Starting phenix.real_space_refine on Wed Mar 12 00:07:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij4_60615/03_2025/9ij4_60615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij4_60615/03_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_60615/03_2025/9ij4_60615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij4_60615/03_2025/9ij4_60615.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij4_60615/03_2025/9ij4_60615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij4_60615/03_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-5624/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: 4.92, per 1000 atoms: 0.69 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: 2.01 Conformation dependent library (CDL) restraints added in 791.7 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: 2.72 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: 3.11 Time building geometry restraints manager: 2.34 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: 0.160 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- 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 : 0.813 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.8959 time to fit residues: 89.6661 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 : 0.741 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172583 restraints weight = 7445.082| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.90 r_work: 0.3970 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.0899 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 : 0.585 7.773 10253 Z= 0.295 Chirality : 0.042 0.173 1202 Planarity : 0.006 0.090 1113 Dihedral : 17.567 126.115 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 114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5124 (OUTLIER) cc_final: 0.4845 (ptpp) REVERT: A 624 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6084 (pt0) outliers start: 26 outliers final: 10 residues processed: 108 average time/residue: 0.9287 time to fit residues: 107.9311 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 : 0.739 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.0010 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.212623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174000 restraints weight = 7494.108| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.91 r_work: 0.3995 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7390 Z= 0.160 Angle : 0.540 8.928 10253 Z= 0.271 Chirality : 0.041 0.176 1202 Planarity : 0.005 0.068 1113 Dihedral : 17.254 85.271 1583 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.59 % Favored : 94.27 % Rotamer: Outliers : 4.57 % Allowed : 27.98 % 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: -0.89 (0.30), residues: 751 helix: 0.81 (0.35), residues: 229 sheet: -0.80 (0.39), residues: 176 loop : -1.40 (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 0.018 0.001 PHE A 950 TYR 0.011 0.001 TYR A 241 ARG 0.008 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 122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.6633 (m-30) cc_final: 0.6329 (m-30) REVERT: A 294 LYS cc_start: 0.5126 (OUTLIER) cc_final: 0.4845 (ptpp) REVERT: A 333 ASP cc_start: 0.7378 (m-30) cc_final: 0.6575 (t0) REVERT: A 369 ASP cc_start: 0.6430 (t0) cc_final: 0.6132 (t0) REVERT: A 392 MET cc_start: 0.5557 (OUTLIER) cc_final: 0.5275 (mpt) REVERT: A 436 PRO cc_start: 0.6135 (Cg_exo) cc_final: 0.5846 (Cg_endo) REVERT: A 601 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.7000 (ttp) REVERT: A 624 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6088 (pt0) REVERT: A 794 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5748 (mm) outliers start: 31 outliers final: 10 residues processed: 113 average time/residue: 0.9383 time to fit residues: 113.6303 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 : 0.671 ------------------------------------------------------------------------------- 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 601 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 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: 6.9990 chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.202263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161483 restraints weight = 7495.525| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.94 r_work: 0.3796 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1858 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= 0.364 Angle : 0.686 9.069 10253 Z= 0.349 Chirality : 0.046 0.183 1202 Planarity : 0.006 0.065 1113 Dihedral : 17.116 84.612 1581 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 6.19 % Allowed : 25.92 % Favored : 67.89 % 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: -1.11 (0.31), residues: 751 helix: 0.49 (0.35), residues: 228 sheet: -0.98 (0.39), residues: 177 loop : -1.39 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 769 HIS 0.008 0.001 HIS A 526 PHE 0.019 0.002 PHE A 835 TYR 0.017 0.002 TYR A 454 ARG 0.006 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 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.730 Fit side-chains REVERT: A 258 MET cc_start: 0.7059 (mmm) cc_final: 0.6641 (mtt) REVERT: A 294 LYS cc_start: 0.5249 (OUTLIER) cc_final: 0.4946 (ptpp) REVERT: A 329 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.6497 (mpp) REVERT: A 333 ASP cc_start: 0.7632 (m-30) cc_final: 0.6750 (t0) REVERT: A 369 ASP cc_start: 0.6709 (t0) cc_final: 0.6498 (t0) REVERT: A 436 PRO cc_start: 0.6217 (Cg_exo) cc_final: 0.5990 (Cg_endo) REVERT: A 495 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 531 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6554 (mm-30) REVERT: A 555 HIS cc_start: 0.7295 (t-90) cc_final: 0.7079 (t-90) REVERT: A 647 ILE cc_start: 0.7136 (mt) cc_final: 0.6844 (mt) REVERT: A 794 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5654 (mm) outliers start: 42 outliers final: 17 residues processed: 123 average time/residue: 0.8373 time to fit residues: 111.1698 Evaluate side-chains 107 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 928 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.204623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.165620 restraints weight = 7381.479| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.09 