828 time to fit residues: 101.8015 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 : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU 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 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 76 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.211742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.172848 restraints weight = 7494.447| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.92 r_work: 0.3984 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7390 Z= 0.167 Angle : 0.544 8.870 10253 Z= 0.274 Chirality : 0.041 0.175 1202 Planarity : 0.005 0.069 1113 Dihedral : 17.247 84.845 1583 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 4.86 % Allowed : 27.69 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.30), residues: 751 helix: 0.78 (0.35), residues: 229 sheet: -0.79 (0.39), residues: 176 loop : -1.41 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 586 HIS 0.003 0.001 HIS A 927 PHE 0.017 0.001 PHE A 950 TYR 0.021 0.001 TYR A 904 ARG 0.009 0.000 ARG A 652 *********************** 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 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.6651 (m-30) cc_final: 0.6343 (m-30) REVERT: A 294 LYS cc_start: 0.5130 (OUTLIER) cc_final: 0.4852 (ptpp) REVERT: A 333 ASP cc_start: 0.7396 (m-30) cc_final: 0.6592 (t0) REVERT: A 369 ASP cc_start: 0.6482 (t0) cc_final: 0.6253 (t0) REVERT: A 392 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.5280 (mpt) REVERT: A 436 PRO cc_start: 0.6044 (Cg_exo) cc_final: 0.5731 (Cg_endo) REVERT: A 624 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6075 (pt0) REVERT: A 794 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5638 (mm) outliers start: 33 outliers final: 11 residues processed: 114 average time/residue: 0.9672 time to fit residues: 118.4757 Evaluate side-chains 98 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 392 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.203289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162806 restraints weight = 7481.286| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.94 r_work: 0.3808 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7390 Z= 0.313 Angle : 0.647 8.904 10253 Z= 0.329 Chirality : 0.045 0.179 1202 Planarity : 0.006 0.064 1113 Dihedral : 17.123 84.688 1582 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 6.19 % Allowed : 26.22 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.31), residues: 751 helix: 0.57 (0.35), residues: 229 sheet: -0.97 (0.39), residues: 177 loop : -1.37 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 769 HIS 0.007 0.001 HIS A 526 PHE 0.017 0.002 PHE A 835 TYR 0.015 0.002 TYR A 454 ARG 0.005 0.001 ARG A 652 *********************** 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 134 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.6990 (mmm) cc_final: 0.6603 (mtt) REVERT: A 294 LYS cc_start: 0.5212 (OUTLIER) cc_final: 0.4917 (ptpp) REVERT: A 329 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.6480 (mpp) REVERT: A 333 ASP cc_start: 0.7561 (m-30) cc_final: 0.6710 (t0) REVERT: A 369 ASP cc_start: 0.6667 (t0) cc_final: 0.6445 (t0) REVERT: A 436 PRO cc_start: 0.6170 (Cg_exo) cc_final: 0.5962 (Cg_endo) REVERT: A 495 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7781 (mm) REVERT: A 531 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6575 (mm-30) REVERT: A 647 ILE cc_start: 0.7089 (mt) cc_final: 0.6805 (mt) REVERT: A 782 ILE cc_start: 0.5964 (OUTLIER) cc_final: 0.5468 (mp) REVERT: A 794 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5602 (mm) outliers start: 42 outliers final: 17 residues processed: 121 average time/residue: 0.8879 time to fit residues: 116.0867 Evaluate side-chains 108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 304 ILE 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.203818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163872 restraints weight = 7386.950| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.95 r_work: 0.3839 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1767 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= 0.240 Angle : 0.599 9.310 10253 Z= 0.303 Chirality : 0.043 0.181 1202 Planarity : 0.005 0.056 1113 Dihedral : 17.186 86.679 1582 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 5.15 % Allowed : 27.69 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.31), residues: 751 helix: 0.76 (0.35), residues: 229 sheet: -0.95 (0.39), residues: 176 loop : -1.36 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 604 HIS 0.006 0.001 HIS A 526 PHE 0.016 0.002 PHE A 835 TYR 0.025 0.002 TYR A 904 ARG 0.005 0.000 ARG A 652 *********************** 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 125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.6600 (mmm) cc_final: 0.6366 (mtt) REVERT: A 294 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4867 (ptpp) REVERT: A 329 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.6150 (mpp) REVERT: A 333 ASP cc_start: 0.7469 (m-30) cc_final: 0.6568 (t0) REVERT: A 369 ASP cc_start: 0.6534 (t0) cc_final: 0.6325 (t0) REVERT: A 392 MET cc_start: 0.5215 (mpt) cc_final: 0.4867 (mpt) REVERT: A 436 PRO cc_start: 0.6277 (Cg_exo) cc_final: 0.6071 (Cg_endo) REVERT: A 531 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6463 (mm-30) REVERT: A 624 GLU cc_start: 0.6650 (mt-10) cc_final: 0.5835 (pt0) REVERT: A 647 ILE cc_start: 0.7114 (mt) cc_final: 0.6839 (mt) REVERT: A 794 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5627 (mm) outliers start: 35 outliers final: 19 residues processed: 113 average time/residue: 0.8826 time to fit residues: 107.6294 Evaluate side-chains 110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 328 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 435 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 0.0570 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.200819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161166 restraints weight = 7516.786| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.07 r_work: 0.3774 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2140 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= 0.367 Angle : 0.694 10.247 10253 Z= 0.352 Chirality : 0.047 0.198 1202 Planarity : 0.006 0.070 1113 Dihedral : 17.172 84.981 1582 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 6.04 % Allowed : 27.