Starting phenix.real_space_refine on Thu Mar 13 13:46:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ost_17164/03_2025/8ost_17164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ost_17164/03_2025/8ost_17164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ost_17164/03_2025/8ost_17164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ost_17164/03_2025/8ost_17164.map" model { file = "/net/cci-nas-00/data/ceres_data/8ost_17164/03_2025/8ost_17164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ost_17164/03_2025/8ost_17164.cif" } resolution = 3.69 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= 0.013 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 69 5.49 5 S 26 5.16 5 C 2856 2.51 5 N 847 2.21 5 O 1097 1.98 5 H 4058 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8955 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 6193 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 21, 'TRANS': 368} Chain breaks: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 604 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 2156 Classifications: {'RNA': 69} Modifications used: {'3*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 25} Link IDs: {'rna2p': 10, 'rna3p': 58} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6242 SG CYS B 139 46.190 33.375 93.580 1.00 95.55 S ATOM 6287 SG CYS B 142 48.791 31.460 95.469 1.00 97.85 S ATOM 6409 SG CYS B 152 49.806 33.602 92.464 1.00 96.98 S ATOM 6549 SG CYS B 161 42.049 17.731 99.911 1.00127.76 S ATOM 6597 SG CYS B 164 44.047 15.621 101.441 1.00131.34 S ATOM 6737 SG CYS B 174 40.227 14.399 101.994 1.00133.57 S Time building chain proxies: 5.82, per 1000 atoms: 0.65 Number of scatterers: 8955 At special positions: 0 Unit cell: (74.7, 74.7, 133.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 26 16.00 P 69 15.00 O 1097 8.00 N 847 7.00 C 2856 6.00 H 4058 1.00 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: 2.44 Conformation dependent library (CDL) restraints added in 452.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 147 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 139 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 152 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 142 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 164 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 161 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 174 " Number of angles added : 3 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 46.5% alpha, 2.5% beta 3 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 275 through 286 removed outlier: 4.332A pdb=" N GLN A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'A' and resid 325 through 343 removed outlier: 3.722A pdb=" N GLU A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.575A pdb=" N THR A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 424 through 439 removed outlier: 3.773A pdb=" N ILE A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 490 removed outlier: 3.778A pdb=" N LEU A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.868A pdb=" N LEU A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 689 through 709 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'B' and resid 170 through 174 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA2, first strand: chain 'A' and resid 446 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.547A pdb=" N ILE A 651 " --> pdb=" O GLU A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 135 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 7 hydrogen bonds 14 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 4040 1.02 - 1.22: 18 1.22 - 1.41: 2099 1.41 - 1.61: 3014 1.61 - 1.81: 33 Bond restraints: 9204 Sorted by residual: bond pdb=" NE2 GLN A 532 " pdb="HE22 GLN A 532 " ideal model delta sigma weight residual 0.860 0.821 0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" CG PRO A 710 " pdb=" CD PRO A 710 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.67e+00 bond pdb=" O4' G C 20 " pdb=" C1' G C 20 " ideal model delta sigma weight residual 1.412 1.395 0.017 1.50e-02 4.44e+03 1.34e+00 bond pdb=" C3' G C 20 " pdb=" C2' G C 20 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.50e-02 4.44e+03 1.33e+00 bond pdb=" CB PRO A 710 " pdb=" CG PRO A 710 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.16e+00 ... (remaining 9199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 16101 1.50 - 3.00: 451 3.00 - 4.50: 40 4.50 - 5.99: 4 5.99 - 7.49: 3 Bond angle restraints: 16599 Sorted by residual: angle pdb=" C3' U C 61 " pdb=" C2' U