Starting phenix.real_space_refine on Tue Feb 11 12:54:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmf_27535/02_2025/8dmf_27535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmf_27535/02_2025/8dmf_27535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmf_27535/02_2025/8dmf_27535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmf_27535/02_2025/8dmf_27535.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmf_27535/02_2025/8dmf_27535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmf_27535/02_2025/8dmf_27535.cif" } resolution = 4.0 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= -0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3589 2.51 5 N 951 2.21 5 O 1093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5670 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5637 Classifications: {'peptide': 718} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 685} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.85, per 1000 atoms: 0.68 Number of scatterers: 5670 At special positions: 0 Unit cell: (75.828, 72.624, 127.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 3 15.00 Mg 1 11.99 O 1093 8.00 N 951 7.00 C 3589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 972.9 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 31.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.531A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.626A pdb=" N THR A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.627A pdb=" N GLY A 170 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 220 Processing helix chain 'A' and resid 235 through 248 removed outlier: 4.231A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.534A pdb=" N PHE A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.512A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 716 removed outlier: 3.553A pdb=" N GLN A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 6.834A pdb=" N LYS A 10 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 79 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 12 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 101 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU A 132 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 103 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN A 134 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 105 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 159 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N CYS A 256 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164 Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 343 removed outlier: 6.964A pdb=" N SER A 302 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.510A pdb=" N LEU A 361 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350 removed outlier: 4.477A pdb=" N ILE A 347 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.585A pdb=" N GLN A 439 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 440 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 400 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 580 Processing sheet with id=AA8, first strand: chain 'A' and resid 482 through 488 removed outlier: 3.539A pdb=" N ALA A 482 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU A 500 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 590 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS A 502 " --> pdb=" O TYR A 588 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 542 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 585 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 544 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 587 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 654 removed outlier: 6.706A pdb=" N VAL A 664 " --> pdb=" O MET A 652 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET A 654 " --> pdb=" O LYS A 662 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS A 662 " --> pdb=" O MET A 654 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1743 1.33 - 1.45: 846 1.45 - 1.57: 3124 1.57 - 1.69: 5 1.69 - 1.81: 61 Bond restraints: 5779 Sorted by residual: bond pdb=" N GLU A 476 " pdb=" CA GLU A 476 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.25e-02 6.40e+03 7.96e+00 bond pdb=" N GLU A 697 " pdb=" CA GLU A 697 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.32e-02 5.74e+03 6.38e+00 bond pdb=" N TYR A 474 " pdb=" CA TYR A 474 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.22e-02 6.72e+03 6.21e+00 bond pdb=" N LYS A 22 " pdb=" CA LYS A 22 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.22e-02 6.72e+03 6.10e+00 bond pdb=" N SER A 695 " pdb=" CA SER A 695 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.21e-02 6.83e+03 5.63e+00 ... (remaining 5774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 7554 1.63 - 3.26: 201 3.26 - 4.89: 30 4.89 - 6.52: 5 6.52 - 8.15: 5 Bond angle restraints: 7795 Sorted by residual: angle pdb=" N GLU A 425 " pdb=" CA GLU A 425 " pdb=" C GLU A 425 " ideal model delta sigma weight residual 111.28 107.47 3.81 1.09e+00 8.42e-01 1.22e+01 angle pdb=" CA GLU A 697 " pdb=" C GLU A 697 " pdb=" O GLU A 697 " ideal model delta sigma weight residual 121.36 118.00 3.36 1.06e+00 8.90e-01 1.00e+01 angle pdb=" N GLU A 424 " pdb=" CA GLU A 424 " pdb=" C GLU A 424 " ideal model delta sigma weight residual 111.71 108.17 3.54 1.15e+00 7.56e-01 9.47e+00 angle pdb=" CA GLU A 476 " pdb=" C GLU A 476 " pdb=" O GLU A 476 " ideal model delta sigma weight residual 121.82 118.12 3.70 1.21e+00 6.83e-01 9.36e+00 angle pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" O TYR A 696 " ideal model delta sigma weight residual 121.55 118.32 3.23 1.06e+00 8.90e-01 9.28e+00 ... (remaining 7790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 3265 22.34 - 44.68: 233 44.68 - 67.02: 10 67.02 - 89.36: 3 89.36 - 111.70: 4 Dihedral angle restraints: 3515 sinusoidal: 1461 harmonic: 2054 Sorted by residual: dihedral pdb=" C8 GTP A 802 " pdb=" C1' GTP A 802 " pdb=" N9 GTP A 802 " pdb=" O4' GTP A 802 " ideal model delta sinusoidal sigma weight residual 104.59 -7.11 111.70 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" C5' GTP A 802 " pdb=" O5' GTP A 802 " pdb=" PA GTP A 802 " pdb=" O3A GTP A 802 " ideal model delta sinusoidal sigma weight residual 69.27 178.40 -109.13 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" CA MET A 224 " pdb=" C MET A 224 " pdb=" N GLU A 225 " pdb=" CA GLU A 225 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 3512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 573 0.037 - 0.073: 172 0.073 - 0.110: 76 0.110 - 0.146: 22 0.146 - 0.183: 3 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA GLU A 424 " pdb=" N GLU A 424 " pdb=" C GLU A 424 " pdb=" CB GLU A 424 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA ARG A 423 " pdb=" N ARG A 423 " pdb=" C ARG A 423 " pdb=" CB ARG A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 843 not shown) Planarity restraints: 1012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 632 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 633 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 276 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 277 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 21 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C GLY A 21 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY A 21 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS A 22 " -0.006 2.00e-02 2.50e+03 ... (remaining 1009 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 65 2.56 - 3.15: 4775 3.15 - 3.73: 9308 3.73 - 4.32: 11920 4.32 - 4.90: 19654 Nonbonded interactions: 45722 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O3A GTP A 802 " model vdw 1.977 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G GTP A 802 " model vdw 2.168 2.170 nonbonded pdb=" N THR A 23 " pdb="MG MG A 801 " model vdw 2.183 2.250 nonbonded pdb=" OH TYR A 400 " pdb=" NH2 ARG A 402 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS A 291 " pdb=" OH TYR A 388 " model vdw 2.267 3.120 ... (remaining 45717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.003 0.035 5779 Z= 0.195 Angle : 0.636 8.154 7795 Z= 0.347 Chirality : 0.046 0.183 846 Planarity : 0.004 0.042 1012 Dihedral : 14.277 111.705 2203 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 (0.33), residues: 716 helix: 1.11 (0.39), residues: 202 sheet: -0.03 (0.41), residues: 195 loop : -0.97 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 455 HIS 0.009 0.001 HIS A 449 PHE 0.011 0.001 PHE A 610 TYR 0.008 0.001 TYR A 696 ARG 0.002 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.8795 (ptm) cc_final: 0.8594 (ttt) REVERT: A 251 MET cc_start: 0.8929 (tmm) cc_final: 0.8647 (tmm) REVERT: A 263 MET cc_start: 0.8783 (mmp) cc_final: 0.8097 (mmp) REVERT: A 323 MET cc_start: 0.8461 (mmp) cc_final: 0.8205 (mmm) REVERT: A 563 MET cc_start: 0.9575 (mmp) cc_final: 0.9122 (mmm) REVERT: A 650 MET cc_start: 0.9167 (mpp) cc_final: 0.8874 (mpp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1578 time to fit residues: 10.6009 Evaluate side-chains 36 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 36 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 443 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.040951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.032700 restraints weight = 45742.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.033835 restraints weight = 27344.