Starting phenix.real_space_refine on Fri Apr 5 21:10:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qkk_18464/04_2024/8qkk_18464.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qkk_18464/04_2024/8qkk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qkk_18464/04_2024/8qkk_18464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qkk_18464/04_2024/8qkk_18464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qkk_18464/04_2024/8qkk_18464.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qkk_18464/04_2024/8qkk_18464.pdb" } 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 Residue "A GLU 271": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.50, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.58 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: 1.78 Time building geometry restraints manager: 2.50 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: 98.44 - 105.56: 148 105.56 - 112.67: 3122 112.67 - 119.79: 1806 119.79 - 126.90: 2596 126.90 - 134.02: 82 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 2.440 nonbonded pdb=" NH1 ARG A 167 " pdb=" OE1 GLN A 444 " model vdw 2.290 2.520 nonbonded pdb=" OG SER A 293 " pdb=" OD1 ASP A 645 " model vdw 2.296 2.440 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 2.520 ... (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: 1.370 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: 7.070 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- 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= 0.147 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.602 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: 0.1880 time to fit residues: 23.0181 Evaluate side-chains 79 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 3.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5696 Z= 0.356 Angle : 0.639 7.409 7754 Z= 0.322 Chirality : 0.044 0.176 926 Planarity : 0.004 0.032 978 Dihedral : 4.147 15.927 774 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.51 % Allowed : 8.74 % Favored : 89.75 % 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: 1.51 (0.24), residues: 500 sheet: 1.05 (0.85), residues: 41 loop : 0.27 (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 0.020 0.002 PHE A 311 TYR 0.010 0.001 TYR A 151 ARG 0.006 0.001 ARG A 281 *********************** 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 92 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 567 MET cc_start: 0.8301 (tmm) cc_final: 0.7926 (ttt) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.1841 time to fit residues: 21.3843 Evaluate side-chains 84 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 680 THR 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 36 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5696 Z= 0.223 Angle : 0.550 6.374 7754 Z= 0.275 Chirality : 0.041 0.157 926 Planarity : 0.004 0.032 978 Dihedral : 4.004 16.676 774 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.68 % Allowed : 9.92 % Favored : 88.40 % 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: 1.81 (0.32), residues: 726 helix: 1.66 (0.24), residues: 494 sheet: 0.87 (0.88), residues: 41 loop : 0.22 (0.48), residues: 191 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 0.017 0.001 PHE A 311 TYR 0.010 0.001 TYR A 151 ARG 0.006 0.000 ARG A 281 *********************** 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 94 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 567 MET cc_start: 0.8315 (tmm) cc_final: 0.7856 (ttt) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.1817 time to fit residues: 22.2520 Evaluate side-chains 81 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 465 ASP Chi-restraints excluded: chain A residue 625 GLN 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 65 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5696 Z= 0.198 Angle : 0.554 6.672 7754 Z= 0.273 Chirality : 0.041 0.303 926 Planarity : 0.004 0.036 978 Dihedral : 3.994 17.010 774 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.85 % Allowed : 10.59 % Favored : 87.56 % 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: 1.79 (0.24), residues: 494 sheet: 0.72 (0.89), residues: 41 loop : 0.15 (0.47), residues: 191 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 0.017 0.001 PHE A 311 TYR 0.010 0.001 TYR A 151 ARG 0.004 0.000 ARG A 281 *********************** 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 96 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 567 MET cc_start: 0.8336 (tmm) cc_final: 0.7830 (ttt) REVERT: A 631 MET cc_start: 0.7977 (mmm) cc_final: 0.7754 (tpp) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.1677 time to fit residues: 20.8335 Evaluate side-chains 86 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 680 THR 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 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.0040 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5696 Z= 0.214 Angle : 0.550 6.187 7754 Z= 0.274 Chirality : 0.041 0.229 926 Planarity : 0.004 0.032 978 Dihedral : 3.989 16.963 774 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.68 % Allowed : 11.43 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.32), residues: 726 helix: 1.75 (0.24), residues: 494 sheet: 0.80 (0.89), residues: 41 loop : 0.12 (0.46), residues: 191 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 0.017 0.001 PHE A 311 TYR 0.010 0.001 TYR A 646 ARG 0.004 0.000 ARG A 266 *********************** 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 fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.582 Fit side-chains REVERT: A 567 MET cc_start: 0.8335 (tmm) cc_final: 0.7824 (ttt) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.1876 time to fit residues: 21.4299 Evaluate side-chains 84 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 680 THR 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 63 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5696 Z= 0.216 Angle : 0.566 9.725 7754 Z= 0.278 Chirality : 0.042 0.384 926 Planarity : 0.004 0.032 978 Dihedral : 3.971 17.012 774 