Starting phenix.real_space_refine on Tue Jan 14 10:58:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3z_18878/01_2025/8r3z_18878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3z_18878/01_2025/8r3z_18878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r3z_18878/01_2025/8r3z_18878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3z_18878/01_2025/8r3z_18878.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3z_18878/01_2025/8r3z_18878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3z_18878/01_2025/8r3z_18878.cif" } resolution = 3.4 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= 0.006 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 73 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 4100 2.51 5 N 1107 2.21 5 O 1157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6389 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6256 Classifications: {'peptide': 755} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 725} Chain breaks: 5 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.78 Number of scatterers: 6389 At special positions: 0 Unit cell: (71.5, 81.9, 105.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 6 15.00 Mg 1 11.99 O 1157 8.00 N 1107 7.00 C 4100 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: 1.90 Conformation dependent library (CDL) restraints added in 864.4 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 37.4% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 154 through 165 Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.996A pdb=" N TRP A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 445 through 463 Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.572A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.508A pdb=" N TYR A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 removed outlier: 3.976A pdb=" N ASP A 537 " --> pdb=" O LYS A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 removed outlier: 3.623A pdb=" N CYS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 644 removed outlier: 3.570A pdb=" N GLN A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 Processing helix chain 'A' and resid 680 through 685 removed outlier: 4.646A pdb=" N GLU A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.672A pdb=" N PHE A 764 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 801 removed outlier: 3.634A pdb=" N ALA A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 3.611A pdb=" N LEU A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 812' Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 392 removed outlier: 3.934A pdb=" N ILE A 389 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 31 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 391 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP A 28 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 706 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 138 removed outlier: 4.897A pdb=" N LEU A 332 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 217 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A 330 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG A 244 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.547A pdb=" N ASN A 203 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.657A pdb=" N ILE A 43 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR A 112 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 45 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.583A pdb=" N THR A 719 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 731 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 749 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 692 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN A 755 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 690 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 602 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 407 through 409 removed outlier: 3.538A pdb=" N ILE A 401 " --> pdb=" O PHE A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.116A pdb=" N ILE A 437 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 475 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR A 439 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 528 " --> pdb=" O ILE A 500 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 819 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: 2.24 Time building geometry restraints manager: 2.16 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: 2008 1.34 - 1.46: 1241 1.46 - 1.58: 3251 1.58 - 1.70: 12 1.70 - 1.82: 29 Bond restraints: 6541 Sorted by residual: bond pdb=" N LEU A 774 " pdb=" CA LEU A 774 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.12e+01 bond pdb=" N ILE A 770 " pdb=" CA ILE A 770 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.98e+00 bond pdb=" N ASN A 700 " pdb=" CA ASN A 700 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.69e+00 bond pdb=" N ASN A 203 " pdb=" CA ASN A 203 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.05e+00 bond pdb=" N LEU A 771 " pdb=" CA LEU A 771 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.52e+00 ... (remaining 6536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 8649 1.77 - 3.53: 177 3.53 - 5.30: 26 5.30 - 7.07: 6 7.07 - 8.83: 4 Bond angle restraints: 8862 Sorted by residual: angle pdb=" N ASN A 756 " pdb=" CA ASN A 756 " pdb=" C ASN A 756 " ideal model delta sigma weight residual 114.56 107.72 6.84 1.27e+00 6.20e-01 2.90e+01 angle pdb=" CA PRO A 489 " pdb=" N PRO A 489 " pdb=" CD PRO A 489 " ideal model delta sigma weight residual 112.00 105.82 6.18 1.40e+00 