Starting phenix.real_space_refine on Mon May 12 11:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ost_17164/05_2025/8ost_17164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ost_17164/05_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_17164/05_2025/8ost_17164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ost_17164/05_2025/8ost_17164.map" model { file = "/net/cci-nas-00/data/ceres_data/8ost_17164/05_2025/8ost_17164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ost_17164/05_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-5687/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: 5.32, per 1000 atoms: 0.59 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: 2.88 Conformation dependent library (CDL) restraints added in 549.3 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: 4.04 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: 3.06 Time building geometry restraints manager: 3.35 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: 2.800 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: 0.130 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- 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 0.078 5153 Z= 0.108 Angle : 0.520 6.337 7308 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 Details of bonding type rmsd hydrogen bonds : bond 0.17730 ( 142) hydrogen bonds : angle 6.47354 ( 392) metal coordination : bond 0.02990 ( 7) metal coordination : angle 3.43786 ( 3) covalent geometry : bond 0.00224 ( 5146) covalent geometry : angle 0.51525 ( 7305) *********************** 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 : 0.565 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: 0.4375 time to fit residues: 42.8234 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 : 0.549 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4954 r_free = 0.4954 target = 0.261886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.210462 restraints weight = 19211.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.216807 restraints weight = 10496.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.221100 restraints weight = 6995.033| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5153 Z= 0.130 Angle : 0.549 5.239 7308 Z= 0.290 Chirality : 0.036 0.193 880 Planarity : 0.005 0.061 671 Dihedral : 23.719 106.504 1526 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.53 % Allowed : 19.20 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.40), residues: 422 helix: 2.08 (0.39), residues: 178 sheet: -1.47 (0.93), residues: 34 loop : -1.00 (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 0.022 0.001 PHE A 493 TYR 0.012 0.002 TYR A 640 ARG 0.004 0.001 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 142) hydrogen bonds : angle 4.91479 ( 392) metal coordination : bond 0.02557 ( 7) metal coordination : angle 3.41115 ( 3) covalent geometry : bond 0.00280 ( 5146) covalent geometry : angle 0.54446 ( 7305) *********************** 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 : 0.617 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: A 291 ARG cc_start: 0.6496 (ptm-80) cc_final: 0.6203 (ptm-80) REVERT: A 364 LYS cc_start: 0.5783 (mptt) cc_final: 0.5338 (tttm) REVERT: A 423 MET cc_start: 0.2862 (mmt) cc_final: 0.2035 (mpp) outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.4464 time to fit residues: 33.0799 Evaluate side-chains 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** 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 = 0.4926 r_free = 0.4926 target = 0.258147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.204692 restraints weight = 19464.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.211240 restraints weight = 11085.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.215378 restraints weight = 7476.891| |-----------------------------------------------------------------------------| r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5153 Z= 0.125 Angle : 0.499 4.778 7308 Z= 0.264 Chirality : 0.035 0.169 880 Planarity : 0.004 0.051 671 Dihedral : 23.561 106.619 1526 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.80 % Allowed : 18.93 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.41), residues: 422 helix: 2.17 (0.40), residues: 178 sheet: -2.35 (0.96), residues: 28 loop : -0.92 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 503 HIS 0.007 0.001 HIS A 328 PHE 0.010 0.002 PHE A 493 TYR 0.010 0.002 TYR A 399 ARG 0.003 0.000 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 142) hydrogen bonds : angle 4.70664 ( 392) metal coordination : bond 0.02523 ( 7) metal coordination : angle 3.07732 ( 3) covalent geometry : bond 0.00282 ( 5146) covalent geometry : angle 0.49510 ( 7305) *********************** 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 55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.592 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: A 291 ARG cc_start: 0.6353 (ptm-80) cc_final: 0.6085 (ptm-80) REVERT: A 423 MET cc_start: 0.2608 (mmt) cc_final: 0.1255 (mpp) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.3824 time to fit residues: 25.3126 Evaluate side-chains 51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER 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: 5.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.250906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.200092 restraints weight = 19287.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.205230 restraints weight = 12981.