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.034651 restraints weight = 18824.676| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5779 Z= 0.161 Angle : 0.605 10.196 7795 Z= 0.301 Chirality : 0.045 0.139 846 Planarity : 0.004 0.038 1012 Dihedral : 7.572 111.381 787 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.33 % Allowed : 8.32 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.32), residues: 716 helix: 1.29 (0.37), residues: 206 sheet: -0.11 (0.40), residues: 199 loop : -1.00 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.008 0.001 HIS A 449 PHE 0.011 0.001 PHE A 255 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.570 Fit side-chains REVERT: A 206 MET cc_start: 0.9252 (mmp) cc_final: 0.8970 (mmt) REVERT: A 251 MET cc_start: 0.8837 (tmm) cc_final: 0.8611 (tmm) REVERT: A 263 MET cc_start: 0.8538 (mmp) cc_final: 0.7882 (mmp) REVERT: A 303 LEU cc_start: 0.9320 (mt) cc_final: 0.9054 (mt) REVERT: A 323 MET cc_start: 0.8399 (mmp) cc_final: 0.8144 (mmm) REVERT: A 389 LYS cc_start: 0.8643 (pttm) cc_final: 0.8085 (tppt) REVERT: A 394 LYS cc_start: 0.9306 (tppt) cc_final: 0.9048 (tptp) REVERT: A 563 MET cc_start: 0.9408 (mmp) cc_final: 0.9115 (mmm) REVERT: A 650 MET cc_start: 0.9124 (mpp) cc_final: 0.8713 (mpp) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.1773 time to fit residues: 10.8281 Evaluate side-chains 39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 overall best weight: 6.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031118 restraints weight = 48076.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032175 restraints weight = 28755.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.032956 restraints weight = 19999.483| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5779 Z= 0.264 Angle : 0.614 9.194 7795 Z= 0.310 Chirality : 0.044 0.152 846 Planarity : 0.004 0.034 1012 Dihedral : 7.724 112.103 787 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.31 % Allowed : 11.09 % Favored : 87.60 % 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: -0.09 (0.32), residues: 716 helix: 1.29 (0.36), residues: 207 sheet: 0.01 (0.40), residues: 200 loop : -1.00 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 429 HIS 0.005 0.002 HIS A 449 PHE 0.012 0.001 PHE A 255 TYR 0.014 0.001 TYR A 121 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9313 (mmp) cc_final: 0.9038 (mmt) REVERT: A 251 MET cc_start: 0.8870 (tmm) cc_final: 0.8635 (tmm) REVERT: A 263 MET cc_start: 0.8667 (mmp) cc_final: 0.7919 (mmp) REVERT: A 394 LYS cc_start: 0.9345 (tppt) cc_final: 0.9112 (tptp) REVERT: A 422 MET cc_start: 0.9542 (mmm) cc_final: 0.9275 (mmm) REVERT: A 563 MET cc_start: 0.9344 (mmp) cc_final: 0.9122 (mmm) REVERT: A 567 MET cc_start: 0.9354 (mpp) cc_final: 0.9133 (mpp) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.1749 time to fit residues: 10.9003 Evaluate side-chains 40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.039179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.031095 restraints weight = 49222.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032178 restraints weight = 29188.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.032954 restraints weight = 20151.488| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5779 Z= 0.201 Angle : 0.583 8.886 7795 Z= 0.289 Chirality : 0.043 0.194 846 Planarity : 0.004 0.033 1012 Dihedral : 7.461 107.943 787 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.14 % Allowed : 12.72 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.32), residues: 716 helix: 1.52 (0.37), residues: 207 sheet: 0.11 (0.43), residues: 178 loop : -1.04 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 429 HIS 0.006 0.001 HIS A 449 PHE 0.016 0.001 PHE A 255 TYR 0.011 0.001 TYR A 121 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9180 (mmp) cc_final: 0.8896 (mmp) REVERT: A 251 MET cc_start: 0.8813 (tmm) cc_final: 0.8559 (tmm) REVERT: A 263 MET cc_start: 0.8615 (mmp) cc_final: 0.7907 (mmp) REVERT: A 323 MET cc_start: 0.8709 (mmm) cc_final: 0.8278 (mmm) REVERT: A 422 MET cc_start: 0.9535 (mmm) cc_final: 0.9193 (mmm) REVERT: A 563 MET cc_start: 0.9384 (mmp) cc_final: 0.9103 (mmm) REVERT: A 567 MET cc_start: 0.9312 (mpp) cc_final: 0.9097 (mpp) REVERT: A 650 MET cc_start: 0.9183 (mpp) cc_final: 0.8931 (mpp) REVERT: A 691 MET cc_start: 0.8776 (ttm) cc_final: 0.8527 (ttt) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.1660 time to fit residues: 10.1566 Evaluate side-chains 42 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.038678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.030547 restraints weight = 48845.