Starting phenix.real_space_refine on Thu Jul 2 02:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ooy_17033/07_2026/8ooy_17033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooy_17033/07_2026/8ooy_17033.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/8ooy_17033/07_2026/8ooy_17033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooy_17033/07_2026/8ooy_17033.map" model { file = "/net/cci-nas-00/data/ceres_data/8ooy_17033/07_2026/8ooy_17033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooy_17033/07_2026/8ooy_17033.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ooy_17033/07_2026/8ooy_17033.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ooy_17033/07_2026/8ooy_17033.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 3520 2.51 5 N 1029 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4782 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 575} Chain: "T" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.26 Number of scatterers: 5828 At special positions: 0 Unit cell: (89.452, 96.14, 78.584, 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 15 16.00 P 51 15.00 Mg 1 11.99 O 1212 8.00 N 1029 7.00 C 3520 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: 0.61 Conformation dependent library (CDL) restraints added in 337.3 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 62.7% alpha, 5.6% beta 23 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.673A pdb=" N LYS A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.604A pdb=" N LEU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.605A pdb=" N ASP A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.944A pdb=" N GLU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.045A pdb=" N ILE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.647A pdb=" N GLN A 488 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 519 Proline residue: A 514 - end of helix removed outlier: 3.555A pdb=" N HIS A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 532 through 544 removed outlier: 4.405A pdb=" N VAL A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.831A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.628A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.032A pdb=" N LYS A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 636 " --> pdb=" O GLY A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.799A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 removed outlier: 3.877A pdb=" N ILE A 679 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 745 through 749 Processing helix chain 'A' and resid 750 through 767 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 795 through 812 removed outlier: 3.734A pdb=" N LEU A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 871 removed outlier: 3.743A pdb=" N ALA A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.570A pdb=" N ALA A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.620A pdb=" N TYR A 382 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 375 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.262A pdb=" N PHE A 352 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS A 416 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.587A pdb=" N SER A 670 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 699 through 702 252 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.77 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: 1534 1.33 - 1.45: 1226 1.45 - 1.57: 3153 1.57 - 1.69: 99 1.69 - 1.81: 29 Bond restraints: 6041 Sorted by residual: bond pdb=" C3' C T 21 " pdb=" C2' C T 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.06e+00 bond pdb=" C3' DG D 12 " pdb=" C2' DG D 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.71e+00 bond pdb=" N VAL A 663 " pdb=" CA VAL A 663 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.48e+00 bond pdb=" C3' G T 17 " pdb=" C2' G T 17 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.91e+00 bond pdb=" N THR A 664 " pdb=" CA THR A 664 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.88e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 7951 1.55 - 3.09: 382 3.09 - 4.64: 45 4.64 - 6.18: 7 6.18 - 7.73: 6 Bond angle restraints: 8391 Sorted by residual: angle pdb=" N3 DT P 10 " pdb=" C4 DT P 10 " pdb=" O4 DT P 10 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT P 8 " pdb=" C4 DT P 8 " pdb=" O4 DT P 8 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 8386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2879 17.28 - 34.57: 390 34.57 - 51.85: 194 51.85 - 69.13: 65 69.13 - 86.41: 7 Dihedral angle restraints: 3535 sinusoidal: 1772 harmonic: 1763 Sorted by residual: dihedral pdb=" CA VAL A 815 " pdb=" C VAL A 815 " pdb=" N GLU A 816 " pdb=" CA GLU A 816 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP A 892 " pdb=" CB ASP A 892 " pdb=" CG ASP A 892 " pdb=" OD1 ASP A 892 " ideal model delta sinusoidal sigma weight residual -30.00 -85.98 55.98 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU A 917 " pdb=" CG GLU A 917 " pdb=" CD GLU A 917 " pdb=" OE1 GLU A 917 " ideal model delta sinusoidal sigma weight residual 0.00 86.41 -86.41 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 3532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 644 0.042 - 0.083: 210 0.083 - 0.125: 81 0.125 - 0.167: 7 0.167 - 0.208: 2 Chirality restraints: 944 Sorted by residual: chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 779 " pdb=" N ILE A 779 " pdb=" C ILE A 779 " pdb=" CB ILE A 779 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 941 not shown) Planarity restraints: 913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 521 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 522 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 779 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 780 