Starting phenix.real_space_refine on Fri Aug 22 16:04:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qkk_18464/08_2025/8qkk_18464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qkk_18464/08_2025/8qkk_18464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qkk_18464/08_2025/8qkk_18464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qkk_18464/08_2025/8qkk_18464.map" model { file = "/net/cci-nas-00/data/ceres_data/8qkk_18464/08_2025/8qkk_18464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qkk_18464/08_2025/8qkk_18464.cif" } resolution = 3.23 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= 0.072 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3622 2.51 5 N 922 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5581 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5581 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 36, 'TRANS': 693} Chain breaks: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.21 Number of scatterers: 5581 At special positions: 0 Unit cell: (69.6, 71.775, 105.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1011 8.00 N 922 7.00 C 3622 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: 0.37 Conformation dependent library (CDL) restraints added in 185.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 3 sheets defined 76.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 4.000A pdb=" N TRP A 5 " --> pdb=" O GLY A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 33 through 36 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 64 through 67 removed outlier: 4.189A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.077A pdb=" N ASP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 101 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 159 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 171 through 205 removed outlier: 3.845A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 212 through 234 Processing helix chain 'A' and resid 241 through 272 removed outlier: 4.091A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 285 through 302 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 332 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 343 through 346 removed outlier: 3.748A pdb=" N ASP A 346 " --> pdb=" O PRO A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 350 through 356 removed outlier: 4.159A pdb=" N ILE A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.691A pdb=" N ARG A 367 " --> pdb=" O GLN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 400 through 416 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 470 through 484 removed outlier: 3.725A pdb=" N VAL A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.857A pdb=" N LYS A 496 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A 497 " --> pdb=" O PRO A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 497' Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.572A pdb=" N ASP A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 584 Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 587 through 612 Processing helix chain 'A' and resid 629 through 660 removed outlier: 3.829A pdb=" N GLY A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 695 removed outlier: 4.910A pdb=" N ARG A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 722 removed outlier: 4.639A pdb=" N ILE A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 removed outlier: 3.605A pdb=" N ALA A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 500 404 hydrogen bonds defined for protein. 1158 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: 0.87 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1799 1.34 - 1.46: 1211 1.46 - 1.58: 2636 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5696 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.44e+00 bond pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.49e-01 bond pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.16e-01 bond pdb=" CA ILE A 194 " pdb=" CB ILE A 194 " ideal model delta sigma weight residual 1.539 1.536 0.003 5.40e-03 3.43e+04 3.66e-01 bond pdb=" CA TRP A 362 " pdb=" CB TRP A 362 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.69e-02 3.50e+03 3.62e-01 ... (remaining 5691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 7511 1.18 - 2.37: 190 2.37 - 3.55: 36 3.55 - 4.73: 15 4.73 - 5.92: 2 Bond angle restraints: 7754 Sorted by residual: angle pdb=" N VAL A 586 " pdb=" CA VAL A 586 " pdb=" C VAL A 586 " ideal model delta sigma weight residual 112.96 110.87 2.09 1.00e+00 1.00e+00 4.37e+00 angle pdb=" C THR A 133 " pdb=" N PHE A 134 " pdb=" CA PHE A 134 " ideal model delta sigma weight residual 121.75 118.99 2.76 1.73e+00 3.34e-01 2.55e+00 angle pdb=" C ASN A 361 " pdb=" N TRP A 362 " pdb=" CA TRP A 362 " ideal model delta sigma weight residual 121.54 124.52 -2.98 1.91e+00 2.74e-01 2.43e+00 angle pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " pdb=" CD LYS A 187 " ideal model delta sigma weight residual 111.30 114.68 -3.38 2.30e+00 1.89e-01 2.16e+00 angle pdb=" C VAL A 302 " pdb=" N PRO A 303 " pdb=" CD PRO A 303 " ideal model delta sigma weight residual 125.00 130.92 -5.92 4.10e+00 5.95e-02 2.08e+00 ... (remaining 7749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3063 17.18 - 34.36: 260 34.36 - 51.55: 41 51.55 - 68.73: 13 68.73 - 85.91: 11 Dihedral angle restraints: 3388 sinusoidal: 1309 harmonic: 2079 Sorted by residual: dihedral pdb=" CA THR A 717 " pdb=" C THR A 717 " pdb=" N ILE A 718 " pdb=" CA ILE A 718 " ideal model delta harmonic sigma weight residual 