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.30), residues: 751 helix: 0.45 (0.35), residues: 232 sheet: -1.14 (0.39), residues: 177 loop : -1.47 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 769 HIS 0.006 0.001 HIS A 242 PHE 0.021 0.002 PHE A 835 TYR 0.015 0.002 TYR A 342 ARG 0.005 0.001 ARG A 652 *********************** 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 133 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.724 Fit side-chains REVERT: A 258 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6678 (mtt) REVERT: A 294 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4966 (ptpp) REVERT: A 329 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.6494 (mpp) REVERT: A 333 ASP cc_start: 0.7626 (m-30) cc_final: 0.6791 (t0) REVERT: A 369 ASP cc_start: 0.6622 (t0) cc_final: 0.6418 (t0) REVERT: A 431 ASP cc_start: 0.6372 (t70) cc_final: 0.6084 (t70) REVERT: A 436 PRO cc_start: 0.6184 (Cg_exo) cc_final: 0.5982 (Cg_endo) REVERT: A 531 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6526 (mm-30) REVERT: A 562 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: A 647 ILE cc_start: 0.7175 (mt) cc_final: 0.6838 (mt) REVERT: A 794 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.5597 (mm) REVERT: A 918 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.5876 (ttp) outliers start: 41 outliers final: 26 residues processed: 120 average time/residue: 0.8984 time to fit residues: 115.9727 Evaluate side-chains 122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 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 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 765 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4343 r_free = 0.4343 target = 0.202181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162963 restraints weight = 7476.518| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.08 r_work: 0.3799 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2155 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= 0.287 Angle : 0.647 11.089 10253 Z= 0.325 Chirality : 0.045 0.187 1202 Planarity : 0.005 0.058 1113 Dihedral : 17.239 85.988 1582 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 6.04 % Allowed : 27.69 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.31), residues: 751 helix: 0.55 (0.35), residues: 232 sheet: -1.12 (0.39), residues: 176 loop : -1.43 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 769 HIS 0.005 0.001 HIS A 242 PHE 0.018 0.002 PHE A 835 TYR 0.013 0.002 TYR A 342 ARG 0.005 0.000 ARG A 652 *********************** 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 132 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.721 Fit side-chains REVERT: A 258 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6689 (mtt) REVERT: A 294 LYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4935 (ptpp) REVERT: A 329 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.6301 (mpp) REVERT: A 333 ASP cc_start: 0.7751 (m-30) cc_final: 0.6904 (t0) REVERT: A 431 ASP cc_start: 0.6432 (t70) cc_final: 0.6139 (t70) REVERT: A 531 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6599 (mm-30) REVERT: A 647 ILE cc_start: 0.7148 (mt) cc_final: 0.6852 (mt) REVERT: A 794 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.5723 (mm) REVERT: A 918 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5875 (ttp) outliers start: 41 outliers final: 25 residues processed: 118 average time/residue: 0.8833 time to fit residues: 112.2428 Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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 765 THR 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 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 32 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 963 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.204212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164526 restraints weight = 7566.347| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.92 r_work: 0.3834 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7390 Z= 0.229 Angle : 0.620 11.615 10253 Z= 0.310 Chirality : 0.044 0.184 1202 Planarity : 0.005 0.052 1113 Dihedral : 17.247 86.453 1582 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 6.04 % Allowed : 28.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.31), residues: 751 helix: 0.71 (0.35), residues: 232 sheet: -1.12 (0.38), residues: 176 loop : -1.33 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 604 HIS 0.005 0.001 HIS A 526 PHE 0.015 0.002 PHE A 835 TYR 0.013 0.002 TYR A 425 ARG 0.003 0.000 ARG A 646 *********************** 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 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.744 Fit side-chains REVERT: A 294 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4929 (ptpp) REVERT: A 333 ASP cc_start: 0.7594 (m-30) cc_final: 0.6780 (t0) REVERT: A 431 ASP cc_start: 0.6422 (t70) cc_final: 0.6149 (t70) REVERT: A 515 LEU cc_start: 0.6781 (tp) cc_final: 0.6361 (tp) REVERT: A 531 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6538 (mm-30) REVERT: A 562 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6954 (mt-10) REVERT: A 647 ILE cc_start: 0.7171 (mt) cc_final: 0.6890 (mt) REVERT: A 666 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.7024 (tpp) REVERT: A 782 ILE cc_start: 0.5927 (OUTLIER) cc_final: 0.5536 (mp) REVERT: A 794 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5653 (mm) REVERT: A 918 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5889 (ttp) outliers start: 41 outliers final: 25 residues processed: 117 average time/residue: 0.8768 time to fit residues: 110.5989 Evaluate side-chains 120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 328 VAL 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 666 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 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 918 MET Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 353 HIS ** 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 = 0.4314 r_free = 0.4314 target = 0.199015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.160395 restraints weight = 7530.141| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.98 r_work: 0.3763 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7390 Z= 0.393 Angle : 0.731 12.403 10253 Z= 0.367 Chirality : 0.049 0.193 1202 Planarity : 0.006 0.066 1113 Dihedral : 17.253 83.709 1582 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.32 % Favored : 92.54 % Rotamer: Outliers : 5.89 % Allowed : 28.13 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.30), residues: 751 helix: 0.31 (0.35), residues: 231 sheet: -1.24 (0.38), residues: 176 loop : -1.43 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 550 HIS 0.006 0.001 HIS A 242 PHE 0.022 0.002 PHE A 835 TYR 0.029 0.003 TYR A 904 ARG 0.004 0.001 ARG A 646 *********************** 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 129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.720 Fit side-chains REVERT: A 294 LYS cc_start: 0.5217 (OUTLIER) cc_final: 0.4929 (ptpp) REVERT: A 329 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.6366 (mpp) REVERT: A 333 ASP cc_start: 0.7630 (m-30) cc_final: 0.6848 (t0) REVERT: A 435 THR cc_start: 0.2964 (OUTLIER) cc_final: 0.2671 (t) REVERT: A 531 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: A 562 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: A 647 ILE cc_start: 0.7275 (mt) cc_final: 0.6900 (mt) REVERT: A 794 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5567 (mm) REVERT: A 918 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5957 (ttp) outliers start: 40 outliers final: 27 residues processed: 118 average time/residue: 0.8714 time to fit residues: 111.5955 Evaluate side-chains 120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 328 VAL Chi-restraints excluded: chain A residue 329 MET 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 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 765 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.207096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168044 restraints weight = 7625.675| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.93 r_work: 0.3870 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2202 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= 0.199 Angle : 0.617 12.428 10253 Z= 0.305 Chirality : 0.044 0.190 1202 Planarity : 0.005 0.059 1113 Dihedral : 17.306 87.389 1582 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 4.42 % Allowed : 29.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.31), residues: 751 helix: 0.76 (0.35), residues: 230 sheet: -1.20 (0.37), residues: 177 loop : -1.30 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 604 HIS 0.006 0.001 HIS A 526 PHE 0.014 0.002 PHE A 950 TYR 0.024 0.002 TYR A 420 ARG 0.004 0.000 ARG A 366 ********************** 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 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.702 Fit side-chains REVERT: A 294 LYS cc_start: 0.5136 (OUTLIER) cc_final: 0.4849 (ptpp) REVERT: A 333 ASP cc_start: 0.7616 (m-30) cc_final: 0.6797 (t0) REVERT: A 562 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: A 647 ILE cc_start: 0.7129 (mt) cc_final: 0.6854 (mt) REVERT: A 652 ARG cc_start: 0.6746 (mmp-170) cc_final: 0.6544 (mmp80) REVERT: A 782 ILE cc_start: 0.5813 (OUTLIER) cc_final: 0.5571 (mp) REVERT: A 794 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5646 (mm) REVERT: A 918 MET cc_start: 0.6179 (OUTLIER) cc_final: 0.5739 (ttp) outliers start: 30 outliers final: 21 residues processed: 111 average time/residue: 0.8565 time to fit residues: 102.4135 Evaluate side-chains 113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 421 ASN 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 562 GLU Chi-restraints excluded: chain A residue 634 ILE 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 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 41 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.208194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169134 restraints weight = 7587.653| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.94 r_work: 0.3881 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7390 Z= 0.187 Angle : 0.618 11.607 10253 Z= 0.305 Chirality : 0.044 0.184 1202 Planarity : 0.005 0.053 1113 Dihedral : 17.295 86.453 1582 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 3.53 % Allowed : 30.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.31), residues: 751 helix: 0.89 (0.35), residues: 231 sheet: -1.10 (0.38), residues: 175 loop : -1.23 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 769 HIS 0.005 0.001 HIS A 526 PHE 0.015 0.002 PHE A 835 TYR 0.022 0.002 TYR A 420 ARG 0.007 0.000 ARG A 937 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5164.78 seconds wall clock time: 92 minutes 3.07 seconds (5523.07 seconds total)