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 780 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 780 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 901 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C HIS A 901 " 0.026 2.00e-02 2.50e+03 pdb=" O HIS A 901 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 902 " -0.009 2.00e-02 2.50e+03 ... (remaining 910 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5044 3.17 - 3.75: 10010 3.75 - 4.32: 13143 4.32 - 4.90: 20807 Nonbonded interactions: 49064 Sorted by model distance: nonbonded pdb=" OD1 ASP A 355 " pdb="MG MG A1001 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASN A 524 " pdb=" ND2 ASN A 528 " model vdw 2.201 3.120 nonbonded pdb=" NE2 HIS A 555 " pdb=" OE2 GLU A 685 " model vdw 2.206 3.120 nonbonded pdb=" OE1 GLU A 729 " pdb=" NZ LYS A 731 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 817 " pdb=" OG1 THR A 851 " model vdw 2.231 3.040 ... (remaining 49059 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: 1.620 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.004 0.039 6041 Z= 0.344 Angle : 0.738 7.727 8391 Z= 0.517 Chirality : 0.047 0.208 944 Planarity : 0.004 0.045 913 Dihedral : 20.016 86.412 2395 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.79 % Allowed : 0.39 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.35), residues: 602 helix: 0.59 (0.30), residues: 315 sheet: -3.34 (0.66), residues: 47 loop : -1.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 806 TYR 0.015 0.001 TYR A 814 PHE 0.016 0.002 PHE A 354 TRP 0.006 0.001 TRP A 465 HIS 0.011 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.34 ( 6041) covalent geometry : angle 0.73757 / 0.52 ( 8391) hydrogen bonds : bond 0.14500 / 9.74 ( 311) hydrogen bonds : angle 6.35157 / 4.16 ( 853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 679 ILE cc_start: 0.8365 (mm) cc_final: 0.8088 (mm) REVERT: A 848 MET cc_start: 0.7811 (mmm) cc_final: 0.7189 (mmm) outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.0596 time to fit residues: 6.2718 Evaluate side-chains 53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083774 restraints weight = 14716.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084383 restraints weight = 11205.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085407 restraints weight = 8872.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085555 restraints weight = 7075.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085793 restraints weight = 7524.310| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6041 Z= 0.148 Angle : 0.643 9.064 8391 Z= 0.352 Chirality : 0.043 0.192 944 Planarity : 0.005 0.051 913 Dihedral : 21.953 65.701 1200 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.38 % Allowed : 6.89 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.35), residues: 602 helix: 0.72 (0.29), residues: 325 sheet: -3.20 (0.64), residues: 49 loop : -1.52 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 806 TYR 0.020 0.002 TYR A 814 PHE 0.019 0.002 PHE A 886 TRP 0.004 0.001 TRP A 342 HIS 0.008 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 6041) covalent geometry : angle 0.64299 / 0.35 ( 8391) hydrogen bonds : bond 0.04449 / 2.95 ( 311) hydrogen bonds : angle 5.13328 / 3.50 ( 853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8323 (mt) cc_final: 0.8024 (mt) REVERT: A 506 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 713 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 848 MET cc_start: 0.7585 (mmm) cc_final: 0.7133 (mmm) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.0640 time to fit residues: 6.1476 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.083950 restraints weight = 14648.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085820 restraints weight = 13633.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086419 restraints weight = 10341.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086378 restraints weight = 7939.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086542 restraints weight = 8648.036| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6041 Z= 0.139 Angle : 0.601 7.714 8391 Z= 0.330 Chirality : 0.041 0.159 944 Planarity : 0.004 0.049 913 Dihedral : 21.911 64.468 1200 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.77 % Allowed : 11.61 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.35), residues: 602 helix: 0.84 (0.29), residues: 325 sheet: -3.17 (0.66), residues: 49 loop : -1.41 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 806 TYR 0.018 0.001 TYR A 814 PHE 0.018 0.002 PHE A 886 TRP 0.004 0.001 TRP A 866 HIS 0.006 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 6041) covalent geometry : angle 0.60075 / 0.33 ( 8391) hydrogen bonds : bond 0.04058 / 2.68 ( 311) hydrogen bonds : angle 4.87111 / 3.33 ( 853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8276 (mm) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.0651 time to fit residues: 6.3996 Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083131 restraints weight = 14635.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083836 restraints weight = 11056.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084822 restraints weight = 8835.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084860 restraints weight = 7219.