Starting phenix.real_space_refine on Fri Feb 14 08:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8a_22724/02_2025/7k8a_22724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8a_22724/02_2025/7k8a_22724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k8a_22724/02_2025/7k8a_22724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8a_22724/02_2025/7k8a_22724.map" model { file = "/net/cci-nas-00/data/ceres_data/7k8a_22724/02_2025/7k8a_22724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8a_22724/02_2025/7k8a_22724.cif" } resolution = 3.65 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 ------------------------------------------------------------------------------- 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= 0.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5513 atoms to isotropic. 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 28 5.16 5 C 3570 2.51 5 N 913 2.21 5 O 1002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5513 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5513 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 37, 'TRANS': 685} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.55, per 1000 atoms: 0.64 Number of scatterers: 5513 At special positions: 0 Unit cell: (92.22, 99.64, 100.7, 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 28 16.00 O 1002 8.00 N 913 7.00 C 3570 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: 1.19 Conformation dependent library (CDL) restraints added in 793.0 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 71.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.661A pdb=" N TRP A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 31 removed outlier: 4.589A pdb=" N VAL A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.914A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 4.347A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 68' Processing helix chain 'A' and resid 83 through 101 removed outlier: 4.169A pdb=" N GLN A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 160 removed outlier: 3.566A pdb=" N ILE A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 170 through 206 removed outlier: 3.734A pdb=" N LEU A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 207 through 233 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 241 through 271 removed outlier: 3.529A pdb=" N VAL A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.774A pdb=" N SER A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 342 removed outlier: 4.998A pdb=" N ALA A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.254A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 415 Proline residue: A 407 - end of helix removed outlier: 3.678A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.503A pdb=" N LYS A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 563 Processing helix chain 'A' and resid 563 through 583 removed outlier: 3.530A pdb=" N MET A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 612 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.536A pdb=" N PHE A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 692 removed outlier: 4.275A pdb=" N ALA A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 722 removed outlier: 3.791A pdb=" N ILE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.624A pdb=" N TRP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 removed outlier: 4.402A pdb=" N VAL A 745 " --> pdb=" O TRP A 741 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.967A pdb=" N THR A 133 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 518 removed outlier: 3.523A pdb=" N ILE A 516 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 518 " --> pdb=" O LEU A 457 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1053 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: 1.46 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1661 1.34 - 1.46: 864 1.46 - 1.58: 3045 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 5624 Sorted by residual: bond pdb=" N ASP A 78 " pdb=" CA ASP A 78 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.33e-02 5.65e+03 1.16e+01 bond pdb=" CA THR A 74 " pdb=" C THR A 74 " ideal model delta sigma weight residual 1.519 1.558 -0.039 1.28e-02 6.10e+03 9.24e+00 bond pdb=" CA ASP A 78 " pdb=" C ASP A 78 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.43e-02 4.89e+03 8.40e+00 bond pdb=" C THR A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.38e+00 bond pdb=" C VAL A 302 " pdb=" N PRO A 303 " ideal model delta sigma weight residual 1.337 1.361 -0.024 1.11e-02 8.12e+03 4.82e+00 ... (remaining 5619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 7413 2.20 - 4.41: 176 4.41 - 6.61: 50 6.61 - 8.82: 13 8.82 - 11.02: 1 Bond angle restraints: 7653 Sorted by residual: angle pdb=" N PRO A 75 " pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 110.70 117.53 -6.83 1.22e+00 6.72e-01 3.13e+01 angle pdb=" N LEU A 73 " pdb=" CA LEU A 73 " pdb=" C LEU A 73 " ideal model delta sigma weight residual 109.46 116.61 -7.15 1.66e+00 3.63e-01 1.86e+01 angle pdb=" C PRO A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 