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.206512 restraints weight = 9078.062| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5153 Z= 0.174 Angle : 0.563 6.010 7308 Z= 0.297 Chirality : 0.036 0.144 880 Planarity : 0.005 0.055 671 Dihedral : 23.474 108.521 1526 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.40 % Allowed : 21.60 % 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 (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: -0.01 (0.39), residues: 422 helix: 1.64 (0.38), residues: 177 sheet: -2.83 (0.88), residues: 29 loop : -1.01 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 570 HIS 0.013 0.002 HIS A 328 PHE 0.024 0.002 PHE A 644 TYR 0.016 0.002 TYR A 399 ARG 0.004 0.001 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 142) hydrogen bonds : angle 4.70873 ( 392) metal coordination : bond 0.02459 ( 7) metal coordination : angle 2.81510 ( 3) covalent geometry : bond 0.00407 ( 5146) covalent geometry : angle 0.56021 ( 7305) *********************** 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 62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.7964 (m-30) cc_final: 0.7756 (t0) REVERT: A 302 CYS cc_start: 0.5972 (p) cc_final: 0.5598 (p) REVERT: A 365 GLU cc_start: 0.4828 (mm-30) cc_final: 0.4323 (mm-30) REVERT: A 412 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.4210 (m-30) REVERT: A 423 MET cc_start: 0.2798 (mmt) cc_final: 0.1518 (mpp) REVERT: A 706 TYR cc_start: 0.6920 (t80) cc_final: 0.6516 (t80) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.3944 time to fit residues: 30.0422 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.252392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.203482 restraints weight = 18919.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.205937 restraints weight = 14173.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.206716 restraints weight = 9458.447| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3810 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= 0.114 Angle : 0.492 5.056 7308 Z= 0.258 Chirality : 0.034 0.140 880 Planarity : 0.004 0.046 671 Dihedral : 23.410 107.668 1526 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.20 (0.40), residues: 422 helix: 1.89 (0.39), residues: 177 sheet: -2.61 (0.91), residues: 29 loop : -0.99 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.006 0.001 HIS A 328 PHE 0.015 0.001 PHE A 644 TYR 0.011 0.002 TYR A 399 ARG 0.003 0.000 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 142) hydrogen bonds : angle 4.44248 ( 392) metal coordination : bond 0.02446 ( 7) metal coordination : angle 2.22950 ( 3) covalent geometry : bond 0.00257 ( 5146) covalent geometry : angle 0.49048 ( 7305) *********************** 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 54 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2620 (mmt) cc_final: 0.1374 (mpp) REVERT: A 644 PHE cc_start: 0.4540 (OUTLIER) cc_final: 0.3623 (p90) REVERT: A 706 TYR cc_start: 0.6812 (t80) cc_final: 0.6423 (t80) REVERT: B 151 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5740 (mp0) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.3968 time to fit residues: 25.5805 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4834 r_free = 0.4834 target = 0.248997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.193489 restraints weight = 18880.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.199043 restraints weight = 11656.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.202661 restraints weight = 8379.256| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5153 Z= 0.160 Angle : 0.517 4.426 7308 Z= 0.278 Chirality : 0.035 0.144 880 Planarity : 0.004 0.045 671 Dihedral : 23.391 108.571 1526 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.93 % Allowed : 20.53 % 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: -0.08 (0.39), residues: 422 helix: 1.56 (0.38), residues: 178 sheet: -2.54 (0.92), residues: 29 loop : -1.10 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 PHE 0.017 0.002 PHE A 644 TYR 0.012 0.002 TYR A 399 ARG 0.003 0.001 ARG A 669 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 142) hydrogen bonds : angle 4.65985 ( 392) metal coordination : bond 0.02156 ( 7) metal coordination : angle 2.62380 ( 3) covalent geometry : bond 0.00369 ( 5146) covalent geometry : angle 0.51417 ( 7305) *********************** 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 55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.4147 (m-30) REVERT: A 423 MET cc_start: 0.2665 (mmt) cc_final: 0.1425 (mpp) REVERT: A 563 VAL cc_start: 0.7270 (t) cc_final: 0.6093 (m) REVERT: A 706 TYR cc_start: 0.7004 (t80) cc_final: 0.6673 (t80) REVERT: B 151 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5708 (mp0) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 0.3916 time to fit residues: 25.7830 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 : 0.589 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4844 r_free = 0.4844 target = 0.249928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.200443 restraints weight = 19025.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.205337 restraints weight = 13805.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.205992 restraints weight = 10523.503| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5153 Z= 0.123 Angle : 0.498 8.500 7308 Z= 0.264 Chirality : 0.035 0.158 880 Planarity : 0.004 0.038 671 Dihedral : 23.327 107.991 1526 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: 0.05 (0.40), residues: 422 helix: 1.69 (0.38), residues: 179 sheet: -2.39 (0.95), residues: 29 loop : -1.08 (0.39), residues: 214 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 0.012 0.001 PHE A 522 TYR 0.009 0.001 TYR A 693 ARG 0.003 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 142) hydrogen bonds : angle 4.37594 ( 392) metal coordination : bond 0.02388 ( 7) metal coordination : angle 2.29022 ( 3) covalent geometry : bond 0.00278 ( 5146) covalent geometry : angle 0.49572 ( 7305) *********************** 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 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.2682 (mmt) cc_final: 0.1423 (mpp) REVERT: A 706 TYR cc_start: 0.6936 (t80) cc_final: 0.6649 (t80) REVERT: B 148 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.6417 (m-70) REVERT: B 151 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5764 (mp0) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.4142 time to fit residues: 26.2487 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 : 0.652 ------------------------------------------------------------------------------- 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 B residue 148 HIS 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: 2.9990 chunk 45 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 39 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 24 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.4853 r_free = 0.4853 target = 0.250891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.200620 restraints weight = 18948.