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084980 restraints weight = 6723.130| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6041 Z= 0.141 Angle : 0.579 7.747 8391 Z= 0.320 Chirality : 0.041 0.186 944 Planarity : 0.004 0.047 913 Dihedral : 21.944 63.446 1200 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.97 % Allowed : 12.99 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.35), residues: 602 helix: 0.88 (0.29), residues: 326 sheet: -3.18 (0.62), residues: 49 loop : -1.36 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.018 0.001 TYR A 814 PHE 0.019 0.002 PHE A 792 TRP 0.005 0.001 TRP A 342 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 6041) covalent geometry : angle 0.57917 / 0.32 ( 8391) hydrogen bonds : bond 0.03893 / 2.56 ( 311) hydrogen bonds : angle 4.70440 / 3.22 ( 853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8272 (mm) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.0727 time to fit residues: 6.5821 Evaluate side-chains 62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084668 restraints weight = 14932.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085254 restraints weight = 12129.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086150 restraints weight = 9615.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086263 restraints weight = 7890.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086384 restraints weight = 7344.795| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6041 Z= 0.131 Angle : 0.577 7.745 8391 Z= 0.315 Chirality : 0.041 0.170 944 Planarity : 0.004 0.048 913 Dihedral : 21.932 61.893 1200 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.36 % Allowed : 14.37 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.35), residues: 602 helix: 0.96 (0.29), residues: 326 sheet: -3.00 (0.63), residues: 48 loop : -1.29 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 754 TYR 0.017 0.001 TYR A 630 PHE 0.015 0.001 PHE A 886 TRP 0.005 0.001 TRP A 342 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 6041) covalent geometry : angle 0.57660 / 0.31 ( 8391) hydrogen bonds : bond 0.03716 / 2.45 ( 311) hydrogen bonds : angle 4.55877 / 3.12 ( 853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 755 ARG cc_start: 0.8234 (ppt170) cc_final: 0.7939 (ppt170) REVERT: A 768 MET cc_start: 0.7823 (ppp) cc_final: 0.7230 (ppp) REVERT: A 788 MET cc_start: 0.7460 (mtm) cc_final: 0.7194 (mtm) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.0706 time to fit residues: 6.9983 Evaluate side-chains 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.081744 restraints weight = 14920.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082526 restraints weight = 11124.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083371 restraints weight = 8970.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.083527 restraints weight = 7262.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083639 restraints weight = 6795.708| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6041 Z= 0.197 Angle : 0.633 7.927 8391 Z= 0.341 Chirality : 0.043 0.184 944 Planarity : 0.005 0.045 913 Dihedral : 22.141 68.499 1200 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.95 % Allowed : 14.57 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.35), residues: 602 helix: 0.97 (0.29), residues: 326 sheet: -2.83 (0.62), residues: 47 loop : -1.42 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 682 TYR 0.020 0.002 TYR A 814 PHE 0.017 0.002 PHE A 886 TRP 0.005 0.001 TRP A 866 HIS 0.006 0.002 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 6041) covalent geometry : angle 0.63264 / 0.34 ( 8391) hydrogen bonds : bond 0.04295 / 2.82 ( 311) hydrogen bonds : angle 4.63116 / 3.15 ( 853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8308 (mt) cc_final: 0.8015 (mt) REVERT: A 506 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8324 (mm) REVERT: A 755 ARG cc_start: 0.8238 (ppt170) cc_final: 0.7838 (ppt170) outliers start: 15 outliers final: 9 residues processed: 69 average time/residue: 0.0589 time to fit residues: 5.5649 Evaluate side-chains 61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082217 restraints weight = 14890.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082745 restraints weight = 11977.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083353 restraints weight = 10669.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.083935 restraints weight = 7514.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084165 restraints weight = 6863.909| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6041 Z= 0.143 Angle : 0.619 8.609 8391 Z= 0.332 Chirality : 0.042 0.163 944 Planarity : 0.005 0.047 913 Dihedral : 22.114 70.265 1200 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.36 % Allowed : 15.94 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.35), residues: 602 helix: 0.89 (0.29), residues: 326 sheet: -2.93 (0.60), residues: 48 loop : -1.26 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.018 0.001 TYR A 814 PHE 0.015 0.001 PHE A 886 TRP 0.005 0.001 TRP A 866 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 6041) covalent geometry : angle 0.61910 / 0.33 ( 8391) hydrogen bonds : bond 0.03926 / 2.58 ( 311) hydrogen bonds : angle 4.59564 / 3.12 ( 853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8238 (mt) cc_final: 0.7955 (mt) REVERT: A 506 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8330 (mm) REVERT: A 755 ARG cc_start: 0.8181 (ppt170) cc_final: 0.7814 (ppt170) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.0609 time to fit residues: 5.5861 Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.103797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082214 restraints weight = 14860.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082297 restraints weight = 11764.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083276 restraints weight = 9842.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083478 restraints weight = 7801.