119.84 114.51 5.33 1.25e+00 6.40e-01 1.82e+01 angle pdb=" C ILE A 719 " pdb=" N ARG A 720 " pdb=" CA ARG A 720 " ideal model delta sigma weight residual 122.38 115.10 7.28 1.81e+00 3.05e-01 1.62e+01 angle pdb=" N PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta sigma weight residual 110.28 116.18 -5.90 1.55e+00 4.16e-01 1.45e+01 ... (remaining 7648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3073 17.99 - 35.98: 235 35.98 - 53.97: 45 53.97 - 71.96: 3 71.96 - 89.95: 4 Dihedral angle restraints: 3360 sinusoidal: 1302 harmonic: 2058 Sorted by residual: dihedral pdb=" N PHE A 649 " pdb=" C PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta harmonic sigma weight residual 122.80 139.31 -16.51 0 2.50e+00 1.60e-01 4.36e+01 dihedral pdb=" C PHE A 649 " pdb=" N PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta harmonic sigma weight residual -122.60 -139.03 16.43 0 2.50e+00 1.60e-01 4.32e+01 dihedral pdb=" CA PHE A 722 " pdb=" C PHE A 722 " pdb=" N LEU A 723 " pdb=" CA LEU A 723 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 905 0.135 - 0.270: 8 0.270 - 0.405: 0 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 914 Sorted by residual: chirality pdb=" CA PHE A 649 " pdb=" N PHE A 649 " pdb=" C PHE A 649 " pdb=" CB PHE A 649 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CB ILE A 137 " pdb=" CA ILE A 137 " pdb=" CG1 ILE A 137 " pdb=" CG2 ILE A 137 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 911 not shown) Planarity restraints: 967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 406 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO A 407 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 417 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 418 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 649 " 0.016 2.00e-02 2.50e+03 1.29e-02 2.91e+00 pdb=" CG PHE A 649 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 649 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 649 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 649 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 649 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 649 " 0.001 2.00e-02 2.50e+03 ... (remaining 964 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 936 2.76 - 3.30: 5906 3.30 - 3.83: 9048 3.83 - 4.37: 10106 4.37 - 4.90: 16840 Nonbonded interactions: 42836 Sorted by model distance: nonbonded pdb=" N ASP A 142 " pdb=" OE2 GLU A 146 " model vdw 2.226 3.120 nonbonded pdb=" O MET A 610 " pdb=" OH TYR A 622 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" O VAL A 513 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR A 680 " pdb=" NH2 ARG A 720 " model vdw 2.305 3.120 nonbonded pdb=" O GLY A 426 " pdb=" OH TYR A 431 " model vdw 2.306 3.040 ... (remaining 42831 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 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: 0.050 Process input model: 16.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5624 Z= 0.265 Angle : 0.918 11.022 7653 Z= 0.501 Chirality : 0.052 0.675 914 Planarity : 0.006 0.075 967 Dihedral : 13.382 89.947 2036 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.17 % Allowed : 1.19 % Favored : 98.64 % 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: -1.30 (0.30), residues: 719 helix: -0.15 (0.24), residues: 457 sheet: -3.15 (0.69), residues: 31 loop : -1.78 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 737 HIS 0.005 0.001 HIS A 540 PHE 0.029 0.002 PHE A 649 TYR 0.025 0.002 TYR A 151 ARG 0.006 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.547 Fit side-chains REVERT: A 128 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7275 (tp-100) REVERT: A 147 ILE cc_start: 0.8233 (pt) cc_final: 0.7427 (pt) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1512 time to fit residues: 26.1849 Evaluate side-chains 117 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.263254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.245168 restraints weight = 9178.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.250285 restraints weight = 7627.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.252509 restraints weight = 4108.396| |-----------------------------------------------------------------------------| r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5624 Z= 0.257 Angle : 0.811 8.292 7653 Z= 0.410 Chirality : 0.046 0.190 914 Planarity : 0.006 0.067 967 Dihedral : 5.458 24.451 769 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.87 % Favored : 94.99 % Rotamer: Outliers : 3.23 % Allowed : 11.73 % Favored : 85.03 % 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: -1.28 (0.30), residues: 719 helix: -0.05 (0.23), residues: 458 sheet: -3.30 (0.68), residues: 30 loop : -1.98 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 737 HIS 0.006 0.001 HIS A 540 PHE 0.020 0.002 PHE A 649 TYR 0.017 0.002 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) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.659 Fit side-chains REVERT: A 44 TYR cc_start: 0.7232 (m-10) cc_final: 0.6789 (m-10) REVERT: A 128 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7133 (tp-100) REVERT: A 419 LEU cc_start: 0.6399 (pp) cc_final: 0.6195 (pp) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.1701 time to fit residues: 28.3024 Evaluate side-chains 127 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.262546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.245904 restraints weight = 9238.