180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 190 " pdb=" CG GLU A 190 " pdb=" CD GLU A 190 " pdb=" OE1 GLU A 190 " ideal model delta sinusoidal sigma weight residual 0.00 -85.91 85.91 1 3.00e+01 1.11e-03 9.91e+00 dihedral pdb=" CB MET A 701 " pdb=" CG MET A 701 " pdb=" SD MET A 701 " pdb=" CE MET A 701 " ideal model delta sinusoidal sigma weight residual -180.00 -122.31 -57.69 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 546 0.025 - 0.049: 223 0.049 - 0.074: 94 0.074 - 0.099: 39 0.099 - 0.123: 24 Chirality restraints: 926 Sorted by residual: chirality pdb=" CA VAL A 460 " pdb=" N VAL A 460 " pdb=" C VAL A 460 " pdb=" CB VAL A 460 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA VAL A 484 " pdb=" N VAL A 484 " pdb=" C VAL A 484 " pdb=" CB VAL A 484 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 923 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 221 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C ALA A 221 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA A 221 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 222 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 246 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C VAL A 246 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 246 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 247 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 223 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA A 223 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 223 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 224 " -0.008 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 93 2.69 - 3.24: 6018 3.24 - 3.79: 9052 3.79 - 4.35: 11642 4.35 - 4.90: 20149 Nonbonded interactions: 46954 Sorted by model distance: nonbonded pdb=" OG1 THR A 127 " pdb=" OD1 ASP A 129 " model vdw 2.132 3.040 nonbonded pdb=" NH1 ARG A 167 " pdb=" OE1 GLN A 444 " model vdw 2.290 3.120 nonbonded pdb=" OG SER A 293 " pdb=" OD1 ASP A 645 " model vdw 2.296 3.040 nonbonded pdb=" O GLN A 473 " pdb=" OD1 ASP A 476 " model vdw 2.309 3.040 nonbonded pdb=" NH2 ARG A 288 " pdb=" O ALA A 582 " model vdw 2.328 3.120 ... (remaining 46949 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: 2.020 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: 5.840 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5696 Z= 0.106 Angle : 0.493 5.917 7754 Z= 0.257 Chirality : 0.038 0.123 926 Planarity : 0.003 0.027 978 Dihedral : 14.137 85.910 2050 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.34), residues: 726 helix: 1.88 (0.25), residues: 490 sheet: 1.27 (0.85), residues: 41 loop : 0.79 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.009 0.001 TYR A 151 PHE 0.014 0.001 PHE A 134 TRP 0.005 0.001 TRP A 736 HIS 0.002 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5696) covalent geometry : angle 0.49338 ( 7754) hydrogen bonds : bond 0.12242 ( 404) hydrogen bonds : angle 5.66002 ( 1158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 496 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7894 (ptpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0695 time to fit residues: 8.4477 Evaluate side-chains 79 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.216529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188824 restraints weight = 5746.845| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.53 r_work: 0.3878 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5696 Z= 0.148 Angle : 0.586 6.520 7754 Z= 0.295 Chirality : 0.042 0.175 926 Planarity : 0.004 0.033 978 Dihedral : 3.930 16.362 774 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.01 % Allowed : 8.07 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.33), residues: 726 helix: 1.76 (0.24), residues: 500 sheet: 1.17 (0.87), residues: 41 loop : 0.34 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 281 TYR 0.009 0.001 TYR A 151 PHE 0.018 0.001 PHE A 134 TRP 0.013 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5696) covalent geometry : angle 0.58568 ( 7754) hydrogen bonds : bond 0.03634 ( 404) hydrogen bonds : angle 4.57948 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7800 (mtm-85) REVERT: A 567 MET cc_start: 0.8266 (tmm) cc_final: 0.7901 (ttt) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.0640 time to fit residues: 7.5480 Evaluate side-chains 82 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.213955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.184679 restraints weight = 5677.578| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.53 r_work: 0.3843 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5696 Z= 0.158 Angle : 0.578 7.420 7754 Z= 0.290 Chirality : 0.042 0.159 926 Planarity : 0.004 0.031 978 Dihedral : 3.948 16.286 774 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.68 % Allowed : 9.08 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.32), residues: 726 helix: 1.57 (0.23), residues: 500 sheet: 0.91 (0.87), residues: 41 loop : 0.27 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 281 TYR 0.010 0.001 TYR A 151 PHE 0.017 0.001 PHE A 311 TRP 0.012 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5696) covalent geometry : angle 0.57846 ( 7754) hydrogen bonds : bond 0.03480 ( 404) hydrogen bonds : angle 4.54980 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7745 (mtm-85) REVERT: A 496 LYS cc_start: 0.7987 (ptpp) cc_final: 0.7704 (ptpp) REVERT: A 567 MET cc_start: 0.8308 (tmm) cc_final: 0.7926 (ttt) REVERT: A 658 ARG cc_start: 0.7645 (tpp-160) cc_final: 0.7402 (tpt90) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.0809 time