Starting phenix.real_space_refine on Thu Jul 2 14:01:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ost_17164/07_2026/8ost_17164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ost_17164/07_2026/8ost_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ost_17164/07_2026/8ost_17164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ost_17164/07_2026/8ost_17164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ost_17164/07_2026/8ost_17164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ost_17164/07_2026/8ost_17164.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 7, 'GLN:plan1': 1, 'PHE:plan': 1} 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: 1.32, per 1000 atoms: 0.15 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: 0.58 Conformation dependent library (CDL) restraints added in 216.9 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: 1.22 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: 1.47 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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: 3.780 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 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 0.078 5153 Z= 0.117 Angle : 0.520 6.337 7308 Z= 0.318 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (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 ARG 0.003 0.000 ARG A 533 TYR 0.005 0.001 TYR A 299 PHE 0.004 0.001 PHE A 700 TRP 0.002 0.000 TRP A 570 HIS 0.001 0.000 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 5146) covalent geometry : angle 0.51528 / 0.32 ( 7305) hydrogen bonds : bond 0.17730 / 12.24 ( 142) hydrogen bonds : angle 6.47354 / 4.40 ( 392) metal coordination : bond 0.02990 / 1.49 ( 7) metal coordination : angle 3.43786 / 1.93 ( 3) *********************** 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 : 0.206 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: 0.5412 (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: 0.1751 time to fit residues: 17.1439 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.0020 chunk 16 optimal weight: 0.0370 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 overall best weight: 0.1266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4987 r_free = 0.4987 target = 0.265863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.216023 restraints weight = 19241.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.222573 restraints weight = 10270.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.226805 restraints weight = 6737.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.229686 restraints weight = 5157.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.231288 restraints weight = 4333.712| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 5153 Z= 0.125 Angle : 0.522 5.096 7308 Z= 0.288 Chirality : 0.037 0.204 880 Planarity : 0.004 0.061 671 Dihedral : 23.790 111.117 1526 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 20.53 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.40), residues: 422 helix: 2.16 (0.39), residues: 178 sheet: -1.47 (0.91), residues: 34 loop : -1.02 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.008 0.001 TYR A 693 PHE 0.015 0.001 PHE A 493 TRP 0.003 0.001 TRP A 666 HIS 0.011 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 5146) covalent geometry : angle 0.51747 / 0.29 ( 7305) hydrogen bonds : bond 0.05117 / 3.49 ( 142) hydrogen bonds : angle 5.11718 / 3.72 ( 392) metal coordination : bond 0.02903 / 1.45 ( 7) metal coordination : angle 3.32394 / 1.90 ( 3) *********************** 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 58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.297 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 364 LYS cc_start: 0.5761 (mptt) cc_final: 0.5328 (tttm) REVERT: A 406 PHE cc_start: 0.6161 (m-10) cc_final: 0.5831 (m-10) REVERT: A 423 MET cc_start: 0.2857 (mmt) cc_final: 0.1999 (mpp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1504 time to fit residues: 11.1924 Evaluate side-chains 51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4939 r_free = 0.4939 target = 0.260045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.207004 restraints weight = 19200.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.213356 restraints weight = 10759.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.217481 restraints weight = 7263.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.219414 restraints weight = 5652.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.221604 restraints weight = 4933.120| |-----------------------------------------------------------------------------| r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5153 Z= 0.146 Angle : 0.510 5.099 7308 Z= 0.282 Chirality : 0.036 0.189 880 Planarity : 0.005 0.074 671 Dihedral : 23.691 107.258 1526 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.07 % Allowed : 19.