r_work: 0.3826 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.1840 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= 0.240 Angle : 0.605 9.769 10253 Z= 0.306 Chirality : 0.043 0.181 1202 Planarity : 0.005 0.057 1113 Dihedral : 17.198 86.824 1581 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 5.01 % Allowed : 27.25 % Favored : 67.75 % 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: -0.98 (0.31), residues: 751 helix: 0.73 (0.35), residues: 229 sheet: -1.01 (0.39), residues: 177 loop : -1.35 (0.33), residues: 345 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 0.015 0.002 TYR A 425 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: 34 poor density : 91 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6593 (mtt) REVERT: A 294 LYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4921 (ptpp) REVERT: A 329 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.6162 (mpp) REVERT: A 333 ASP cc_start: 0.7564 (m-30) cc_final: 0.6705 (t0) REVERT: A 369 ASP cc_start: 0.6645 (t0) cc_final: 0.6443 (t0) REVERT: A 392 MET cc_start: 0.5341 (mpt) cc_final: 0.4986 (mpt) REVERT: A 436 PRO cc_start: 0.6243 (Cg_exo) cc_final: 0.6032 (Cg_endo) REVERT: A 515 LEU cc_start: 0.6808 (tp) cc_final: 0.6433 (tp) REVERT: A 531 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6630 (mm-30) REVERT: A 647 ILE cc_start: 0.7098 (mt) cc_final: 0.6819 (mt) REVERT: A 794 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.5792 (mm) outliers start: 34 outliers final: 18 residues processed: 114 average time/residue: 0.8768 time to fit residues: 107.5945 Evaluate side-chains 111 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 0.0070 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN A 954 GLN A 963 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.202294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.162391 restraints weight = 7512.051| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.18 r_work: 0.3780 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7390 Z= 0.310 Angle : 0.653 10.818 10253 Z= 0.331 Chirality : 0.045 0.181 1202 Planarity : 0.005 0.068 1113 Dihedral : 17.162 85.617 1581 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 6.19 % Allowed : 26.95 % 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: -1.11 (0.31), residues: 751 helix: 0.61 (0.35), residues: 231 sheet: -1.12 (0.39), residues: 177 loop : -1.42 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 769 HIS 0.006 0.001 HIS A 242 PHE 0.020 0.002 PHE A 835 TYR 0.014 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 136 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 0.702 Fit side-chains REVERT: A 258 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6662 (mtt) REVERT: A 294 LYS cc_start: 0.5246 (OUTLIER) cc_final: 0.4940 (ptpp) REVERT: A 329 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.6387 (mpp) REVERT: A 333 ASP cc_start: 0.7608 (m-30) cc_final: 0.6768 (t0) REVERT: A 436 PRO cc_start: 0.6184 (Cg_exo) cc_final: 0.5979 (Cg_endo) REVERT: A 531 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6487 (mm-30) REVERT: A 562 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: A 647 ILE cc_start: 0.7166 (mt) cc_final: 0.6878 (mt) REVERT: A 782 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5539 (mp) REVERT: A 794 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5707 (mm) REVERT: A 918 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5867 (ttp) outliers start: 42 outliers final: 23 residues processed: 123 average time/residue: 0.8902 time to fit residues: 117.6697 Evaluate side-chains 119 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 17 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 776 GLN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.196078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155063 restraints weight = 7484.225| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.96 r_work: 0.3728 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 7390 Z= 0.519 Angle : 0.824 11.230 10253 Z= 0.419 Chirality : 0.052 0.229 1202 Planarity : 0.007 0.060 1113 Dihedral : 17.297 82.652 1581 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 6.48 % Allowed : 26.95 % 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 (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: -1.66 (0.30), residues: 751 helix: -0.15 (0.34), residues: 228 sheet: -1.37 (0.38), residues: 176 loop : -1.53 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 769 HIS 0.008 0.002 HIS A 242 PHE 0.027 0.003 PHE A 835 TYR 0.019 0.003 TYR A 342 ARG 0.005 0.001 ARG A 536 *********************** 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 138 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 294 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.5008 (ptpp) REVERT: A 329 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.6834 (mpp) REVERT: A 333 ASP cc_start: 0.7621 (m-30) cc_final: 0.6857 (t0) REVERT: A 515 LEU cc_start: 0.6826 (tp) cc_final: 0.6464 (tp) REVERT: A 531 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: A 555 HIS cc_start: 0.7203 (t-90) cc_final: 0.6961 (t-90) REVERT: A 562 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: A 794 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5484 (mm) REVERT: A 918 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6160 (ttp) outliers start: 44 outliers final: 24 residues processed: 125 average time/residue: 0.8954 time to fit residues: 121.1271 Evaluate side-chains 119 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 742 MET Chi-restraints excluded: chain A residue 755 VAL 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 964 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.206402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.167297 restraints weight = 7606.146| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.92 r_work: 0.3861 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2286 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= 0.196 Angle : 0.627 11.776 10253 Z= 0.312 Chirality : 0.044 0.196 1202 Planarity : 0.005 0.054 1113 Dihedral : 17.379 87.839 1581 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 3.98 % Allowed : 29.46 % 