Starting phenix.real_space_refine on Thu Jun 5 07:02:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qkk_18464/06_2025/8qkk_18464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qkk_18464/06_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_18464/06_2025/8qkk_18464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qkk_18464/06_2025/8qkk_18464.map" model { file = "/net/cci-nas-00/data/ceres_data/8qkk_18464/06_2025/8qkk_18464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qkk_18464/06_2025/8qkk_18464.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.51, per 1000 atoms: 0.81 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: 1.50 Conformation dependent library (CDL) restraints added in 825.6 milliseconds 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: 0.56 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: 1.99 Time building geometry restraints manager: 1.72 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.140 Process input model: 18.460 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- 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 : 9.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP A 736 HIS 0.002 0.001 HIS A 68 PHE 0.014 0.001 PHE A 134 TYR 0.009 0.001 TYR A 151 ARG 0.002 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.12242 ( 404) hydrogen bonds : angle 5.66002 ( 1158) covalent geometry : bond 0.00220 ( 5696) covalent geometry : angle 0.49338 ( 7754) *********************** 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 : 0.549 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: 0.1742 time to fit residues: 21.2310 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 : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.213713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.187804 restraints weight = 5671.326| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.47 r_work: 0.3857 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5696 Z= 0.173 Angle : 0.616 6.878 7754 Z= 0.311 Chirality : 0.044 0.179 926 Planarity : 0.004 0.035 978 Dihedral : 4.034 15.985 774 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 8.40 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.32), residues: 726 helix: 1.63 (0.24), residues: 500 sheet: 1.09 (0.87), residues: 41 loop : 0.30 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 PHE 0.018 0.002 PHE A 311 TYR 0.010 0.001 TYR A 151 ARG 0.006 0.001 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 404) hydrogen bonds : angle 4.64192 ( 1158) covalent geometry : bond 0.00428 ( 5696) covalent geometry : angle 0.61565 ( 7754) *********************** 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 : 0.590 Fit side-chains revert: symmetry clash REVERT: A 61 TYR cc_start: 0.7641 (m-80) cc_final: 0.6983 (m-80) REVERT: A 167 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7734 (mtm-85) REVERT: A 567 MET cc_start: 0.8258 (tmm) cc_final: 0.7924 (ttt) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.1772 time to fit residues: 20.9378 Evaluate side-chains 82 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 461 MET 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 68 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.214092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.188170 restraints weight = 5680.685| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.41 r_work: 0.3858 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5696 Z= 0.145 Angle : 0.569 6.666 7754 Z= 0.285 Chirality : 0.042 0.156 926 Planarity : 0.004 0.032 978 Dihedral : 3.985 16.539 774 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.02 % Allowed : 9.75 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.32), residues: 726 helix: 1.56 (0.23), residues: 500 sheet: 0.82 (0.87), residues: 41 loop : 0.22 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 736 HIS 0.006 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.009 0.001 TYR A 151 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 404) hydrogen bonds : angle 4.54655 ( 1158) covalent geometry : bond 0.00354 ( 5696) covalent geometry : angle 0.56870 ( 7754) *********************** 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 96 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7762 (mtm-85) REVERT: A 496 LYS cc_start: 0.7982 (ptpp) cc_final: 0.7703 (ptpp) REVERT: A 567 MET cc_start: 0.8252 (tmm) cc_final: 0.7863 (ttt) outliers start: 12 outliers final: 5 residues processed: 93 average time/residue: 0.1894 time to fit residues: 22.7130 Evaluate side-chains 84 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.212372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180400 restraints weight = 5835.523| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.66 r_work: 0.3799 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5696 Z= 0.145 Angle : 0.576 6.793 7754 Z= 0.285 Chirality : 0.042 0.321 926 Planarity : 0.004 0.032 978 Dihedral : 4.021 16.628 774 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.34 % Allowed : 10.76 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.32), residues: 726 helix: 1.55 (0.23), residues: 500 sheet: 0.73 (0.88), residues: 41 loop : 0.20 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.010 0.001 TYR A 646 ARG 0.004 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 404) hydrogen bonds : angle 4.51498 ( 1158) covalent geometry : bond 0.00355 ( 5696) covalent geometry : angle 0.57636 ( 7754) *********************** 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 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7649 (mtm-85) REVERT: A 