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031588 restraints weight = 29449.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.032343 restraints weight = 20531.977| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5779 Z= 0.272 Angle : 0.612 8.054 7795 Z= 0.308 Chirality : 0.043 0.183 846 Planarity : 0.004 0.034 1012 Dihedral : 7.672 109.135 787 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.63 % Allowed : 14.36 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.32), residues: 716 helix: 1.40 (0.37), residues: 207 sheet: 0.05 (0.41), residues: 191 loop : -1.11 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 429 HIS 0.005 0.001 HIS A 449 PHE 0.014 0.001 PHE A 525 TYR 0.014 0.001 TYR A 121 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9160 (mmp) cc_final: 0.8935 (mmp) REVERT: A 251 MET cc_start: 0.8869 (tmm) cc_final: 0.8633 (tmm) REVERT: A 263 MET cc_start: 0.8769 (mmp) cc_final: 0.8096 (mmp) REVERT: A 323 MET cc_start: 0.8686 (mmm) cc_final: 0.8424 (mmm) REVERT: A 422 MET cc_start: 0.9615 (mmm) cc_final: 0.9410 (mmm) REVERT: A 650 MET cc_start: 0.9131 (mpp) cc_final: 0.8726 (mpp) outliers start: 10 outliers final: 6 residues processed: 41 average time/residue: 0.1398 time to fit residues: 8.5794 Evaluate side-chains 40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 51 optimal weight: 0.0270 chunk 16 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 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 = 0.3089 r_free = 0.3089 target = 0.039767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.031533 restraints weight = 47401.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.032616 restraints weight = 28460.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.033416 restraints weight = 19786.604| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5779 Z= 0.153 Angle : 0.575 8.446 7795 Z= 0.281 Chirality : 0.044 0.189 846 Planarity : 0.003 0.033 1012 Dihedral : 7.188 104.644 787 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.14 % Allowed : 15.82 % Favored : 83.03 % 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 (0.33), residues: 716 helix: 1.77 (0.38), residues: 208 sheet: 0.13 (0.43), residues: 178 loop : -1.12 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.005 0.001 HIS A 449 PHE 0.009 0.001 PHE A 255 TYR 0.009 0.001 TYR A 626 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8800 (tmm) cc_final: 0.8564 (tmm) REVERT: A 263 MET cc_start: 0.8425 (mmp) cc_final: 0.7781 (mmp) REVERT: A 303 LEU cc_start: 0.9366 (mt) cc_final: 0.9092 (mt) REVERT: A 323 MET cc_start: 0.8733 (mmm) cc_final: 0.8233 (mmm) REVERT: A 422 MET cc_start: 0.9526 (mmm) cc_final: 0.9295 (mmm) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.1515 time to fit residues: 9.8197 Evaluate side-chains 41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.039701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031425 restraints weight = 47505.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.032494 restraints weight = 28708.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.033271 restraints weight = 20003.271| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5779 Z= 0.185 Angle : 0.597 8.667 7795 Z= 0.291 Chirality : 0.043 0.191 846 Planarity : 0.003 0.033 1012 Dihedral : 7.205 104.688 787 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.14 % Allowed : 16.97 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.33), residues: 716 helix: 1.77 (0.37), residues: 207 sheet: 0.19 (0.43), residues: 183 loop : -1.18 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.004 0.001 HIS A 449 PHE 0.010 0.001 PHE A 545 TYR 0.010 0.001 TYR A 626 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8837 (tmm) cc_final: 0.8561 (tmm) REVERT: A 303 LEU cc_start: 0.9367 (mt) cc_final: 0.9067 (mt) REVERT: A 323 MET cc_start: 0.8744 (mmm) cc_final: 0.8269 (mmm) REVERT: A 422 MET cc_start: 0.9563 (mmm) cc_final: 0.9314 (mmm) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.1451 time to fit residues: 8.7980 Evaluate side-chains 41 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 0.0170 chunk 38 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 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 = 0.3088 r_free = 0.3088 target = 0.039723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.031362 restraints weight = 47380.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032430 restraints weight = 28718.