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.251359 restraints weight = 7897.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.253172 restraints weight = 3570.506| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5624 Z= 0.241 Angle : 0.782 8.169 7653 Z= 0.393 Chirality : 0.046 0.303 914 Planarity : 0.006 0.052 967 Dihedral : 5.407 22.760 767 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.70 % Favored : 94.16 % Rotamer: Outliers : 4.59 % Allowed : 14.29 % Favored : 81.12 % 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: -1.23 (0.30), residues: 719 helix: 0.04 (0.24), residues: 459 sheet: -3.30 (0.67), residues: 42 loop : -1.98 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 737 HIS 0.006 0.002 HIS A 540 PHE 0.022 0.002 PHE A 449 TYR 0.020 0.002 TYR A 151 ARG 0.007 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.592 Fit side-chains REVERT: A 44 TYR cc_start: 0.7314 (m-10) cc_final: 0.6849 (m-10) REVERT: A 128 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7173 (tp-100) REVERT: A 480 LYS cc_start: 0.6006 (mmtm) cc_final: 0.5037 (mttm) REVERT: A 664 THR cc_start: 0.3463 (OUTLIER) cc_final: 0.2304 (m) REVERT: A 742 MET cc_start: -0.1771 (tpt) cc_final: -0.3242 (tpt) outliers start: 27 outliers final: 20 residues processed: 135 average time/residue: 0.1618 time to fit residues: 28.7069 Evaluate side-chains 140 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.266238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.247814 restraints weight = 9269.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.253400 restraints weight = 8485.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.255870 restraints weight = 4222.288| |-----------------------------------------------------------------------------| r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5624 Z= 0.195 Angle : 0.732 7.639 7653 Z= 0.360 Chirality : 0.044 0.312 914 Planarity : 0.005 0.043 967 Dihedral : 5.093 21.780 767 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.87 % Favored : 94.99 % Rotamer: Outliers : 4.42 % Allowed : 17.35 % Favored : 78.23 % 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: -0.94 (0.31), residues: 719 helix: 0.27 (0.24), residues: 466 sheet: -3.11 (0.69), residues: 42 loop : -1.95 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.003 0.001 HIS A 37 PHE 0.019 0.002 PHE A 265 TYR 0.017 0.001 TYR A 151 ARG 0.008 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.568 Fit side-chains REVERT: A 44 TYR cc_start: 0.7230 (m-10) cc_final: 0.6793 (m-10) REVERT: A 128 GLN cc_start: 0.7446 (tp-100) cc_final: 0.6957 (tp-100) REVERT: A 253 ILE cc_start: 0.7273 (mm) cc_final: 0.7042 (mm) REVERT: A 273 TYR cc_start: 0.6266 (m-10) cc_final: 0.4945 (m-10) REVERT: A 333 VAL cc_start: 0.5788 (OUTLIER) cc_final: 0.5550 (t) REVERT: A 742 MET cc_start: -0.2043 (tpt) cc_final: -0.3278 (tpt) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 0.1780 time to fit residues: 30.2652 Evaluate side-chains 132 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 52 optimal weight: 0.2980 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 = 0.4676 r_free = 0.4676 target = 0.260564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.243357 restraints weight = 9264.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.248439 restraints weight = 8309.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.250884 restraints weight = 4144.179| |-----------------------------------------------------------------------------| r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5624 Z= 0.267 Angle : 0.795 7.353 7653 Z= 0.399 Chirality : 0.045 0.252 914 Planarity : 0.006 0.043 967 Dihedral : 5.344 23.388 767 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.46 % Rotamer: Outliers : 5.95 % Allowed : 18.54 % Favored : 75.51 % 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: -1.04 (0.31), residues: 719 helix: 0.20 (0.24), residues: 461 sheet: -3.41 (0.67), residues: 34 loop : -2.01 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.005 0.001 HIS A 540 PHE 0.024 0.002 PHE A 649 TYR 0.018 0.002 TYR A 151 ARG 0.015 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.546 Fit side-chains REVERT: A 44 TYR cc_start: 0.7447 (m-10) cc_final: 0.6756 (m-10) REVERT: A 128 GLN cc_start: 0.7648 (tp-100) cc_final: 0.7222 (tp-100) REVERT: A 480 LYS cc_start: 0.6131 (mmtm) cc_final: 0.5216 (mttm) REVERT: A 534 ARG cc_start: 0.7129 (mmt-90) cc_final: 0.6885 (mmt-90) REVERT: A 664 THR cc_start: 0.3452 (OUTLIER) cc_final: 0.2305 (m) REVERT: A 693 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.6016 (m-10) REVERT: A 742 MET cc_start: -0.1918 (tpt) cc_final: -0.3312 (tpt) outliers start: 35 outliers final: 25 residues processed: 136 average time/residue: 0.1765 time to fit residues: 31.1722 Evaluate side-chains 142 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.256419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.238848 restraints weight = 9053.