496 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7639 (ptpp) REVERT: A 567 MET cc_start: 0.8240 (tmm) cc_final: 0.7783 (ttt) REVERT: A 700 MET cc_start: 0.8223 (mtm) cc_final: 0.7944 (mtm) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1993 time to fit residues: 24.0744 Evaluate side-chains 86 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 5 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 chunk 3 optimal weight: 0.0470 chunk 61 optimal weight: 0.0010 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.0170 chunk 19 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.2122 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.216841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.185937 restraints weight = 5680.874| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.66 r_work: 0.3841 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5696 Z= 0.112 Angle : 0.546 7.443 7754 Z= 0.271 Chirality : 0.040 0.208 926 Planarity : 0.004 0.032 978 Dihedral : 3.883 17.338 774 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.34 % Allowed : 12.77 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.32), residues: 726 helix: 1.86 (0.24), residues: 495 sheet: 0.95 (0.89), residues: 41 loop : 0.26 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.016 0.001 PHE A 311 TYR 0.009 0.001 TYR A 151 ARG 0.004 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 404) hydrogen bonds : angle 4.38252 ( 1158) covalent geometry : bond 0.00243 ( 5696) covalent geometry : angle 0.54585 ( 7754) *********************** 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 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.622 Fit side-chains REVERT: A 167 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7638 (mtm-85) REVERT: A 496 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7618 (ptpp) REVERT: A 712 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7650 (mm) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 0.1954 time to fit residues: 22.9582 Evaluate side-chains 86 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 461 MET 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 Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 48 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.211655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.179993 restraints weight = 5744.433| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.63 r_work: 0.3801 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1789 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= 0.165 Angle : 0.615 10.872 7754 Z= 0.301 Chirality : 0.044 0.378 926 Planarity : 0.004 0.031 978 Dihedral : 3.993 16.642 774 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.02 % Allowed : 12.10 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.32), residues: 726 helix: 1.54 (0.24), residues: 499 sheet: 0.81 (0.89), residues: 41 loop : 0.18 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.018 0.001 PHE A 311 TYR 0.012 0.001 TYR A 646 ARG 0.003 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 404) hydrogen bonds : angle 4.48743 ( 1158) covalent geometry : bond 0.00409 ( 5696) covalent geometry : angle 0.61536 ( 7754) *********************** 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 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.659 Fit side-chains REVERT: A 167 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7686 (mtm-85) REVERT: A 444 GLN cc_start: 0.7676 (tt0) cc_final: 0.7439 (tt0) REVERT: A 567 MET cc_start: 0.8314 (tmm) cc_final: 0.7697 (ttt) REVERT: A 625 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.5222 (pm20) REVERT: A 658 ARG cc_start: 0.7692 (tpp-160) cc_final: 0.7336 (tpt90) REVERT: A 700 MET cc_start: 0.8323 (mtm) cc_final: 0.8047 (mtm) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.2081 time to fit residues: 25.1227 Evaluate side-chains 89 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.211918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180239 restraints weight = 5760.403| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.68 r_work: 0.3806 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5696 Z= 0.145 Angle : 0.609 14.263 7754 Z= 0.295 Chirality : 0.043 0.342 926 Planarity : 0.004 0.032 978 Dihedral : 4.020 17.137 774 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.85 % Allowed : 13.28 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.32), residues: 726 helix: 1.52 (0.24), residues: 499 sheet: 0.74 (0.89), residues: 41 loop : 0.17 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.012 0.001 TYR A 646 ARG 0.003 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 404) hydrogen bonds : angle 4.49324 ( 1158) covalent geometry : bond 0.00353 ( 5696) covalent geometry : angle 0.60865 ( 7754) *********************** 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 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.583 Fit side-chains REVERT: A 167 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7567 (mtm-85) REVERT: A 567 MET cc_start: 0.8320 (tmm) cc_final: 0.7704 (ttt) REVERT: A 700 MET cc_start: 0.8316 (mtm) cc_final: 0.8014 (mtm) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.1834 time to fit residues: 22.0466 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 : 0.532 ------------------------------------------------------------------------------- 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 461 MET 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 60 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.214096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182909 restraints weight = 5696.005| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.65 r_work: 0.3809 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5696 Z= 0.122 Angle : 0.602 15.123 7754 Z= 0.287 Chirality : 0.042 0.297 926 Planarity : 0.004 0.031 978 Dihedral : 3.975 17.464 774 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.18 % Allowed : 13.