Starting phenix.real_space_refine on Tue Mar 3 12:45:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz2_15032/03_2026/7zz2_15032.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz2_15032/03_2026/7zz2_15032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz2_15032/03_2026/7zz2_15032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz2_15032/03_2026/7zz2_15032.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz2_15032/03_2026/7zz2_15032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz2_15032/03_2026/7zz2_15032.cif" } resolution = 2.48 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= 0.009 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 Mn 1 7.51 5 Mg 1 5.21 5 S 19 5.16 5 C 2739 2.51 5 N 731 2.21 5 O 875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4366 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4301 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 65 Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1} Classifications: {'undetermined': 3, 'water': 57} Link IDs: {None: 59} Time building chain proxies: 1.06, per 1000 atoms: 0.24 Number of scatterers: 4366 At special positions: 0 Unit cell: (67.84, 76.32, 78.44, 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) Mn 1 24.99 S 19 16.00 Mg 1 11.99 O 875 8.00 N 731 7.00 C 2739 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: 0.39 Conformation dependent library (CDL) restraints added in 264.6 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 62.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.818A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 617 through 632 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.318A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.515A pdb=" N TYR A 685 " --> pdb=" O ASN A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 725 Processing helix chain 'A' and resid 734 through 738 removed outlier: 4.622A pdb=" N SER A 737 " --> pdb=" O HIS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.790A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 826 through 840 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 860 Processing helix chain 'A' and resid 868 through 883 Processing helix chain 'A' and resid 886 through 894 Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 919 through 927 Processing helix chain 'A' and resid 945 through 958 Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 1000 Processing sheet with id=AA1, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.885A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 633 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: 0.73 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1418 1.34 - 1.46: 878 1.46 - 1.58: 2068 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 4401 Sorted by residual: bond pdb=" C1 PYR A1203 " pdb=" C2 PYR A1203 " ideal model delta sigma weight residual 1.558 1.388 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C2 PYR A1203 " pdb=" O3 PYR A1203 " ideal model delta sigma weight residual 1.210 1.309 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1 PYR A1203 " pdb=" O1 PYR A1203 " ideal model delta sigma weight residual 1.239 1.307 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 PYR A1203 " pdb=" O2 PYR A1203 " ideal model delta sigma weight residual 1.243 1.308 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 4396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 5844 2.28 - 4.55: 88 4.55 - 6.83: 19 6.83 - 9.10: 3 9.10 - 11.38: 3 Bond angle restraints: 5957 Sorted by residual: angle pdb=" CB MET A 982 " pdb=" CG MET A 982 " pdb=" SD MET A 982 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA GLN A 817 " pdb=" CB GLN A 817 " pdb=" CG GLN A 817 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CB MET A 858 " pdb=" CG MET A 858 " pdb=" SD MET A 858 " ideal model delta sigma weight residual 112.70 123.53 -10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA LYS A 921 " pdb=" CB LYS A 921 " pdb=" CG LYS A 921 " ideal model delta sigma weight residual 114.10 121.14 -7.04 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CB GLU A 960 " pdb=" CG GLU A 960 " pdb=" CD GLU A 960 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 ... (remaining 5952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2293 17.82 - 35.65: 263 35.65 - 53.47: 62 53.47 - 71.30: 23 71.30 - 89.12: 6 Dihedral angle restraints: 2647 sinusoidal: 1078 harmonic: 1569 Sorted by residual: dihedral pdb=" CA ARG A 533 " pdb=" C ARG A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual -180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 918 " pdb=" C PHE A 918 " pdb=" N PRO A 919 " pdb=" CA PRO A 919 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU A 583 " pdb=" CG GLU A 583 " pdb=" CD GLU A 583 " pdb=" OE1 GLU A 583 " ideal model delta sinusoidal sigma weight residual 0.00 89.12 -89.12 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 480 0.047 - 0.094: 137 0.094 - 0.141: 28 0.141 - 0.188: 4 0.188 - 0.235: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 552 " pdb=" CA ILE A 552 " pdb=" CG1 ILE A 552 " pdb=" CG2 ILE A 552 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB VAL A 840 " pdb=" CA VAL A 840 " pdb=" CG1 VAL A 840 " pdb=" CG2 VAL A 840 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 647 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 899 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 900 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 900 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 900 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 749 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CD GLN A 749 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLN A 749 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 749 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 768 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 769 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " -0.020 5.00e-02 4.00e+02 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 140 2.69 - 3.24: 4250 3.24 - 3.79: 7930 3.79 - 4.35: 10233 4.35 - 4.90: 16234 Nonbonded interactions: 38787 Sorted by model distance: nonbonded pdb=" OQ1 KCX A 703 " pdb="MN MN A1202 " model vdw 2.132 2.320 nonbonded pdb="MN MN A1202 " pdb=" O HOH A1308 " model vdw 2.176 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1202 " model vdw 2.202 2.400 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1202 " model vdw 2.213 2.320 nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1202 " model vdw 2.216 2.320 ... (remaining 38782 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.230 Find NCS groups from input model: 0.020 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:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 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 : 0.005 0.170 4401 Z= 0.259 Angle : 0.764 11.381 5957 Z= 0.407 Chirality : 0.046 0.235 650 Planarity : 0.005 0.040 779 Dihedral : 17.253 89.122 1643 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.27 % Allowed : 18.95 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.33), residues: 536 helix: -0.15 (0.27), residues: 299 sheet: -0.07 (0.79), residues: 43 loop : 0.01 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 485 TYR 0.010 0.002 TYR A 578 PHE 0.011 0.002 PHE A 997 TRP 0.005 0.001 TRP A 586 HIS 0.009 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 4401) covalent geometry : angle 0.76372 ( 5957) hydrogen bonds : bond 0.15166 ( 218) hydrogen bonds : angle 7.81649 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.105 Fit side-chains REVERT: A 596 MET cc_start: 0.9184 (mtp) cc_final: 0.8926 (mtm) outliers start: 15 outliers final: 14 residues processed: 45 average time/residue: 0.4084 time to fit residues: 19.3283 Evaluate side-chains 44 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 934 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.0270 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 999 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049452 restraints weight = 15659.149| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.98 r_work: 0.2963 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4401 Z= 0.111 Angle : 0.474 5.443 5957 Z= 0.252 Chirality : 0.040 0.137 650 Planarity : 0.004 0.033 779 Dihedral : 6.981 58.694 615 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.70 % Allowed : 16.12 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.35), residues: 536 helix: 1.03 (0.29), residues: 300 sheet: -0.09 (0.78), residues: 43 loop : 0.36 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 783 TYR 0.006 0.001 TYR A 776 PHE 0.008 0.001 PHE A 636 TRP 0.004 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4401) covalent geometry : angle 0.47448 ( 5957) hydrogen bonds : bond 0.03814 ( 218) hydrogen bonds : angle 5.95955 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.195 Fit side-chains REVERT: A 568 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8125 (ppp) outliers start: 17 outliers final: 7 residues processed: 41 average time/residue: 0.4499 time to fit residues: 19.5095 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048874 restraints weight = 15563.649| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.96 r_work: 0.2942 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4401 Z= 0.129 Angle : 0.483 5.677 5957 Z= 0.255 Chirality : 0.040 0.131 650 Planarity : 0.004 0.032 779 Dihedral : 6.148 57.819 602 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.70 % Allowed : 17.65 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.36), residues: 536 helix: 1.40 (0.30), residues: 301 sheet: -0.14 (0.76), residues: 43 loop : 0.39 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 485 TYR 0.007 0.001 TYR A 680 PHE 0.008 0.001 PHE A 636 TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4401) covalent geometry : angle 0.48283 ( 5957) hydrogen bonds : bond 0.03971 ( 218) hydrogen bonds : angle 5.70913 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 28 time to evaluate : 0.145 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 39 average time/residue: 0.4828 time to fit residues: 19.6876 Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.054502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048669 restraints weight = 15554.318| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.95 r_work: 0.2938 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4401 Z= 0.133 Angle : 0.481 6.427 5957 Z= 0.252 Chirality : 0.040 0.130 650 Planarity : 0.003 0.031 779 Dihedral : 6.132 57.574 602 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.14 % Allowed : 17.21 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.36), residues: 536 helix: 1.66 (0.30), residues: 295 sheet: -0.24 (0.75), residues: 43 loop : 0.57 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 593 TYR 0.008 0.001 TYR A 680 PHE 0.008 0.001 PHE A 636 TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4401) covalent geometry : angle 0.48130 ( 5957) hydrogen bonds : bond 0.03945 ( 218) hydrogen bonds : angle 5.60160 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 0.152 Fit side-chains REVERT: A 596 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8949 (mtm) outliers start: 19 outliers final: 11 residues processed: 41 average time/residue: 0.5662 time to fit residues: 24.1383 Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 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 = 0.3243 r_free = 0.3243 target = 0.055069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049201 restraints weight = 15621.087| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.96 r_work: 0.2954 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4401 Z= 0.112 Angle : 0.466 5.781 5957 Z= 0.246 Chirality : 0.040 0.131 650 Planarity : 0.003 0.029 779 Dihedral : 6.108 58.276 602 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.27 % Allowed : 17.65 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.36), residues: 536 helix: 1.74 (0.30), residues: 295 sheet: -0.32 (0.74), residues: 43 loop : 0.55 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 845 TYR 0.006 0.001 TYR A 680 PHE 0.008 0.001 PHE A 636 TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4401) covalent geometry : angle 0.46587 ( 5957) hydrogen bonds : bond 0.03657 ( 218) hydrogen bonds : angle 5.51813 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.110 Fit side-chains REVERT: A 596 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8922 (mtm) outliers start: 15 outliers final: 10 residues processed: 40 average time/residue: 0.4280 time to fit residues: 17.9154 Evaluate side-chains 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.0970 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.053771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047872 restraints weight = 15998.405| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.99 r_work: 0.2922 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4401 Z= 0.161 