C 61 " pdb=" C1' U C 61 " ideal model delta sigma weight residual 101.50 104.37 -2.87 1.00e+00 1.00e+00 8.22e+00 angle pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " ideal model delta sigma weight residual 102.60 105.43 -2.83 1.00e+00 1.00e+00 7.98e+00 angle pdb=" O3' A C 19 " pdb=" C3' A C 19 " pdb=" C2' A C 19 " ideal model delta sigma weight residual 113.70 117.89 -4.19 1.50e+00 4.44e-01 7.79e+00 angle pdb=" CA PRO A 710 " pdb=" N PRO A 710 " pdb=" CD PRO A 710 " ideal model delta sigma weight residual 112.00 108.12 3.88 1.40e+00 5.10e-01 7.69e+00 angle pdb=" C4' U C 61 " pdb=" C3' U C 61 " pdb=" C2' U C 61 " ideal model delta sigma weight residual 102.60 105.34 -2.74 1.00e+00 1.00e+00 7.51e+00 ... (remaining 16594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 3980 28.38 - 56.76: 324 56.76 - 85.14: 118 85.14 - 113.52: 17 113.52 - 141.90: 2 Dihedral angle restraints: 4441 sinusoidal: 2957 harmonic: 1484 Sorted by residual: dihedral pdb=" O4' G C 20 " pdb=" C2' G C 20 " pdb=" C1' G C 20 " pdb=" C3' G C 20 " ideal model delta sinusoidal sigma weight residual 25.00 -18.72 43.72 1 8.00e+00 1.56e-02 4.16e+01 dihedral pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " pdb=" C1' G C 20 " ideal model delta sinusoidal sigma weight residual 36.00 0.06 35.94 1 8.00e+00 1.56e-02 2.86e+01 dihedral pdb=" C4' G C 20 " pdb=" O4' G C 20 " pdb=" C1' G C 20 " pdb=" C2' G C 20 " ideal model delta sinusoidal sigma weight residual 3.00 -31.89 34.89 1 8.00e+00 1.56e-02 2.70e+01 ... (remaining 4438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 716 0.041 - 0.083: 116 0.083 - 0.124: 43 0.124 - 0.165: 4 0.165 - 0.206: 1 Chirality restraints: 880 Sorted by residual: chirality pdb=" C3' A C 19 " pdb=" C4' A C 19 " pdb=" O3' A C 19 " pdb=" C2' A C 19 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1' U C 14 " pdb=" O4' U C 14 " pdb=" C2' U C 14 " pdb=" N1 U C 14 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" C1' G C 15 " pdb=" O4' G C 15 " pdb=" C2' G C 15 " pdb=" N9 G C 15 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 877 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 532 " -0.062 2.00e-02 2.50e+03 7.96e-02 9.50e+01 pdb=" CD GLN A 532 " 0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN A 532 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 532 " 0.126 2.00e-02 2.50e+03 pdb="HE21 GLN A 532 " 0.012 2.00e-02 2.50e+03 pdb="HE22 GLN A 532 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 414 " 0.036 2.00e-02 2.50e+03 6.09e-02 5.57e+01 pdb=" CG ASN A 414 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 414 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 414 " 0.103 2.00e-02 2.50e+03 pdb="HD21 ASN A 414 " 0.007 2.00e-02 2.50e+03 pdb="HD22 ASN A 414 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 709 " 0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 710 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 710 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 710 " 0.061 5.00e-02 4.00e+02 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 57 2.06 - 2.69: 12485 2.69 - 3.33: 24556 3.33 - 3.96: 31326 3.96 - 4.60: 46429 Nonbonded interactions: 114853 Sorted by model distance: nonbonded pdb=" HE1 HIS B 147 " pdb="ZN ZN B 301 " model vdw 1.422 1.408 nonbonded pdb="HD22 ASN A 424 " pdb=" OD2 ASP A 427 " model vdw 1.598 2.450 nonbonded pdb="HO2' A C 35 " pdb=" O4' U C 36 " model vdw 1.680 2.450 nonbonded pdb=" OD1 ASP A 675 " pdb=" HG SER A 678 " model vdw 1.804 2.450 nonbonded pdb=" O MET A 525 " pdb=" HH TYR A 640 " model vdw 1.817 2.450 ... (remaining 114848 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.150 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.810 Find NCS groups from input model: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 5146 Z= 0.145 Angle : 0.515 6.337 7305 Z= 0.290 Chirality : 0.037 0.206 880 Planarity : 0.006 0.113 671 Dihedral : 22.671 121.299 2369 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.27 % Allowed : 18.40 % Favored : 81.33 % 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: 0.21 (0.40), residues: 422 helix: 1.96 (0.41), residues: 168 sheet: -1.89 (0.87), residues: 34 loop : -0.99 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 570 HIS 0.001 0.000 HIS A 351 PHE 0.004 0.001 PHE A 700 TYR 0.005 0.001 TYR A 299 ARG 0.003 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.6349 (mptt) cc_final: 0.5411 (ttpt) REVERT: A 423 MET cc_start: 0.2818 (mmt) cc_final: 0.1685 (mpp) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.4572 time to fit residues: 44.5068 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN ** B 147 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 = 0.4950 r_free = 0.4950 target = 0.261376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.209485 restraints weight = 19218.