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083602 restraints weight = 7466.356| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6041 Z= 0.173 Angle : 0.659 12.835 8391 Z= 0.350 Chirality : 0.043 0.220 944 Planarity : 0.005 0.046 913 Dihedral : 22.175 72.047 1200 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.17 % Allowed : 16.54 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.35), residues: 602 helix: 0.83 (0.29), residues: 327 sheet: -2.73 (0.61), residues: 47 loop : -1.33 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.019 0.002 TYR A 814 PHE 0.064 0.003 PHE A 792 TRP 0.004 0.001 TRP A 866 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 6041) covalent geometry : angle 0.65939 / 0.35 ( 8391) hydrogen bonds : bond 0.04081 / 2.70 ( 311) hydrogen bonds : angle 4.68054 / 3.19 ( 853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8303 (mt) cc_final: 0.8038 (mt) REVERT: A 506 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8332 (mm) REVERT: A 614 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 755 ARG cc_start: 0.8262 (ppt170) cc_final: 0.7844 (ppt170) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.0779 time to fit residues: 6.8235 Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.105188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083393 restraints weight = 14938.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083590 restraints weight = 12966.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084529 restraints weight = 10687.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084686 restraints weight = 8756.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084794 restraints weight = 8053.180| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6041 Z= 0.137 Angle : 0.631 11.864 8391 Z= 0.336 Chirality : 0.043 0.247 944 Planarity : 0.005 0.047 913 Dihedral : 22.118 72.937 1200 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.17 % Allowed : 16.54 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.35), residues: 602 helix: 0.90 (0.29), residues: 326 sheet: -2.85 (0.58), residues: 53 loop : -1.10 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.016 0.001 TYR A 814 PHE 0.017 0.002 PHE A 886 TRP 0.005 0.001 TRP A 866 HIS 0.004 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 6041) covalent geometry : angle 0.63081 / 0.34 ( 8391) hydrogen bonds : bond 0.03786 / 2.53 ( 311) hydrogen bonds : angle 4.54136 / 3.10 ( 853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8292 (mt) cc_final: 0.8019 (mt) REVERT: A 506 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8335 (mm) REVERT: A 614 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7705 (mm) REVERT: A 685 GLU cc_start: 0.7180 (mp0) cc_final: 0.6927 (pm20) REVERT: A 755 ARG cc_start: 0.8237 (ppt170) cc_final: 0.7835 (ppt170) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.0690 time to fit residues: 6.0490 Evaluate side-chains 63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.104239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082506 restraints weight = 14966.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082373 restraints weight = 13469.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083237 restraints weight = 12628.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083709 restraints weight = 9040.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.083910 restraints weight = 8577.630| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6041 Z= 0.163 Angle : 0.651 11.843 8391 Z= 0.347 Chirality : 0.043 0.195 944 Planarity : 0.005 0.046 913 Dihedral : 22.159 74.283 1200 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.97 % Allowed : 17.13 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.35), residues: 602 helix: 0.95 (0.29), residues: 326 sheet: -2.80 (0.59), residues: 53 loop : -1.10 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.017 0.002 TYR A 814 PHE 0.019 0.002 PHE A 792 TRP 0.004 0.001 TRP A 465 HIS 0.005 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6041) covalent geometry : angle 0.65112 / 0.35 ( 8391) hydrogen bonds : bond 0.04019 / 2.66 ( 311) hydrogen bonds : angle 4.63867 / 3.15 ( 853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8313 (mt) cc_final: 0.8036 (mt) REVERT: A 506 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 614 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 685 GLU cc_start: 0.7201 (mp0) cc_final: 0.6952 (pm20) REVERT: A 755 ARG cc_start: 0.8244 (ppt170) cc_final: 0.7835 (ppt170) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.0629 time to fit residues: 5.3294 Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 ASN A 761 ASN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.102873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081954 restraints weight = 14905.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081496 restraints weight = 13900.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082418 restraints weight = 12415.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082585 restraints weight = 9632.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083180 restraints weight = 8887.223| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.005 0.050 6041 Z= 0.213 Angle : 0.693 11.344 8391 Z= 0.369 Chirality : 0.045 0.199 944 Planarity : 0.005 0.046 913 Dihedral : 22.336 77.231 1200 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.97 % Allowed : 17.32 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.35), residues: 602 helix: 0.78 (0.29), residues: 323 sheet: -2.94 (0.59), residues: 53 loop : -1.22 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 682 TYR 0.020 0.002 TYR A 814 PHE 0.021 0.002 PHE A 792 TRP 0.007 0.001 TRP A 465 HIS 0.006 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 6041) covalent geometry : angle 0.69318 / 0.37 ( 8391) hydrogen bonds : bond 0.04436 / 2.95 ( 311) hydrogen bonds : angle 4.77789 / 3.23 ( 853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 930.93 seconds wall clock time: 16 minutes 44.79 seconds (1004.79 seconds total)