to fit residues: 9.6505 Evaluate side-chains 82 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 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 = 0.4302 r_free = 0.4302 target = 0.212987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181749 restraints weight = 5716.448| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.63 r_work: 0.3813 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5696 Z= 0.144 Angle : 0.562 6.240 7754 Z= 0.282 Chirality : 0.041 0.150 926 Planarity : 0.004 0.033 978 Dihedral : 3.994 16.536 774 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.01 % Allowed : 11.60 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.32), residues: 726 helix: 1.58 (0.24), residues: 500 sheet: 0.79 (0.87), residues: 41 loop : 0.22 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.009 0.001 TYR A 151 PHE 0.023 0.001 PHE A 134 TRP 0.012 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5696) covalent geometry : angle 0.56151 ( 7754) hydrogen bonds : bond 0.03316 ( 404) hydrogen bonds : angle 4.49783 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7632 (mtm-85) REVERT: A 496 LYS cc_start: 0.7946 (ptpp) cc_final: 0.7652 (ptpp) REVERT: A 567 MET cc_start: 0.8220 (tmm) cc_final: 0.7773 (ttt) REVERT: A 658 ARG cc_start: 0.7768 (tpp-160) cc_final: 0.7526 (tpt90) outliers start: 6 outliers final: 4 residues processed: 94 average time/residue: 0.0778 time to fit residues: 9.3320 Evaluate side-chains 83 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.211029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.178900 restraints weight = 5846.136| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.70 r_work: 0.3771 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5696 Z= 0.156 Angle : 0.596 10.307 7754 Z= 0.297 Chirality : 0.044 0.326 926 Planarity : 0.004 0.032 978 Dihedral : 4.046 16.709 774 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.51 % Allowed : 12.27 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.32), residues: 726 helix: 1.52 (0.24), residues: 500 sheet: 0.71 (0.87), residues: 41 loop : 0.16 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.011 0.001 TYR A 646 PHE 0.018 0.001 PHE A 134 TRP 0.010 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5696) covalent geometry : angle 0.59595 ( 7754) hydrogen bonds : bond 0.03381 ( 404) hydrogen bonds : angle 4.53923 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7571 (mtm-85) REVERT: A 496 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7594 (ptpp) REVERT: A 567 MET cc_start: 0.8244 (tmm) cc_final: 0.7798 (ttt) REVERT: A 658 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7524 (tpt90) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.0864 time to fit residues: 10.0390 Evaluate side-chains 86 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.211678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179192 restraints weight = 5790.003| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.72 r_work: 0.3772 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5696 Z= 0.146 Angle : 0.590 11.353 7754 Z= 0.291 Chirality : 0.042 0.266 926 Planarity : 0.004 0.032 978 Dihedral : 4.039 16.849 774 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.85 % Allowed : 13.11 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.32), residues: 726 helix: 1.53 (0.24), residues: 500 sheet: 0.53 (0.88), residues: 42 loop : 0.18 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.012 0.001 TYR A 646 PHE 0.019 0.001 PHE A 134 TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5696) covalent geometry : angle 0.58966 ( 7754) hydrogen bonds : bond 0.03316 ( 404) hydrogen bonds : angle 4.53227 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7540 (mtm-85) REVERT: A 496 LYS cc_start: 0.7973 (ptpp) cc_final: 0.7655 (ptpp) REVERT: A 567 MET cc_start: 0.8243 (tmm) cc_final: 0.7782 (ttt) REVERT: A 625 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.5370 (pm20) REVERT: A 658 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7519 (tpt90) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 0.0687 time to fit residues: 8.6842 Evaluate side-chains 90 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.210203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.178607 restraints weight = 5884.050| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.67 r_work: 0.3772 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5696 Z= 0.169 Angle : 0.630 11.616 7754 Z= 0.309 Chirality : 0.045 0.395 926 Planarity : 0.004 0.032 978 Dihedral : 4.132 16.826 774 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.85 % Allowed : 14.12 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.32), residues: 726 helix: 1.40 (0.23), residues: 499 sheet: 0.63 (0.87), residues: 41 loop : 0.11 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 266 TYR 0.013 0.001 TYR A 646 PHE 0.020 0.001 PHE A 134 TRP 0.009 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 5696) covalent geometry : angle 0.62953 ( 7754) hydrogen bonds : bond 0.03423 ( 404) hydrogen bonds : angle 4.60351 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7558 (mtm-85) REVERT: A 496 LYS cc_start: 0.7996 (ptpp) cc_final: 0.7680 (ptpp) REVERT: A 567 MET cc_start: 0.8228 (tmm) cc_final: 0.7800 (ttt) REVERT: A 658 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7552 (tpt90) outliers start: 11 outliers final: 9 residues processed: 96 average time/residue: 0.0752 time to fit residues: 9.4312 Evaluate side-chains 96 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 