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.215946 restraints weight = 10522.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.220226 restraints weight = 6973.293| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5146 Z= 0.191 Angle : 0.539 4.742 7305 Z= 0.288 Chirality : 0.036 0.194 880 Planarity : 0.005 0.065 671 Dihedral : 23.739 106.799 1526 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.53 % Allowed : 19.73 % Favored : 79.73 % 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: 0.47 (0.41), residues: 422 helix: 2.09 (0.39), residues: 178 sheet: -1.46 (0.93), residues: 34 loop : -0.99 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 666 HIS 0.011 0.002 HIS B 169 PHE 0.020 0.001 PHE A 493 TYR 0.012 0.002 TYR A 640 ARG 0.005 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6505 (ptm-80) cc_final: 0.6214 (ptm-80) REVERT: A 364 LYS cc_start: 0.5810 (mptt) cc_final: 0.5361 (tttm) REVERT: A 423 MET cc_start: 0.2885 (mmt) cc_final: 0.2044 (mpp) outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.4578 time to fit residues: 34.0092 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 686 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** 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 = 0.4889 r_free = 0.4889 target = 0.253837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.203607 restraints weight = 19237.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.207130 restraints weight = 12529.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.208269 restraints weight = 8996.294| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5146 Z= 0.273 Angle : 0.553 4.881 7305 Z= 0.298 Chirality : 0.036 0.163 880 Planarity : 0.005 0.063 671 Dihedral : 23.622 107.761 1526 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 20.27 % Favored : 78.13 % 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: 0.08 (0.40), residues: 422 helix: 1.75 (0.39), residues: 178 sheet: -2.60 (0.87), residues: 29 loop : -1.03 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 503 HIS 0.011 0.002 HIS A 328 PHE 0.019 0.002 PHE A 493 TYR 0.017 0.002 TYR A 399 ARG 0.003 0.001 ARG A 670 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6287 (ptm-80) cc_final: 0.6024 (ptm-80) REVERT: A 412 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.4290 (m-30) REVERT: A 423 MET cc_start: 0.2687 (mmt) cc_final: 0.1831 (mpp) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.3738 time to fit residues: 27.4883 Evaluate side-chains 56 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** 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 = 0.4875 r_free = 0.4875 target = 0.252605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.203509 restraints weight = 19141.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.206923 restraints weight = 12464.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.207491 restraints weight = 8630.345| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5146 Z= 0.216 Angle : 0.509 4.382 7305 Z= 0.274 Chirality : 0.035 0.148 880 Planarity : 0.004 0.055 671 Dihedral : 23.505 107.552 1526 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 21.33 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.40), residues: 422 helix: 1.86 (0.39), residues: 177 sheet: -2.64 (0.89), residues: 29 loop : -1.07 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 503 HIS 0.007 0.001 HIS A 328 PHE 0.017 0.002 PHE A 567 TYR 0.011 0.002 TYR A 640 ARG 0.002 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2636 (mmt) cc_final: 0.1364 (mpp) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.3947 time to fit residues: 27.3903 Evaluate side-chains 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 HIS ** B 147 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 = 0.4869 r_free = 0.4869 target = 0.252588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.205654 restraints weight = 18646.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.207317 restraints weight = 11308.