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 (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: -1.09 (0.31), residues: 751 helix: 0.67 (0.35), residues: 230 sheet: -1.22 (0.38), residues: 177 loop : -1.36 (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 0.018 0.002 PHE A 245 TYR 0.015 0.002 TYR A 425 ARG 0.004 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.661 Fit side-chains REVERT: A 294 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4986 (ptpp) REVERT: A 333 ASP cc_start: 0.7568 (m-30) cc_final: 0.6774 (t0) REVERT: A 515 LEU cc_start: 0.6622 (tp) cc_final: 0.6307 (tp) REVERT: A 647 ILE cc_start: 0.7019 (mt) cc_final: 0.6724 (mt) REVERT: A 782 ILE cc_start: 0.6011 (OUTLIER) cc_final: 0.5629 (mp) REVERT: A 794 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5697 (mm) REVERT: A 918 MET cc_start: 0.6160 (ttp) cc_final: 0.5758 (ttp) outliers start: 27 outliers final: 13 residues processed: 112 average time/residue: 0.8325 time to fit residues: 100.7203 Evaluate side-chains 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 435 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 634 ILE 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 813 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL 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: 9.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 801 ASN A 963 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.201924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.164267 restraints weight = 7548.048| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.89 r_work: 0.3799 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2395 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= 0.292 Angle : 0.669 12.081 10253 Z= 0.334 Chirality : 0.046 0.192 1202 Planarity : 0.005 0.065 1113 Dihedral : 17.291 84.906 1581 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 3.83 % Allowed : 29.31 % 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: -1.07 (0.31), residues: 751 helix: 0.63 (0.35), residues: 231 sheet: -1.15 (0.38), residues: 175 loop : -1.35 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 586 HIS 0.005 0.001 HIS A 242 PHE 0.018 0.002 PHE A 835 TYR 0.030 0.002 TYR A 420 ARG 0.007 0.001 ARG A 510 *********************** 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 116 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.721 Fit side-chains REVERT: A 294 LYS cc_start: 0.5279 (OUTLIER) cc_final: 0.4979 (ptpp) REVERT: A 329 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.6357 (mpp) REVERT: A 333 ASP cc_start: 0.7615 (m-30) cc_final: 0.6848 (t0) REVERT: A 513 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.5750 (tppp) REVERT: A 647 ILE cc_start: 0.7179 (mt) cc_final: 0.6860 (mt) REVERT: A 782 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5700 (mp) REVERT: A 794 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5696 (mm) REVERT: A 918 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5934 (ttp) outliers start: 26 outliers final: 15 residues processed: 109 average time/residue: 0.8512 time to fit residues: 100.0726 Evaluate side-chains 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 513 LYS Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 734 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.204219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164526 restraints weight = 7597.115| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.93 r_work: 0.3823 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2363 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= 0.237 Angle : 0.645 11.836 10253 Z= 0.320 Chirality : 0.045 0.187 1202 Planarity : 0.005 0.059 1113 Dihedral : 17.313 85.961 1581 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 3.39 % Allowed : 30.19 % Favored : 66.42 % 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: -1.02 (0.31), residues: 751 helix: 0.67 (0.36), residues: 232 sheet: -1.15 (0.38), residues: 175 loop : -1.30 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 884 HIS 0.004 0.001 HIS A 526 PHE 0.017 0.002 PHE A 835 TYR 0.030 0.002 TYR A 420 ARG 0.008 0.001 ARG A 510 ********************** 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 113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.693 Fit side-chains REVERT: A 294 LYS cc_start: 0.5183 (OUTLIER) cc_final: 0.4895 (ptpp) REVERT: A 329 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6149 (mpp) REVERT: A 333 ASP cc_start: 0.7639 (m-30) cc_final: 0.6838 (t0) REVERT: A 415 ILE cc_start: 0.7322 (mp) cc_final: 0.6823 (mt) REVERT: A 647 ILE cc_start: 0.7146 (mt) cc_final: 0.6834 (mt) REVERT: A 782 ILE cc_start: 0.5955 (OUTLIER) cc_final: 0.5589 (mp) REVERT: A 794 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.5654 (mm) REVERT: A 918 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5758 (ttp) outliers start: 23 outliers final: 14 residues processed: 105 average time/residue: 0.9397 time to fit residues: 106.1311 Evaluate side-chains 108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 734 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 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: 0.7980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.202334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162380 restraints weight = 7554.200| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.95 r_work: 0.3810 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2408 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= 0.274 Angle : 0.668 11.816 10253 Z= 0.332 Chirality : 0.046 0.187 1202 Planarity : 0.005 0.055 1113 Dihedral : 17.313 85.237 1581 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 3.09 % Allowed : 30.34 % 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 (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: -1.10 (0.31), residues: 751 helix: 0.62 (0.35), residues: 231 sheet: -1.15 (0.38), residues: 175 loop : -1.38 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 884 HIS 0.005 0.001 HIS A 242 PHE 0.019 0.002 PHE A 835 TYR 0.029 0.002 TYR A 420 ARG 0.009 0.001 ARG A 510 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5300.76 seconds wall clock time: 91 minutes 3.42 seconds (5463.42 seconds total)