0.0050 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4332 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.212837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.181537 restraints weight = 5700.014| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.65 r_work: 0.3800 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5696 Z= 0.125 Angle : 0.601 11.909 7754 Z= 0.291 Chirality : 0.043 0.345 926 Planarity : 0.004 0.032 978 Dihedral : 4.058 17.797 774 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.02 % Allowed : 14.29 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.32), residues: 726 helix: 1.63 (0.24), residues: 493 sheet: 0.69 (0.88), residues: 41 loop : 0.10 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.011 0.001 TYR A 646 PHE 0.019 0.001 PHE A 134 TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5696) covalent geometry : angle 0.60060 ( 7754) hydrogen bonds : bond 0.03220 ( 404) hydrogen bonds : angle 4.53430 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.127 Fit side-chains REVERT: A 167 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7510 (mtm-85) REVERT: A 496 LYS cc_start: 0.7996 (ptpp) cc_final: 0.7678 (ptpp) REVERT: A 567 MET cc_start: 0.8224 (tmm) cc_final: 0.7758 (ttt) REVERT: A 625 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.5623 (pm20) REVERT: A 658 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7526 (tpt90) REVERT: A 700 MET cc_start: 0.8227 (mtm) cc_final: 0.7981 (mtm) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.0704 time to fit residues: 8.4147 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.213335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.181918 restraints weight = 5752.356| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.66 r_work: 0.3812 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.003 0.030 5696 Z= 0.130 Angle : 0.609 11.908 7754 Z= 0.294 Chirality : 0.043 0.333 926 Planarity : 0.004 0.031 978 Dihedral : 4.058 17.392 774 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.02 % Allowed : 14.29 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.32), residues: 726 helix: 1.65 (0.24), residues: 493 sheet: 0.69 (0.88), residues: 41 loop : 0.18 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.013 0.001 TYR A 646 PHE 0.018 0.001 PHE A 134 TRP 0.010 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5696) covalent geometry : angle 0.60923 ( 7754) hydrogen bonds : bond 0.03224 ( 404) hydrogen bonds : angle 4.50936 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.268 Fit side-chains REVERT: A 167 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7480 (mtm-85) REVERT: A 567 MET cc_start: 0.8219 (tmm) cc_final: 0.7603 (ttt) REVERT: A 658 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7460 (tpt90) REVERT: A 700 MET cc_start: 0.8207 (mtm) cc_final: 0.7928 (mtm) outliers start: 12 outliers final: 11 residues processed: 91 average time/residue: 0.0682 time to fit residues: 8.3202 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.211787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.179725 restraints weight = 5810.098| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.70 r_work: 0.3789 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5696 Z= 0.149 Angle : 0.620 11.401 7754 Z= 0.303 Chirality : 0.043 0.331 926 Planarity : 0.004 0.031 978 Dihedral : 4.075 17.403 774 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 14.45 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.32), residues: 726 helix: 1.51 (0.24), residues: 499 sheet: 0.63 (0.88), residues: 41 loop : 0.16 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 266 TYR 0.016 0.001 TYR A 646 PHE 0.018 0.001 PHE A 134 TRP 0.010 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5696) covalent geometry : angle 0.62023 ( 7754) hydrogen bonds : bond 0.03325 ( 404) hydrogen bonds : angle 4.55364 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.197 Fit side-chains REVERT: A 167 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7420 (mtm-85) REVERT: A 567 MET cc_start: 0.8235 (tmm) cc_final: 0.7783 (ttt) REVERT: A 658 ARG cc_start: 0.7773 (tpp-160) cc_final: 0.7450 (tpt90) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.0848 time to fit residues: 9.8545 Evaluate side-chains 90 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 0.0070 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.0670 chunk 42 optimal weight: 0.0570 chunk 72 optimal weight: 0.0270 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.1512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.215786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184985 restraints weight = 5723.873| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.63 r_work: 0.3835 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5696 Z= 0.115 Angle : 0.598 11.262 7754 Z= 0.290 Chirality : 0.042 0.322 926 Planarity : 0.004 0.052 978 Dihedral : 4.006 17.942 774 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 14.45 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.32), residues: 726 helix: 1.74 (0.24), residues: 493 sheet: 0.75 (0.89), residues: 41 loop : 0.21 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.012 0.001 TYR A 646 PHE 0.017 0.001 PHE A 134 TRP 0.013 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5696) covalent geometry : angle 0.59777 ( 7754) hydrogen bonds : bond 0.03164 ( 404) hydrogen bonds : angle 4.46944 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.99 seconds wall clock time: 22 minutes 30.26 seconds (1350.26 seconds total)