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.207073 restraints weight = 10148.046| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5146 Z= 0.200 Angle : 0.505 10.293 7305 Z= 0.270 Chirality : 0.035 0.142 880 Planarity : 0.004 0.048 671 Dihedral : 23.435 107.452 1526 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.40 % Allowed : 21.07 % Favored : 76.53 % 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: 0.18 (0.40), residues: 422 helix: 1.90 (0.39), residues: 177 sheet: -2.51 (0.93), residues: 29 loop : -1.04 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.007 0.001 HIS A 328 PHE 0.016 0.002 PHE A 644 TYR 0.010 0.002 TYR A 640 ARG 0.002 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2706 (mmt) cc_final: 0.1460 (mpp) REVERT: A 644 PHE cc_start: 0.4532 (OUTLIER) cc_final: 0.3454 (p90) REVERT: B 151 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5800 (mp0) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.4168 time to fit residues: 28.5856 Evaluate side-chains 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 151 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 41 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 147 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 = 0.4865 r_free = 0.4865 target = 0.252314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.204097 restraints weight = 18537.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.208672 restraints weight = 13000.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.209406 restraints weight = 10122.900| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5146 Z= 0.168 Angle : 0.482 5.128 7305 Z= 0.253 Chirality : 0.034 0.144 880 Planarity : 0.004 0.039 671 Dihedral : 23.327 107.379 1526 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.93 % Allowed : 19.73 % Favored : 77.33 % 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: 0.42 (0.40), residues: 422 helix: 1.95 (0.39), residues: 179 sheet: -2.70 (1.00), residues: 24 loop : -0.80 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 570 HIS 0.004 0.001 HIS A 328 PHE 0.010 0.001 PHE A 567 TYR 0.009 0.001 TYR A 640 ARG 0.004 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.3176 (m-30) REVERT: A 423 MET cc_start: 0.2606 (mmt) cc_final: 0.1409 (mpp) REVERT: A 644 PHE cc_start: 0.4504 (OUTLIER) cc_final: 0.3825 (p90) REVERT: A 706 TYR cc_start: 0.6838 (t80) cc_final: 0.6452 (t80) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.4108 time to fit residues: 25.4726 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** 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 = 0.4845 r_free = 0.4845 target = 0.250102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.202860 restraints weight = 18708.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.203846 restraints weight = 13186.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.205855 restraints weight = 10332.822| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5146 Z= 0.204 Angle : 0.491 5.125 7305 Z= 0.263 Chirality : 0.035 0.147 880 Planarity : 0.004 0.039 671 Dihedral : 23.286 108.328 1526 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.67 % Allowed : 19.73 % Favored : 77.60 % 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: 0.16 (0.40), residues: 422 helix: 1.75 (0.38), residues: 178 sheet: -2.38 (0.94), residues: 29 loop : -0.97 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 PHE 0.016 0.002 PHE A 644 TYR 0.011 0.002 TYR A 399 ARG 0.006 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6479 (OUTLIER) cc_final: 0.4237 (m-30) REVERT: A 423 MET cc_start: 0.2640 (mmt) cc_final: 0.1358 (mpp) REVERT: A 644 PHE cc_start: 0.5082 (OUTLIER) cc_final: 0.4603 (p90) REVERT: A 706 TYR cc_start: 0.6848 (t80) cc_final: 0.6453 (t80) REVERT: B 151 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5981 (mp0) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.4005 time to fit residues: 25.9009 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 151 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** 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 = 0.4849 r_free = 0.4849 target = 0.250457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.194669 restraints weight = 18821.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.200663 restraints weight = 10985.