5.10e-01 1.95e+01 angle pdb=" CA ASN A 756 " pdb=" C ASN A 756 " pdb=" N THR A 757 " ideal model delta sigma weight residual 119.26 115.57 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N ASN A 700 " pdb=" CA ASN A 700 " pdb=" C ASN A 700 " ideal model delta sigma weight residual 112.59 108.92 3.67 1.22e+00 6.72e-01 9.06e+00 angle pdb=" CB MET A 224 " pdb=" CG MET A 224 " pdb=" SD MET A 224 " ideal model delta sigma weight residual 112.70 121.53 -8.83 3.00e+00 1.11e-01 8.67e+00 ... (remaining 8857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 3348 17.46 - 34.91: 457 34.91 - 52.37: 117 52.37 - 69.83: 38 69.83 - 87.28: 7 Dihedral angle restraints: 3967 sinusoidal: 1731 harmonic: 2236 Sorted by residual: dihedral pdb=" CA SER A 390 " pdb=" C SER A 390 " pdb=" N MET A 391 " pdb=" CA MET A 391 " ideal model delta harmonic sigma weight residual -180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLU A 30 " pdb=" C GLU A 30 " pdb=" N MET A 31 " pdb=" CA MET A 31 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU A 181 " pdb=" C LEU A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta harmonic sigma weight residual 180.00 164.19 15.81 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 3964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 766 0.051 - 0.101: 175 0.101 - 0.152: 41 0.152 - 0.203: 3 0.203 - 0.253: 1 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB ILE A 500 " pdb=" CA ILE A 500 " pdb=" CG1 ILE A 500 " pdb=" CG2 ILE A 500 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE A 770 " pdb=" N ILE A 770 " pdb=" C ILE A 770 " pdb=" CB ILE A 770 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA LEU A 771 " pdb=" N LEU A 771 " pdb=" C LEU A 771 " pdb=" CB LEU A 771 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 983 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 488 " -0.083 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO A 489 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 568 " 0.014 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP A 568 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 568 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 568 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 568 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 568 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 121 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LEU A 121 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A 121 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 122 " 0.012 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 52 2.53 - 3.12: 4732 3.12 - 3.71: 10155 3.71 - 4.31: 13771 4.31 - 4.90: 23114 Nonbonded interactions: 51824 Sorted by model distance: nonbonded pdb=" OP3 U B 1 " pdb="MG MG A1000 " model vdw 1.932 2.170 nonbonded pdb=" O LYS A 697 " pdb=" NH2 ARG A 783 " model vdw 2.241 3.120 nonbonded pdb=" NE2 GLN A 354 " pdb=" O PHE A 742 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS A 86 " pdb=" O VAL A 379 " model vdw 2.256 3.120 nonbonded pdb=" OG1 THR A 157 " pdb=" OD2 ASP A 372 " model vdw 2.259 3.040 ... (remaining 51819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.091 6541 Z= 0.216 Angle : 0.653 8.835 8862 Z= 0.367 Chirality : 0.046 0.253 986 Planarity : 0.005 0.123 1098 Dihedral : 17.436 87.284 2517 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.29 % Allowed : 27.82 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.30), residues: 743 helix: 0.92 (0.33), residues: 252 sheet: -0.36 (0.35), residues: 193 loop : -0.80 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 568 HIS 0.008 0.001 HIS A 687 PHE 0.011 0.001 PHE A 481 TYR 0.032 0.002 TYR A 57 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8747 (mmmt) REVERT: A 416 ASN cc_start: 0.8505 (p0) cc_final: 0.7929 (p0) REVERT: A 417 TRP cc_start: 0.6963 (m100) cc_final: 0.6463 (m100) outliers start: 2 outliers final: 0 residues processed: 85 average time/residue: 0.1792 time to fit residues: 21.1684 Evaluate side-chains 67 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.0570 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 GLN A 551 GLN A 707 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.128064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.098984 restraints weight = 15096.720| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 4.45 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6541 Z= 0.212 Angle : 0.540 7.131 8862 Z= 0.285 Chirality : 0.044 0.174 986 Planarity : 0.004 0.067 1098 Dihedral : 9.372 63.836 916 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.14 % Allowed : 25.53 % Favored : 70.33 % 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: 0.05 (0.30), residues: 743 helix: 1.21 (0.33), residues: 250 sheet: -0.16 (0.36), residues: 187 loop : -0.76 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 568 HIS 0.006 0.001 HIS A 687 PHE 0.013 0.001 PHE A 408 TYR 0.015 0.001 TYR A 816 ARG 0.002 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8983 (pttm) REVERT: A 84 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: A 85 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: A 224 MET cc_start: 0.9141 (mmm) cc_final: 0.8561 (mmm) REVERT: A 391 MET cc_start: 0.6701 (ttt) cc_final: 0.6390 (ttt) REVERT: A 417 TRP cc_start: 0.6920 (m100) cc_final: 0.6402 (m100) REVERT: A 438 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6313 (tp) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.1680 time to fit residues: 23.3443 Evaluate side-chains 84 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 774 