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.205120 restraints weight = 12707.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205991 restraints weight = 9528.382| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5153 Z= 0.106 Angle : 0.471 5.397 7308 Z= 0.248 Chirality : 0.034 0.144 880 Planarity : 0.004 0.038 671 Dihedral : 23.214 107.373 1526 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.87 % Allowed : 20.53 % 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: 0.21 (0.40), residues: 422 helix: 1.84 (0.38), residues: 179 sheet: -2.25 (0.98), residues: 29 loop : -1.01 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.001 PHE A 522 TYR 0.008 0.001 TYR A 706 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 142) hydrogen bonds : angle 4.19117 ( 392) metal coordination : bond 0.02381 ( 7) metal coordination : angle 2.32040 ( 3) covalent geometry : bond 0.00241 ( 5146) covalent geometry : angle 0.46875 ( 7305) *********************** 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 : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.5906 (mptt) cc_final: 0.5515 (tttm) REVERT: A 423 MET cc_start: 0.2503 (mmt) cc_final: 0.1251 (mpp) REVERT: A 706 TYR cc_start: 0.6900 (t80) cc_final: 0.6629 (t80) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.4403 time to fit residues: 25.2202 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 480 THR Chi-restraints excluded: chain A residue 570 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.248688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.197852 restraints weight = 18782.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.201138 restraints weight = 13953.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.201339 restraints weight = 11184.455| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5153 Z= 0.141 Angle : 0.509 5.008 7308 Z= 0.272 Chirality : 0.035 0.158 880 Planarity : 0.004 0.036 671 Dihedral : 23.232 108.526 1526 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.87 % Allowed : 20.53 % 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: 0.03 (0.40), residues: 422 helix: 1.61 (0.38), residues: 179 sheet: -2.31 (0.98), residues: 29 loop : -1.03 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.008 0.001 HIS A 328 PHE 0.012 0.001 PHE A 644 TYR 0.013 0.002 TYR A 399 ARG 0.004 0.001 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 142) hydrogen bonds : angle 4.40805 ( 392) metal coordination : bond 0.02346 ( 7) metal coordination : angle 2.32622 ( 3) covalent geometry : bond 0.00328 ( 5146) covalent geometry : angle 0.50666 ( 7305) *********************** 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 : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.5859 (mptt) cc_final: 0.5503 (tttm) REVERT: A 423 MET cc_start: 0.2611 (mmt) cc_final: 0.1374 (mpp) REVERT: A 706 TYR cc_start: 0.7011 (t80) cc_final: 0.6727 (t80) REVERT: B 151 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6001 (mp0) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.4243 time to fit residues: 26.4550 Evaluate side-chains 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 27 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.249829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.198970 restraints weight = 18591.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.204022 restraints weight = 12434.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.204428 restraints weight = 9485.805| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5153 Z= 0.108 Angle : 0.483 5.979 7308 Z= 0.256 Chirality : 0.035 0.158 880 Planarity : 0.004 0.039 671 Dihedral : 23.201 108.594 1526 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: 0.22 (0.40), residues: 422 helix: 1.75 (0.38), residues: 179 sheet: -2.14 (1.00), residues: 29 loop : -0.93 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.003 0.001 HIS A 328 PHE 0.008 0.001 PHE A 529 TYR 0.009 0.001 TYR A 693 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 142) hydrogen bonds : angle 4.21813 ( 392) metal coordination : bond 0.02530 ( 7) metal coordination : angle 2.17918 ( 3) covalent geometry : bond 0.00247 ( 5146) covalent geometry : angle 0.48078 ( 7305) ********************** 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 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.5934 (mptt) cc_final: 0.5511 (tttm) REVERT: A 423 MET cc_start: 0.2489 (mmt) cc_final: 0.1255 (mpp) REVERT: A 706 TYR cc_start: 0.6920 (t80) cc_final: 0.6664 (t80) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.4554 time to fit residues: 26.3769 Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 480 THR Chi-restraints excluded: chain A residue 570 TRP 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: 0.0570 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.4840 r_free = 0.4840 target = 0.249147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.198299 restraints weight = 18905.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.203075 restraints weight = 13315.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.203661 restraints weight = 10004.580| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5153 Z= 0.121 Angle : 0.491 5.682 7308 Z= 0.261 Chirality : 0.035 0.163 880 Planarity : 0.004 0.035 671 Dihedral : 23.206 112.431 1526 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.33 % Allowed : 21.87 % 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: 0.19 (0.40), residues: 422 helix: 1.72 (0.38), residues: 179 sheet: -2.11 (1.02), residues: 29 loop : -0.94 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.011 0.001 HIS A 322 PHE 0.009 0.001 PHE A 567 TYR 0.010 0.001 TYR A 399 ARG 0.003 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 142) hydrogen bonds : angle 4.23065 ( 392) metal coordination : bond 0.02300 ( 7) metal coordination : angle 2.21429 ( 3) covalent geometry : bond 0.00279 ( 5146) covalent geometry : angle 0.48912 ( 7305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.00 seconds wall clock time: 69 minutes 36.99 seconds (4176.99 seconds total)