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.243664 restraints weight = 8396.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.245660 restraints weight = 4322.175| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5624 Z= 0.349 Angle : 0.881 7.683 7653 Z= 0.451 Chirality : 0.050 0.463 914 Planarity : 0.007 0.066 967 Dihedral : 5.951 27.485 767 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.37 % Favored : 92.49 % Rotamer: Outliers : 5.61 % Allowed : 20.41 % Favored : 73.98 % 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: -1.51 (0.30), residues: 719 helix: -0.11 (0.24), residues: 457 sheet: -3.50 (0.67), residues: 34 loop : -2.29 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 737 HIS 0.009 0.002 HIS A 540 PHE 0.030 0.003 PHE A 389 TYR 0.019 0.002 TYR A 151 ARG 0.016 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7489 (m-10) cc_final: 0.6800 (m-10) REVERT: A 128 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7161 (tp-100) REVERT: A 419 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5954 (pp) REVERT: A 480 LYS cc_start: 0.6358 (mmtm) cc_final: 0.5371 (mmtm) REVERT: A 552 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6183 (mp) REVERT: A 664 THR cc_start: 0.3727 (OUTLIER) cc_final: 0.2730 (m) REVERT: A 742 MET cc_start: -0.1986 (tpt) cc_final: -0.3218 (tpt) outliers start: 33 outliers final: 25 residues processed: 137 average time/residue: 0.1630 time to fit residues: 29.3786 Evaluate side-chains 143 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.259095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.240407 restraints weight = 9329.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.246116 restraints weight = 9108.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.248251 restraints weight = 4476.569| |-----------------------------------------------------------------------------| r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5624 Z= 0.254 Angle : 0.804 7.463 7653 Z= 0.400 Chirality : 0.046 0.250 914 Planarity : 0.006 0.051 967 Dihedral : 5.643 26.420 767 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.74 % Rotamer: Outliers : 5.44 % Allowed : 21.26 % Favored : 73.30 % 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: -1.25 (0.30), residues: 719 helix: 0.04 (0.24), residues: 452 sheet: -3.53 (0.70), residues: 34 loop : -2.00 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 86 HIS 0.005 0.001 HIS A 540 PHE 0.021 0.002 PHE A 265 TYR 0.019 0.002 TYR A 151 ARG 0.011 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6974 (mpt-90) cc_final: 0.6731 (mpt-90) REVERT: A 128 GLN cc_start: 0.7524 (tp-100) cc_final: 0.7271 (tp-100) REVERT: A 419 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6123 (pp) REVERT: A 480 LYS cc_start: 0.6230 (mmtm) cc_final: 0.5318 (mmtm) REVERT: A 534 ARG cc_start: 0.6928 (mmt-90) cc_final: 0.6636 (mmt-90) REVERT: A 664 THR cc_start: 0.3441 (OUTLIER) cc_final: 0.2345 (m) REVERT: A 742 MET cc_start: -0.2184 (tpt) cc_final: -0.3323 (tpt) outliers start: 32 outliers final: 24 residues processed: 138 average time/residue: 0.1705 time to fit residues: 30.6931 Evaluate side-chains 142 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 0.0060 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 overall best weight: 3.3802 ------------------------------------------------------------------------------- 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 = 0.4667 r_free = 0.4667 target = 0.259839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.240915 restraints weight = 9045.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.246644 restraints weight = 8789.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.248826 restraints weight = 4266.994| |-----------------------------------------------------------------------------| r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5624 Z= 0.247 Angle : 0.798 9.493 7653 Z= 0.398 Chirality : 0.046 0.244 914 Planarity : 0.006 0.048 967 Dihedral : 5.502 23.091 767 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.68 % Favored : 93.18 % Rotamer: Outliers : 5.44 % Allowed : 20.92 % Favored : 73.64 % 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: -1.28 (0.30), residues: 719 helix: 0.03 (0.24), residues: 458 sheet: -3.56 (0.70), residues: 34 loop : -2.09 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.005 0.001 HIS A 540 PHE 0.020 0.002 PHE A 265 TYR 0.019 0.002 TYR A 151 ARG 0.008 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.595 Fit side-chains REVERT: A 44 TYR cc_start: 0.7676 (m-10) cc_final: 0.6937 (m-10) REVERT: A 63 ARG cc_start: 0.7108 (mtm110) cc_final: 0.6804 (mtm110) REVERT: A 128 GLN cc_start: 0.7708 (tp-100) cc_final: 0.7412 (tp-100) REVERT: A 419 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.6032 (pp) REVERT: A 480 LYS cc_start: 0.6061 (mmtm) cc_final: 0.5126 (mmtm) REVERT: A 642 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7316 (tt) REVERT: A 664 THR cc_start: 0.3562 (OUTLIER) cc_final: 0.2461 (m) REVERT: A 742 MET cc_start: -0.2344 (tpt) cc_final: -0.3449 (tpt) outliers start: 32 outliers final: 25 residues processed: 135 average time/residue: 0.1715 time to fit residues: 30.0847 Evaluate side-chains 144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 721 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 = 0.4673 r_free = 0.4673 target = 0.260574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.241761 restraints weight = 8956.