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN A 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.129428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.100126 restraints weight = 15660.438| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.75 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6541 Z= 0.147 Angle : 0.507 7.193 8862 Z= 0.262 Chirality : 0.043 0.145 986 Planarity : 0.003 0.045 1098 Dihedral : 9.247 63.835 916 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.99 % Allowed : 26.11 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.30), residues: 743 helix: 1.45 (0.33), residues: 243 sheet: -0.16 (0.36), residues: 191 loop : -0.65 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.005 0.001 HIS A 687 PHE 0.020 0.001 PHE A 408 TYR 0.012 0.001 TYR A 816 ARG 0.007 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: A 208 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 224 MET cc_start: 0.9227 (mmm) cc_final: 0.8795 (mmm) REVERT: A 355 MET cc_start: 0.7985 (mpp) cc_final: 0.7512 (mpp) REVERT: A 391 MET cc_start: 0.6909 (ttt) cc_final: 0.6654 (ttt) REVERT: A 416 ASN cc_start: 0.8579 (p0) cc_final: 0.8226 (p0) REVERT: A 417 TRP cc_start: 0.6848 (m100) cc_final: 0.6506 (m100) REVERT: A 438 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6208 (tp) REVERT: A 498 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7564 (pm20) outliers start: 28 outliers final: 15 residues processed: 93 average time/residue: 0.1521 time to fit residues: 20.2824 Evaluate side-chains 85 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 774 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.0050 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.126789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.096978 restraints weight = 16236.774| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 4.84 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6541 Z= 0.224 Angle : 0.516 5.776 8862 Z= 0.268 Chirality : 0.043 0.139 986 Planarity : 0.003 0.034 1098 Dihedral : 9.175 63.834 916 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.71 % Allowed : 25.39 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.30), residues: 743 helix: 1.46 (0.33), residues: 248 sheet: -0.02 (0.37), residues: 185 loop : -0.67 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 417 HIS 0.007 0.001 HIS A 687 PHE 0.019 0.001 PHE A 408 TYR 0.011 0.001 TYR A 816 ARG 0.003 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 224 MET cc_start: 0.9230 (mmm) cc_final: 0.8829 (mmm) REVERT: A 352 ASN cc_start: 0.8683 (m-40) cc_final: 0.8210 (m-40) REVERT: A 355 MET cc_start: 0.7990 (mpp) cc_final: 0.7495 (mpp) REVERT: A 416 ASN cc_start: 0.8558 (p0) cc_final: 0.7950 (p0) REVERT: A 417 TRP cc_start: 0.6891 (m100) cc_final: 0.6655 (m100) REVERT: A 498 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7591 (pm20) outliers start: 33 outliers final: 27 residues processed: 92 average time/residue: 0.1466 time to fit residues: 19.5408 Evaluate side-chains 93 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.124311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093477 restraints weight = 15895.808| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.97 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6541 Z= 0.241 Angle : 0.539 7.560 8862 Z= 0.278 Chirality : 0.043 0.149 986 Planarity : 0.003 0.027 1098 Dihedral : 9.268 63.835 916 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.28 % Allowed : 25.68 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.30), residues: 743 helix: 1.43 (0.33), residues: 248 sheet: -0.04 (0.37), residues: 185 loop : -0.63 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 417 HIS 0.010 0.001 HIS A 687 PHE 0.014 0.001 PHE A 408 TYR 0.012 0.001 TYR A 46 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7640 (mp) REVERT: A 85 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: A 224 MET cc_start: 0.9283 (mmm) cc_final: 0.8900 (mmm) REVERT: A 355 MET cc_start: 0.7936 (mpp) cc_final: 0.7351 (mpp) REVERT: A 416 ASN cc_start: 0.8473 (p0) cc_final: 0.8066 (p0) REVERT: A 417 TRP cc_start: 0.6834 (m100) cc_final: 0.6606 (m100) REVERT: A 498 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: A 777 ASN cc_start: 0.8143 (t0) cc_final: 0.7924 (t0) outliers start: 37 outliers final: 26 residues processed: 97 average time/residue: 0.1616 time to fit residues: 22.0613 Evaluate side-chains 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 774 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.122979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.092169 restraints weight = 15940.224| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.95 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6541 Z= 0.278 Angle : 0.550 8.579 8862 Z= 0.286 Chirality : 0.044 0.166 986 Planarity : 0.003 0.027 1098 Dihedral : 9.142 63.979 916 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.14 % Allowed : 25.96 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 743 helix: 1.37 (0.33), residues: 248 sheet: -0.14 (0.37), residues: 179 loop : -0.67 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 417 HIS 0.009 0.001 HIS A 687 PHE 0.013 0.001 PHE A 764 TYR 0.012 0.001 TYR A 46 ARG 0.007 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 82 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8825 (pttm) REVERT: A 224 MET cc_start: 0.9293 (mmm) cc_final: 0.8904 (mmm) REVERT: A 416 ASN cc_start: 0.8444 (p0) cc_final: 0.8071 (p0) REVERT: A 417 TRP cc_start: 0.6812 (m100) cc_final: 0.6585 (m100) outliers start: 36 