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.033189 restraints weight = 20095.159| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5779 Z= 0.175 Angle : 0.615 10.388 7795 Z= 0.297 Chirality : 0.043 0.185 846 Planarity : 0.003 0.033 1012 Dihedral : 7.141 104.243 787 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.47 % Allowed : 17.94 % Favored : 80.59 % 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: 0.04 (0.33), residues: 716 helix: 1.61 (0.38), residues: 208 sheet: 0.25 (0.43), residues: 183 loop : -1.16 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 429 HIS 0.004 0.001 HIS A 449 PHE 0.008 0.001 PHE A 545 TYR 0.009 0.001 TYR A 626 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9387 (mm) REVERT: A 251 MET cc_start: 0.8826 (tmm) cc_final: 0.8551 (tmm) REVERT: A 303 LEU cc_start: 0.9366 (mt) cc_final: 0.9085 (mt) REVERT: A 323 MET cc_start: 0.8746 (mmm) cc_final: 0.8448 (mmm) REVERT: A 422 MET cc_start: 0.9547 (mmm) cc_final: 0.9284 (mmm) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.1804 time to fit residues: 10.8947 Evaluate side-chains 42 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 24 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 29 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031724 restraints weight = 48233.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.032759 restraints weight = 29112.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.033565 restraints weight = 20370.600| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5779 Z= 0.202 Angle : 0.658 14.242 7795 Z= 0.311 Chirality : 0.044 0.217 846 Planarity : 0.003 0.032 1012 Dihedral : 7.227 105.272 787 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.14 % Allowed : 18.76 % Favored : 80.10 % 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: -0.02 (0.33), residues: 716 helix: 1.60 (0.38), residues: 207 sheet: 0.15 (0.44), residues: 173 loop : -1.14 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 429 HIS 0.004 0.001 HIS A 449 PHE 0.009 0.001 PHE A 525 TYR 0.010 0.001 TYR A 626 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9402 (mm) REVERT: A 208 MET cc_start: 0.9079 (ttp) cc_final: 0.8784 (ttt) REVERT: A 251 MET cc_start: 0.8831 (tmm) cc_final: 0.8521 (tmm) REVERT: A 303 LEU cc_start: 0.9372 (mt) cc_final: 0.9080 (mt) REVERT: A 323 MET cc_start: 0.8756 (mmm) cc_final: 0.8453 (mmm) REVERT: A 422 MET cc_start: 0.9552 (mmm) cc_final: 0.9289 (mmm) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.1433 time to fit residues: 8.9604 Evaluate side-chains 40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 488 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.038650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030522 restraints weight = 49294.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.031581 restraints weight = 29888.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.032341 restraints weight = 20761.689| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5779 Z= 0.314 Angle : 0.721 14.275 7795 Z= 0.354 Chirality : 0.045 0.251 846 Planarity : 0.004 0.033 1012 Dihedral : 7.746 109.901 787 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.65 % Allowed : 18.76 % Favored : 80.59 % 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: -0.34 (0.32), residues: 716 helix: 1.19 (0.37), residues: 208 sheet: -0.23 (0.41), residues: 190 loop : -1.15 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 429 HIS 0.004 0.002 HIS A 502 PHE 0.016 0.002 PHE A 525 TYR 0.017 0.002 TYR A 626 ARG 0.003 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9407 (mm) REVERT: A 208 MET cc_start: 0.9116 (ttp) cc_final: 0.8832 (ttt) REVERT: A 251 MET cc_start: 0.8894 (tmm) cc_final: 0.8621 (tmm) REVERT: A 323 MET cc_start: 0.8746 (mmm) cc_final: 0.8196 (mmm) REVERT: A 422 MET cc_start: 0.9600 (mmm) cc_final: 0.9355 (mmm) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.1561 time to fit residues: 9.4398 Evaluate side-chains 39 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030812 restraints weight = 49064.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.031870 restraints weight = 29488.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.032643 restraints weight = 20415.617| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5779 Z= 0.284 Angle : 0.711 13.788 7795 Z= 0.346 Chirality : 0.045 0.236 846 Planarity : 0.004 0.031 1012 Dihedral : 7.639 108.545 787 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.82 % Allowed : 19.09 % Favored : 80.10 % 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: -0.36 (0.32), residues: 716 helix: 1.20 (0.37), residues: 208 sheet: -0.21 (0.41), residues: 188 loop : -1.19 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 429 HIS 0.006 0.001 HIS A 449 PHE 0.015 0.001 PHE A 525 TYR 0.017 0.001 TYR A 626 ARG 0.003 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.31 seconds wall clock time: 28 minutes 34.85 seconds (1714.85 seconds total)