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.32), residues: 726 helix: 1.70 (0.24), residues: 493 sheet: 0.82 (0.90), residues: 41 loop : 0.19 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.016 0.001 PHE A 311 TYR 0.012 0.001 TYR A 646 ARG 0.004 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 404) hydrogen bonds : angle 4.44135 ( 1158) covalent geometry : bond 0.00278 ( 5696) covalent geometry : angle 0.60235 ( 7754) *********************** 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 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.603 Fit side-chains REVERT: A 167 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7645 (mtm-85) REVERT: A 625 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.5392 (pm20) REVERT: A 700 MET cc_start: 0.8204 (mtm) cc_final: 0.7947 (mtm) outliers start: 13 outliers final: 10 residues processed: 89 average time/residue: 0.2084 time to fit residues: 24.3812 Evaluate side-chains 89 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 636 ILE 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 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 34 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.215329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.184246 restraints weight = 5691.767| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.65 r_work: 0.3825 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1988 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= 0.119 Angle : 0.596 14.458 7754 Z= 0.285 Chirality : 0.041 0.267 926 Planarity : 0.004 0.032 978 Dihedral : 3.933 17.546 774 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.18 % Allowed : 13.61 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.32), residues: 726 helix: 1.75 (0.24), residues: 492 sheet: 0.86 (0.90), residues: 41 loop : 0.22 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.016 0.001 PHE A 311 TYR 0.015 0.001 TYR A 646 ARG 0.003 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 404) hydrogen bonds : angle 4.42048 ( 1158) covalent geometry : bond 0.00271 ( 5696) covalent geometry : angle 0.59641 ( 7754) *********************** 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: 13 poor density : 81 time to evaluate : 0.596 Fit side-chains REVERT: A 167 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7755 (mtm-85) outliers start: 13 outliers final: 11 residues processed: 89 average time/residue: 0.1724 time to fit residues: 20.5951 Evaluate side-chains 90 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 636 ILE 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 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.214900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183742 restraints weight = 5773.258| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.66 r_work: 0.3824 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.003 0.029 5696 Z= 0.125 Angle : 0.613 14.794 7754 Z= 0.290 Chirality : 0.042 0.230 926 Planarity : 0.004 0.031 978 Dihedral : 3.913 17.428 774 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.35 % Allowed : 13.78 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.32), residues: 726 helix: 1.73 (0.24), residues: 493 sheet: 0.88 (0.90), residues: 41 loop : 0.25 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.005 0.001 HIS A 37 PHE 0.016 0.001 PHE A 311 TYR 0.014 0.001 TYR A 646 ARG 0.003 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 404) hydrogen bonds : angle 4.42093 ( 1158) covalent geometry : bond 0.00292 ( 5696) covalent geometry : angle 0.61267 ( 7754) ********************** 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 96 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.587 Fit side-chains REVERT: A 61 TYR cc_start: 0.7184 (m-80) cc_final: 0.4589 (m-10) REVERT: A 167 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7637 (mtm-85) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.1846 time to fit residues: 21.9460 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 37 HIS 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 636 ILE 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 58 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.214727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183559 restraints weight = 5750.315| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.64 r_work: 0.3820 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 5696 Z= 0.389 Angle : 1.245 59.196 7754 Z= 0.805 Chirality : 0.051 0.802 926 Planarity : 0.008 0.219 978 Dihedral : 3.922 17.418 774 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.35 % Allowed : 14.29 % Favored : 83.36 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.32), residues: 726 helix: 1.72 (0.24), residues: 493 sheet: 0.89 (0.90), residues: 41 loop : 0.23 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 736 HIS 0.400 0.024 HIS A 37 PHE 0.016 0.001 PHE A 311 TYR 0.013 0.001 TYR A 646 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 404) hydrogen bonds : angle 4.42032 ( 1158) covalent geometry : bond 0.00602 ( 5696) covalent geometry : angle 1.24541 ( 7754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3153.50 seconds wall clock time: 55 minutes 25.48 seconds (3325.48 seconds total)