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.40), residues: 422 helix: 2.07 (0.39), residues: 178 sheet: -1.63 (0.92), residues: 34 loop : -1.02 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 661 TYR 0.023 0.002 TYR A 299 PHE 0.010 0.001 PHE A 500 TRP 0.007 0.001 TRP A 503 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 5146) covalent geometry : angle 0.50536 / 0.28 ( 7305) hydrogen bonds : bond 0.04888 / 3.32 ( 142) hydrogen bonds : angle 4.90859 / 3.63 ( 392) metal coordination : bond 0.02438 / 1.22 ( 7) metal coordination : angle 3.32782 / 1.91 ( 3) *********************** 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 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6271 (ptm-80) cc_final: 0.5978 (ptm-80) REVERT: A 364 LYS cc_start: 0.5683 (mptt) cc_final: 0.5323 (tttm) REVERT: A 423 MET cc_start: 0.2735 (mmt) cc_final: 0.1931 (mpp) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.1660 time to fit residues: 11.4430 Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 686 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 HIS A 663 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.249835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.194769 restraints weight = 19210.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.199534 restraints weight = 11104.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.202988 restraints weight = 7709.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.204607 restraints weight = 6229.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.204807 restraints weight = 5409.196| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5153 Z= 0.222 Angle : 0.614 5.970 7308 Z= 0.343 Chirality : 0.039 0.155 880 Planarity : 0.005 0.069 671 Dihedral : 23.668 109.064 1526 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.67 % Allowed : 20.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.38), residues: 422 helix: 1.21 (0.38), residues: 177 sheet: -3.13 (0.82), residues: 29 loop : -1.34 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 669 TYR 0.018 0.003 TYR A 399 PHE 0.024 0.003 PHE A 644 TRP 0.014 0.002 TRP A 503 HIS 0.018 0.003 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 ( 5146) covalent geometry : angle 0.61018 / 0.34 ( 7305) hydrogen bonds : bond 0.05174 / 3.57 ( 142) hydrogen bonds : angle 5.11129 / 3.86 ( 392) metal coordination : bond 0.02167 / 1.09 ( 7) metal coordination : angle 3.30179 / 1.88 ( 3) *********************** 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 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.4688 (m-30) REVERT: A 423 MET cc_start: 0.2683 (mmt) cc_final: 0.1401 (mpp) REVERT: A 706 TYR cc_start: 0.6938 (t80) cc_final: 0.6528 (t80) REVERT: B 151 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5843 (mp0) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.1426 time to fit residues: 11.7598 Evaluate side-chains 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 38 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4884 r_free = 0.4884 target = 0.253257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.199177 restraints weight = 19209.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.205378 restraints weight = 11158.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.209200 restraints weight = 7699.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.211633 restraints weight = 6091.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.212619 restraints weight = 5255.445| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 5153 Z= 0.110 Angle : 0.485 4.958 7308 Z= 0.266 Chirality : 0.035 0.142 880 Planarity : 0.005 0.051 671 Dihedral : 23.591 107.709 1526 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.80 % Allowed : 24.00 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.39), residues: 422 helix: 1.66 (0.39), residues: 177 sheet: -2.72 (0.87), residues: 29 loop : -1.05 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.009 0.001 TYR A 693 PHE 0.012 0.001 PHE A 644 TRP 0.005 0.001 TRP A 570 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 5146) covalent geometry : angle 0.48251 / 0.27 ( 7305) hydrogen bonds : bond 0.04237 / 2.93 ( 142) hydrogen bonds : angle 4.58286 / 3.45 ( 392) metal coordination : bond 0.02606 / 1.30 ( 7) metal coordination : angle 2.59018 / 1.46 ( 3) *********************** 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 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ARG cc_start: 0.6294 (ptm-80) cc_final: 0.6074 (ptm-80) REVERT: A 423 MET cc_start: 0.2696 (mmt) cc_final: 0.1509 (mpp) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.1502 time to fit residues: 9.2821 Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4858 r_free = 0.4858 target = 0.251146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.197074 restraints weight = 18924.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.202772 restraints weight = 11343.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.206579 restraints weight = 7955.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.208857 restraints weight = 6311.