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.247419 restraints weight = 8545.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.249758 restraints weight = 4181.304| |-----------------------------------------------------------------------------| r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5624 Z= 0.260 Angle : 0.825 8.716 7653 Z= 0.410 Chirality : 0.048 0.419 914 Planarity : 0.006 0.052 967 Dihedral : 5.532 22.383 767 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.95 % Favored : 92.91 % Rotamer: Outliers : 5.27 % Allowed : 22.28 % Favored : 72.45 % 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: -1.22 (0.30), residues: 719 helix: 0.05 (0.24), residues: 454 sheet: -3.68 (0.69), residues: 34 loop : -1.95 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 86 HIS 0.004 0.001 HIS A 540 PHE 0.019 0.002 PHE A 265 TYR 0.018 0.002 TYR A 151 ARG 0.010 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.542 Fit side-chains REVERT: A 44 TYR cc_start: 0.7567 (m-10) cc_final: 0.6814 (m-10) REVERT: A 419 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.6042 (pp) REVERT: A 480 LYS cc_start: 0.6048 (mmtm) cc_final: 0.5126 (mmtm) REVERT: A 642 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7292 (tt) REVERT: A 664 THR cc_start: 0.3510 (OUTLIER) cc_final: 0.2404 (m) REVERT: A 742 MET cc_start: -0.2272 (tpt) cc_final: -0.3400 (tpt) outliers start: 31 outliers final: 25 residues processed: 133 average time/residue: 0.1721 time to fit residues: 29.7283 Evaluate side-chains 141 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 0.0980 chunk 49 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.263233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.245038 restraints weight = 9386.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.248543 restraints weight = 6177.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.250954 restraints weight = 4339.901| |-----------------------------------------------------------------------------| r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5624 Z= 0.221 Angle : 0.802 8.299 7653 Z= 0.392 Chirality : 0.047 0.395 914 Planarity : 0.006 0.076 967 Dihedral : 5.345 20.558 767 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.84 % Favored : 94.02 % Rotamer: Outliers : 4.76 % Allowed : 22.79 % Favored : 72.45 % 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: -1.13 (0.31), residues: 719 helix: 0.17 (0.24), residues: 464 sheet: -3.72 (0.67), residues: 42 loop : -2.00 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.002 0.001 HIS A 540 PHE 0.020 0.002 PHE A 265 TYR 0.039 0.002 TYR A 273 ARG 0.015 0.001 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.599 Fit side-chains REVERT: A 419 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5209 (pp) REVERT: A 480 LYS cc_start: 0.5784 (mmtm) cc_final: 0.4910 (mttm) REVERT: A 604 MET cc_start: 0.6008 (tmm) cc_final: 0.5555 (tmm) REVERT: A 642 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7209 (tt) REVERT: A 662 MET cc_start: 0.5421 (mmm) cc_final: 0.5070 (mmm) REVERT: A 742 MET cc_start: -0.2418 (tpt) cc_final: -0.3489 (tpt) outliers start: 28 outliers final: 25 residues processed: 131 average time/residue: 0.1764 time to fit residues: 29.9219 Evaluate side-chains 141 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.263316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.244785 restraints weight = 9335.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.250676 restraints weight = 8652.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.252928 restraints weight = 4177.765| |-----------------------------------------------------------------------------| r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5624 Z= 0.232 Angle : 0.810 8.144 7653 Z= 0.398 Chirality : 0.046 0.337 914 Planarity : 0.006 0.052 967 Dihedral : 5.395 28.349 767 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.98 % Favored : 93.88 % Rotamer: Outliers : 4.42 % Allowed : 23.30 % Favored : 72.28 % 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: -1.11 (0.31), residues: 719 helix: 0.18 (0.24), residues: 465 sheet: -3.74 (0.66), residues: 42 loop : -1.99 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.003 0.001 HIS A 540 PHE 0.019 0.002 PHE A 265 TYR 0.033 0.002 TYR A 273 ARG 0.016 0.001 ARG A 281 =============================================================================== Job complete usr+sys time: 1707.96 seconds wall clock time: 31 minutes 18.43 seconds (1878.43 seconds total)