Angle : 0.501 7.441 5957 Z= 0.263 Chirality : 0.042 0.134 650 Planarity : 0.003 0.030 779 Dihedral : 6.184 55.880 602 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.27 % Allowed : 18.30 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.36), residues: 536 helix: 1.63 (0.30), residues: 301 sheet: -0.25 (0.74), residues: 43 loop : 0.43 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 845 TYR 0.009 0.001 TYR A 776 PHE 0.009 0.001 PHE A 636 TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4401) covalent geometry : angle 0.50128 ( 5957) hydrogen bonds : bond 0.04189 ( 218) hydrogen bonds : angle 5.61244 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.168 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 39 average time/residue: 0.4857 time to fit residues: 19.8796 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.054360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048485 restraints weight = 15767.800| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.97 r_work: 0.2931 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.140 Angle : 0.499 7.145 5957 Z= 0.262 Chirality : 0.041 0.135 650 Planarity : 0.003 0.030 779 Dihedral : 6.096 51.764 602 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.27 % Allowed : 18.30 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.36), residues: 536 helix: 1.64 (0.30), residues: 301 sheet: -0.32 (0.73), residues: 43 loop : 0.41 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 845 TYR 0.008 0.001 TYR A 680 PHE 0.008 0.001 PHE A 636 TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4401) covalent geometry : angle 0.49941 ( 5957) hydrogen bonds : bond 0.03960 ( 218) hydrogen bonds : angle 5.55527 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.101 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 40 average time/residue: 0.4684 time to fit residues: 19.6171 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048711 restraints weight = 15718.374| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.97 r_work: 0.2937 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4401 Z= 0.128 Angle : 0.501 7.450 5957 Z= 0.260 Chirality : 0.040 0.137 650 Planarity : 0.003 0.030 779 Dihedral : 6.040 50.883 602 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.40 % Allowed : 18.74 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.36), residues: 536 helix: 1.66 (0.30), residues: 301 sheet: -0.31 (0.73), residues: 43 loop : 0.43 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 845 TYR 0.007 0.001 TYR A 680 PHE 0.008 0.001 PHE A 636 TRP 0.005 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4401) covalent geometry : angle 0.50059 ( 5957) hydrogen bonds : bond 0.03821 ( 218) hydrogen bonds : angle 5.50208 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.143 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 36 average time/residue: 0.4238 time to fit residues: 16.0402 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.054943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.049063 restraints weight = 15819.689| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.97 r_work: 0.2950 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4401 Z= 0.113 Angle : 0.491 7.745 5957 Z= 0.254 Chirality : 0.040 0.135 650 Planarity : 0.003 0.030 779 Dihedral : 5.981 51.291 602 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 18.52 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.36), residues: 536 helix: 1.71 (0.30), residues: 301 sheet: -0.31 (0.73), residues: 43 loop : 0.43 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 845 TYR 0.007 0.001 TYR A 680 PHE 0.007 0.001 PHE A 879 TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4401) covalent geometry : angle 0.49093 ( 5957) hydrogen bonds : bond 0.03608 ( 218) hydrogen bonds : angle 5.42276 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.183 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 37 average time/residue: 0.4620 time to fit residues: 17.9498 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 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 = 0.3241 r_free = 0.3241 target = 0.054979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049109 restraints weight = 15623.540| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.96 r_work: 0.2953 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4401 Z= 0.113 Angle : 0.494 7.898 5957 Z= 0.254 Chirality : 0.040 0.136 650 Planarity : 0.003 0.029 779 Dihedral : 5.953 51.288 602 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.40 % Allowed : 19.61 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.36), residues: 536 helix: 1.71 (0.30), residues: 301 sheet: -0.27 (0.74), residues: 43 loop : 0.44 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 845 TYR 0.007 0.001 TYR A 680 PHE 0.007 0.001 PHE A 997 TRP 0.005 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4401) covalent geometry : angle 0.49359 ( 5957) hydrogen bonds : bond 0.03638 ( 218) hydrogen bonds : angle 5.42657 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.128 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 35 average time/residue: 0.4410 time to fit residues: 16.1492 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 50 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.0916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN A 768 GLN ** A 829 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 = 0.3310 r_free = 0.3310 target = 0.057395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.051632 restraints weight = 15615.238| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.95 r_work: 0.3035 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4401 Z= 0.086 Angle : 0.475 8.133 5957 Z= 0.241 Chirality : 0.039 0.136 650 Planarity : 0.003 0.029 779 Dihedral : 5.693 51.195 602 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.74 % Allowed : 20.26 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.37), residues: 536 helix: 1.83 (0.31), residues: 301 sheet: -0.16 (0.80), residues: 43 loop : 0.52 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 783 TYR 0.007 0.001 TYR A 830 PHE 0.008 0.001 PHE A 605 TRP 0.006 0.001 TRP A 644 HIS 0.004 0.000 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 4401) covalent geometry : angle 0.47458 ( 5957) hydrogen bonds : bond 0.02805 ( 218) hydrogen bonds : angle 5.18400 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.85 seconds wall clock time: 25 minutes 27.83 seconds (1527.83 seconds total)