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.209708 restraints weight = 5496.548| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5153 Z= 0.141 Angle : 0.480 4.738 7308 Z= 0.266 Chirality : 0.035 0.148 880 Planarity : 0.004 0.050 671 Dihedral : 23.492 107.488 1526 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.13 % Allowed : 22.93 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.40), residues: 422 helix: 1.75 (0.39), residues: 177 sheet: -2.57 (0.92), residues: 29 loop : -0.98 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 669 TYR 0.011 0.002 TYR A 640 PHE 0.016 0.002 PHE A 644 TRP 0.005 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5146) covalent geometry : angle 0.47748 / 0.27 ( 7305) hydrogen bonds : bond 0.04091 / 2.83 ( 142) hydrogen bonds : angle 4.56839 / 3.42 ( 392) metal coordination : bond 0.02490 / 1.24 ( 7) metal coordination : angle 2.50556 / 1.43 ( 3) *********************** 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 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.7999 (m-30) cc_final: 0.7768 (t0) REVERT: A 423 MET cc_start: 0.2751 (mmt) cc_final: 0.1546 (mpp) REVERT: A 644 PHE cc_start: 0.4780 (OUTLIER) cc_final: 0.3882 (p90) REVERT: A 706 TYR cc_start: 0.6836 (t80) cc_final: 0.6456 (t80) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1414 time to fit residues: 9.2180 Evaluate side-chains 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4849 r_free = 0.4849 target = 0.250174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.195795 restraints weight = 18974.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.201343 restraints weight = 11396.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.204813 restraints weight = 8069.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.207114 restraints weight = 6479.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.207903 restraints weight = 5655.118| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5153 Z= 0.153 Angle : 0.510 7.275 7308 Z= 0.281 Chirality : 0.035 0.167 880 Planarity : 0.004 0.047 671 Dihedral : 23.490 107.858 1526 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.60 % Allowed : 23.20 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.40), residues: 422 helix: 1.63 (0.39), residues: 177 sheet: -2.55 (0.91), residues: 29 loop : -0.97 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.011 0.002 TYR A 640 PHE 0.016 0.001 PHE A 644 TRP 0.006 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 5146) covalent geometry : angle 0.50753 / 0.28 ( 7305) hydrogen bonds : bond 0.04053 / 2.83 ( 142) hydrogen bonds : angle 4.70169 / 3.50 ( 392) metal coordination : bond 0.02311 / 1.16 ( 7) metal coordination : angle 2.50760 / 1.43 ( 3) *********************** 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 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.7996 (m-30) cc_final: 0.7781 (t0) REVERT: A 423 MET cc_start: 0.2705 (mmt) cc_final: 0.1509 (mpp) REVERT: A 644 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.4277 (p90) REVERT: A 706 TYR cc_start: 0.6871 (t80) cc_final: 0.6464 (t80) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.1419 time to fit residues: 8.1369 Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 570 TRP Chi-restraints excluded: chain A residue 644 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.0470 chunk 24 optimal weight: 0.0970 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4860 r_free = 0.4860 target = 0.251652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.203040 restraints weight = 18768.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.205486 restraints weight = 14515.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.206326 restraints weight = 9618.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.207614 restraints weight = 8591.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.207825 restraints weight = 7798.815| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 5153 Z= 0.099 Angle : 0.462 5.387 7308 Z= 0.250 Chirality : 0.035 0.142 880 Planarity : 0.004 0.038 671 Dihedral : 23.416 107.319 1526 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.87 % Allowed : 21.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.41), residues: 422 helix: 1.89 (0.39), residues: 177 sheet: -2.35 (0.95), residues: 29 loop : -0.88 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.009 0.001 TYR A 693 PHE 0.010 0.001 PHE A 529 TRP 0.008 0.001 TRP A 570 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 5146) covalent geometry : angle 0.45939 / 0.25 ( 7305) hydrogen bonds : bond 0.03680 / 2.57 ( 142) hydrogen bonds : angle 4.38489 / 3.26 ( 392) metal coordination : bond 0.02558 / 1.28 ( 7) metal coordination : angle 2.34385 / 1.31 ( 3) *********************** 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 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2584 (mmt) cc_final: 0.1380 (mpp) REVERT: A 644 PHE cc_start: 0.4835 (OUTLIER) cc_final: 0.4196 (p90) REVERT: A 706 TYR cc_start: 0.6764 (t80) cc_final: 0.6390 (t80) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.1504 time to fit residues: 8.9861 Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4848 r_free = 0.4848 target = 0.250474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.204179 restraints weight = 18814.