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.18 % Allowed : 12.27 % Favored : 85.55 % 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: 1.79 (0.32), residues: 726 helix: 1.67 (0.24), residues: 500 sheet: 0.83 (0.89), residues: 41 loop : 0.08 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 736 HIS 0.004 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.011 0.001 TYR A 646 ARG 0.003 0.000 ARG A 281 *********************** 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 94 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.615 Fit side-chains REVERT: A 567 MET cc_start: 0.8344 (tmm) cc_final: 0.7832 (ttt) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.1738 time to fit residues: 21.1840 Evaluate side-chains 89 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 680 THR 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 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5696 Z= 0.218 Angle : 0.570 10.434 7754 Z= 0.280 Chirality : 0.042 0.342 926 Planarity : 0.004 0.032 978 Dihedral : 3.995 17.185 774 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.18 % Allowed : 12.94 % 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: 1.83 (0.32), residues: 726 helix: 1.72 (0.24), residues: 493 sheet: 0.78 (0.89), residues: 41 loop : 0.12 (0.46), residues: 192 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 0.011 0.001 TYR A 646 ARG 0.003 0.000 ARG A 281 *********************** 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 91 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.610 Fit side-chains REVERT: A 567 MET cc_start: 0.8354 (tmm) cc_final: 0.7837 (ttt) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.1663 time to fit residues: 19.5822 Evaluate side-chains 85 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 461 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 680 THR 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 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 0.0870 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5696 Z= 0.195 Angle : 0.594 14.730 7754 Z= 0.283 Chirality : 0.042 0.317 926 Planarity : 0.004 0.032 978 Dihedral : 3.991 17.591 774 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 (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: 1.81 (0.32), residues: 726 helix: 1.69 (0.24), residues: 499 sheet: 0.78 (0.89), residues: 41 loop : 0.09 (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 281 *********************** 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 fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.627 Fit side-chains REVERT: A 567 MET cc_start: 0.8359 (tmm) cc_final: 0.7828 (ttt) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.1656 time to fit residues: 19.9947 Evaluate side-chains 92 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 461 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 470 THR 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 680 THR 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 65 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1938 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= 0.298 Angle : 0.648 15.336 7754 Z= 0.312 Chirality : 0.044 0.313 926 Planarity : 0.004 0.031 978 Dihedral : 4.094 18.154 774 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.02 % Allowed : 14.62 % Favored : 83.36 % 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: 1.59 (0.32), residues: 726 helix: 1.50 (0.23), residues: 499 sheet: 0.61 (0.88), residues: 41 loop : 0.11 (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 0.017 0.001 TYR A 646 ARG 0.004 0.000 ARG A 367 *********************** 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 fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.546 Fit side-chains REVERT: A 567 MET cc_start: 0.8347 (tmm) cc_final: 0.7870 (ttt) outliers start: 12 outliers final: 11 residues processed: 90 average time/residue: 0.1640 time to fit residues: 19.9105 Evaluate side-chains 91 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 465 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5696 Z= 0.240 Angle : 0.624 15.095 7754 Z= 0.299 Chirality : 0.043 0.295 926 Planarity : 0.004 0.032 978 Dihedral : 4.087 17.574 774 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 15.29 % Favored : 82.86 % 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: 1.59 (0.24), residues: 493 sheet: 0.58 (0.87), residues: 41 loop : 0.13 (0.46), residues: 192 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 0.014 0.001 TYR A 646 ARG 0.002 0.000 ARG A 281 ********************** 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 91 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.608 Fit side-chains REVERT: A 567 MET cc_start: 0.8337 (tmm) cc_final: 0.7840 (ttt) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.1603 time to fit residues: 19.2261 Evaluate side-chains 91 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 465 ASP Chi-restraints excluded: chain A residue 470 THR 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 680 THR 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 53 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.211365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.179725 restraints weight = 5652.404| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.65 r_work: 0.3783 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 5696 Z= 0.307 Angle : 1.139 59.198 7754 Z= 0.641 Chirality : 0.045 0.501 926 Planarity : 0.004 0.032 978 Dihedral : 4.085 17.592 774 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.02 % Allowed : 14.96 % Favored : 83.03 % Cbeta Deviations : 0.15 % 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: 1.66 (0.32), residues: 726 helix: 1.59 (0.24), residues: 493 sheet: 0.58 (0.87), residues: 41 loop : 0.10 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 736 HIS 0.004 0.001 HIS A 37 PHE 0.017 0.001 PHE A 311 TYR 0.013 0.001 TYR A 646 ARG 0.005 0.000 ARG A 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1480.03 seconds wall clock time: 27 minutes 28.29 seconds (1648.29 seconds total)