outliers final: 29 residues processed: 94 average time/residue: 0.1571 time to fit residues: 21.4851 Evaluate side-chains 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.121642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.090772 restraints weight = 15993.722| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 4.91 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6541 Z= 0.320 Angle : 0.585 9.501 8862 Z= 0.303 Chirality : 0.045 0.168 986 Planarity : 0.003 0.028 1098 Dihedral : 9.249 64.078 916 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.56 % Allowed : 26.39 % Favored : 68.05 % 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: 0.04 (0.30), residues: 743 helix: 1.30 (0.33), residues: 248 sheet: -0.37 (0.37), residues: 184 loop : -0.68 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 417 HIS 0.013 0.001 HIS A 687 PHE 0.021 0.001 PHE A 408 TYR 0.014 0.002 TYR A 46 ARG 0.006 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 65 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7523 (mp) REVERT: A 82 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8794 (pttm) REVERT: A 416 ASN cc_start: 0.8352 (p0) cc_final: 0.8133 (p0) outliers start: 39 outliers final: 32 residues processed: 97 average time/residue: 0.1445 time to fit residues: 20.6182 Evaluate side-chains 94 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.121296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.090356 restraints weight = 16055.937| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.83 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6541 Z= 0.360 Angle : 0.617 10.538 8862 Z= 0.319 Chirality : 0.046 0.178 986 Planarity : 0.003 0.028 1098 Dihedral : 9.437 64.095 916 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.14 % Allowed : 27.82 % Favored : 67.05 % 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: -0.12 (0.30), residues: 743 helix: 1.15 (0.32), residues: 251 sheet: -0.60 (0.36), residues: 189 loop : -0.66 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 778 HIS 0.008 0.001 HIS A 687 PHE 0.018 0.001 PHE A 408 TYR 0.017 0.002 TYR A 46 ARG 0.005 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 224 MET cc_start: 0.9184 (mmm) cc_final: 0.8599 (mmm) REVERT: A 533 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8940 (tmtt) outliers start: 36 outliers final: 32 residues processed: 92 average time/residue: 0.1588 time to fit residues: 21.1784 Evaluate side-chains 95 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.124139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.093511 restraints weight = 15995.083| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 4.93 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6541 Z= 0.192 Angle : 0.553 8.062 8862 Z= 0.286 Chirality : 0.045 0.176 986 Planarity : 0.003 0.050 1098 Dihedral : 9.301 63.911 916 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.71 % Allowed : 28.53 % Favored : 67.76 % 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: 0.11 (0.30), residues: 743 helix: 1.46 (0.33), residues: 248 sheet: -0.32 (0.37), residues: 184 loop : -0.74 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 568 HIS 0.005 0.001 HIS A 687 PHE 0.012 0.001 PHE A 408 TYR 0.015 0.001 TYR A 46 ARG 0.012 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 224 MET cc_start: 0.9187 (mmm) cc_final: 0.8632 (mmm) outliers start: 26 outliers final: 20 residues processed: 88 average time/residue: 0.1507 time to fit residues: 19.1119 Evaluate side-chains 80 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** 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 = 0.4014 r_free = 0.4014 target = 0.121994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091258 restraints weight = 16156.777| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.91 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6541 Z= 0.280 Angle : 0.589 8.570 8862 Z= 0.305 Chirality : 0.045 0.182 986 Planarity : 0.004 0.058 1098 Dihedral : 9.303 64.001 916 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.28 % Allowed : 28.53 % Favored : 68.19 % 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: 0.11 (0.30), residues: 743 helix: 1.45 (0.32), residues: 248 sheet: -0.32 (0.37), residues: 184 loop : -0.74 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 778 HIS 0.007 0.001 HIS A 687 PHE 0.014 0.001 PHE A 408 TYR 0.013 0.002 TYR A 249 ARG 0.014 0.001 ARG A 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7533 (mp) REVERT: A 224 MET cc_start: 0.9193 (mmm) cc_final: 0.8646 (mmm) outliers start: 23 outliers final: 22 residues processed: 83 average time/residue: 0.1583 time to fit residues: 19.1356 Evaluate side-chains 82 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093776 restraints weight = 16263.286| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.98 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6541 Z= 0.181 Angle : 0.548 7.664 8862 Z= 0.282 Chirality : 0.045 0.175 986 Planarity : 0.003 0.059 1098 Dihedral : 9.219 63.878 916 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.14 % Allowed : 28.67 % Favored : 68.19 % 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: 0.26 (0.30), residues: 743 helix: 1.61 (0.33), residues: 248 sheet: -0.15 (0.37), residues: 183 loop : -0.75 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 568 HIS 0.005 0.001 HIS A 687 PHE 0.012 0.001 PHE A 408 TYR 0.011 0.001 TYR A 46 ARG 0.014 0.000 ARG A 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.03 seconds wall clock time: 50 minutes 58.88 seconds (3058.88 seconds total)