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.209068 restraints weight = 14517.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.209870 restraints weight = 10757.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.210359 restraints weight = 8007.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.210520 restraints weight = 7374.554| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5153 Z= 0.107 Angle : 0.469 5.804 7308 Z= 0.255 Chirality : 0.034 0.143 880 Planarity : 0.004 0.038 671 Dihedral : 23.359 107.378 1526 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.87 % Allowed : 21.87 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.41), residues: 422 helix: 1.84 (0.38), residues: 178 sheet: -2.21 (0.97), residues: 29 loop : -0.87 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.009 0.001 TYR A 693 PHE 0.011 0.001 PHE A 644 TRP 0.006 0.001 TRP A 570 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 5146) covalent geometry : angle 0.46613 / 0.25 ( 7305) hydrogen bonds : bond 0.03653 / 2.55 ( 142) hydrogen bonds : angle 4.37846 / 3.26 ( 392) metal coordination : bond 0.02507 / 1.25 ( 7) metal coordination : angle 2.41433 / 1.37 ( 3) *********************** 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 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2604 (mmt) cc_final: 0.1471 (mpp) REVERT: A 644 PHE cc_start: 0.4756 (OUTLIER) cc_final: 0.4143 (p90) REVERT: A 706 TYR cc_start: 0.6817 (t80) cc_final: 0.6427 (t80) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.1599 time to fit residues: 9.9138 Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 570 TRP Chi-restraints excluded: chain A residue 644 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 40 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 31 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4841 r_free = 0.4841 target = 0.249665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.203014 restraints weight = 18595.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.208417 restraints weight = 14159.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.209087 restraints weight = 10169.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.209446 restraints weight = 7922.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.209596 restraints weight = 7248.988| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5153 Z= 0.120 Angle : 0.482 10.876 7308 Z= 0.263 Chirality : 0.035 0.199 880 Planarity : 0.004 0.039 671 Dihedral : 23.333 107.649 1526 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.87 % Allowed : 22.13 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.40), residues: 422 helix: 1.82 (0.38), residues: 179 sheet: -2.23 (0.98), residues: 29 loop : -0.96 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.009 0.001 TYR A 693 PHE 0.011 0.001 PHE A 644 TRP 0.006 0.001 TRP A 570 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5146) covalent geometry : angle 0.47917 / 0.26 ( 7305) hydrogen bonds : bond 0.03662 / 2.56 ( 142) hydrogen bonds : angle 4.37654 / 3.26 ( 392) metal coordination : bond 0.02496 / 1.25 ( 7) metal coordination : angle 2.38949 / 1.36 ( 3) ********************** 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 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2614 (mmt) cc_final: 0.1466 (mpp) REVERT: A 644 PHE cc_start: 0.4830 (OUTLIER) cc_final: 0.4287 (p90) REVERT: A 706 TYR cc_start: 0.6854 (t80) cc_final: 0.6584 (t80) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.1277 time to fit residues: 7.4885 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4842 r_free = 0.4842 target = 0.249586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.201033 restraints weight = 18766.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.204808 restraints weight = 13631.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.206257 restraints weight = 10588.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.206711 restraints weight = 7679.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.206943 restraints weight = 7163.144| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5153 Z= 0.136 Angle : 0.501 7.724 7308 Z= 0.274 Chirality : 0.035 0.143 880 Planarity : 0.004 0.040 671 Dihedral : 23.318 108.081 1526 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.60 % Allowed : 22.40 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.40), residues: 422 helix: 1.73 (0.38), residues: 179 sheet: -2.24 (0.97), residues: 29 loop : -0.98 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 291 TYR 0.011 0.002 TYR A 399 PHE 0.014 0.001 PHE A 644 TRP 0.006 0.001 TRP A 570 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 5146) covalent geometry : angle 0.49866 / 0.27 ( 7305) hydrogen bonds : bond 0.03766 / 2.63 ( 142) hydrogen bonds : angle 4.44230 / 3.31 ( 392) metal coordination : bond 0.02447 / 1.22 ( 7) metal coordination : angle 2.38831 / 1.36 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.99 seconds wall clock time: 33 minutes 42.53 seconds (2022.53 seconds total)