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.204295 restraints weight = 7649.400| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5146 Z= 0.182 Angle : 0.493 8.663 7305 Z= 0.262 Chirality : 0.035 0.148 880 Planarity : 0.004 0.036 671 Dihedral : 23.239 108.029 1526 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.40 % Allowed : 20.80 % Favored : 76.80 % 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: 0.23 (0.40), residues: 422 helix: 1.79 (0.38), residues: 178 sheet: -2.29 (0.95), residues: 29 loop : -0.91 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.001 PHE A 644 TYR 0.009 0.001 TYR A 640 ARG 0.003 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.5840 (mptt) cc_final: 0.5461 (tttm) REVERT: A 412 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.4071 (m-30) REVERT: A 423 MET cc_start: 0.2557 (mmt) cc_final: 0.1287 (mpp) REVERT: A 706 TYR cc_start: 0.6851 (t80) cc_final: 0.6488 (t80) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.4444 time to fit residues: 26.8288 Evaluate side-chains 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 151 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** 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 = 0.4837 r_free = 0.4837 target = 0.248876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.198700 restraints weight = 18660.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.203213 restraints weight = 13085.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.204051 restraints weight = 10001.212| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5146 Z= 0.206 Angle : 0.501 6.596 7305 Z= 0.269 Chirality : 0.036 0.173 880 Planarity : 0.004 0.035 671 Dihedral : 23.221 108.224 1526 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.13 % Allowed : 20.80 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.40), residues: 422 helix: 1.67 (0.38), residues: 178 sheet: -2.32 (0.95), residues: 29 loop : -0.97 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.007 0.001 HIS A 328 PHE 0.011 0.001 PHE A 493 TYR 0.011 0.002 TYR A 399 ARG 0.005 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.5881 (mptt) cc_final: 0.5463 (tttm) REVERT: A 412 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.4243 (m-30) REVERT: A 423 MET cc_start: 0.2533 (mmt) cc_final: 0.1278 (mpp) REVERT: A 706 TYR cc_start: 0.6915 (t80) cc_final: 0.6539 (t80) REVERT: B 151 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6499 (mt-10) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.4542 time to fit residues: 28.9617 Evaluate side-chains 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** 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 = 0.4836 r_free = 0.4836 target = 0.248807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.198013 restraints weight = 18526.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.202456 restraints weight = 12779.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.203243 restraints weight = 9860.045| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5146 Z= 0.203 Angle : 0.496 7.226 7305 Z= 0.266 Chirality : 0.035 0.155 880 Planarity : 0.004 0.035 671 Dihedral : 23.227 107.882 1526 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.13 % Allowed : 20.80 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.40), residues: 422 helix: 1.69 (0.38), residues: 178 sheet: -2.32 (0.97), residues: 29 loop : -0.94 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE A 493 TYR 0.010 0.002 TYR A 399 ARG 0.003 0.001 ARG A 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LYS 560 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LYS 668 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.4290 (m-30) REVERT: A 423 MET cc_start: 0.2526 (mmt) cc_final: 0.1275 (mpp) REVERT: A 706 TYR cc_start: 0.6955 (t80) cc_final: 0.6619 (t80) REVERT: B 151 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5919 (mp0) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.4047 time to fit residues: 24.3193 Evaluate side-chains 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** 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 = 0.4836 r_free = 0.4836 target = 0.248815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.198653 restraints weight = 18770.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.202441 restraints weight = 14053.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.202983 restraints weight = 10578.018| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5146 Z= 0.192 Angle : 0.499 5.900 7305 Z= 0.267 Chirality : 0.036 0.178 880 Planarity : 0.004 0.036 671 Dihedral : 23.201 109.296 1526 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.13 % Allowed : 20.80 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.40), residues: 422 helix: 1.72 (0.38), residues: 178 sheet: -2.23 (1.00), residues: 29 loop : -0.91 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 PHE 0.013 0.001 PHE A 567 TYR 0.010 0.002 TYR A 399 ARG 0.003 0.000 ARG A 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.25 seconds wall clock time: 72 minutes 29.90 seconds (4349.90 seconds total)