Starting phenix.real_space_refine on Tue Aug 4 19:55:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3z_18878/08_2026/8r3z_18878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3z_18878/08_2026/8r3z_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_18878/08_2026/8r3z_18878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3z_18878/08_2026/8r3z_18878.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3z_18878/08_2026/8r3z_18878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3z_18878/08_2026/8r3z_18878.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 1.36, per 1000 atoms: 0.21 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: 0.40 Conformation dependent library (CDL) restraints added in 311.1 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: 0.12 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: 0.93 Time building geometry restraints manager: 0.55 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: 8636 1.77 - 3.53: 190 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=" O5' A B 3 " pdb=" C5' A B 3 " pdb=" C4' A B 3 " ideal model delta sigma weight residual 109.40 111.82 -2.42 8.00e-01 1.56e+00 9.17e+00 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 ... (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: 760 0.051 - 0.101: 177 0.101 - 0.152: 45 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: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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= 0.179 Angle : 0.660 8.835 8862 Z= 0.376 Chirality : 0.047 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 619 TYR 0.032 0.002 TYR A 57 PHE 0.011 0.001 PHE A 481 TRP 0.039 0.003 TRP A 568 HIS 0.008 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 ( 6541) covalent geometry : angle 0.65998 / 0.38 ( 8862) hydrogen bonds : bond 0.14283 / 9.51 ( 281) hydrogen bonds : angle 6.62200 / 4.77 ( 819) *********************** 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 : 0.171 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: 0.0570 time to fit residues: 6.9015 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS A 707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.127196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098073 restraints weight = 15330.695| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.46 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0949 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= 0.177 Angle : 0.580 7.162 8862 Z= 0.306 Chirality : 0.045 0.182 986 Planarity : 0.004 0.062 1098 Dihedral : 9.373 63.940 916 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.71 % Allowed : 25.25 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.30), residues: 743 helix: 0.99 (0.33), residues: 253 sheet: -0.24 (0.35), residues: 188 loop : -0.79 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 783 TYR 0.012 0.002 TYR A 286 PHE 0.008 0.001 PHE A 764 TRP 0.023 0.002 TRP A 568 HIS 0.008 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 6541) covalent geometry : angle 0.58036 / 0.31 ( 8862) hydrogen bonds : bond 0.04252 / 2.78 ( 281) hydrogen bonds : angle 5.71866 / 4.00 ( 819) *********************** 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 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: A 206 GLU cc_start: 0.8448 (tt0) cc_final: 0.8192 (tt0) REVERT: A 416 ASN cc_start: 0.8542 (p0) cc_final: 0.7932 (p0) REVERT: A 417 TRP cc_start: 0.6966 (m100) cc_final: 0.6528 (m100) REVERT: A 438 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6382 (tp) REVERT: A 498 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7646 (pm20) outliers start: 26 outliers final: 15 residues processed: 95 average time/residue: 0.0516 time to fit residues: 6.9563 Evaluate side-chains 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 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 531 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 633 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4101 r_free = 0.4101 target = 0.125787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096078 restraints weight = 15946.759| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.77 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6541 Z= 0.186 Angle : 0.576 7.107 8862 Z= 0.302 Chirality : 0.045 0.149 986 Planarity : 0.004 0.043 1098 Dihedral : 9.396 64.021 916 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.71 % Allowed : 24.82 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.30), residues: 743 helix: 0.96 (0.32), residues: 252 sheet: -0.21 (0.35), residues: 188 loop : -0.75 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 351 TYR 0.012 0.002 TYR A 816 PHE 0.017 0.001 PHE A 408 TRP 0.012 0.002 TRP A 568 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 6541) covalent geometry : angle 0.57615 / 0.30 ( 8862) hydrogen bonds : bond 0.03846 / 2.49 ( 281) hydrogen bonds : angle 5.55932 / 3.89 ( 819) *********************** 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 102 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 417 TRP cc_start: 0.6886 (m100) cc_final: 0.6483 (m100) REVERT: A 436 MET cc_start: 0.7248 (tpp) cc_final: 0.7035 (tpp) REVERT: A 498 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7626 (pm20) outliers start: 33 outliers final: 24 residues processed: 98 average time/residue: 0.0468 time to fit residues: 6.6296 Evaluate side-chains 91 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 373 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 531 VAL 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 604 THR 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 772 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 GLN A 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.125091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095134 restraints weight = 16144.878| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 4.81 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1540 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= 0.193 Angle : 0.567 6.522 8862 Z= 0.297 Chirality : 0.044 0.141 986 Planarity : 0.004 0.033 1098 Dihedral : 9.353 64.050 916 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.71 % Allowed : 25.11 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.30), residues: 743 helix: 1.03 (0.32), residues: 251 sheet: -0.24 (0.36), residues: 185 loop : -0.72 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.014 0.002 TYR A 512 PHE 0.016 0.001 PHE A 408 TRP 0.011 0.002 TRP A 417 HIS 0.007 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 6541) covalent geometry : angle 0.56679 / 0.30 ( 8862) hydrogen bonds : bond 0.03681 / 2.38 ( 281) hydrogen bonds : angle 5.37973 / 3.76 ( 819) *********************** 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 108 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 82 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8992 (pttm) REVERT: A 84 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: A 85 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: A 416 ASN cc_start: 0.8594 (p0) cc_final: 0.7640 (p0) REVERT: A 417 TRP cc_start: 0.6900 (m100) cc_final: 0.6604 (m100) REVERT: A 436 MET cc_start: 0.7303 (tpp) cc_final: 0.7067 (tpp) REVERT: A 498 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7610 (pm20) outliers start: 40 outliers final: 30 residues processed: 100 average time/residue: 0.0555 time to fit residues: 8.3657 Evaluate side-chains 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 82 LYS 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 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 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 498 GLN Chi-restraints excluded: chain A residue 531 VAL 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 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 660 THR Chi-restraints excluded: chain A residue 695 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN A 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091301 restraints weight = 15732.026| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 4.90 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6541 Z= 0.195 Angle : 0.562 8.173 8862 Z= 0.293 Chirality : 0.044 0.141 986 Planarity : 0.003 0.032 1098 Dihedral : 9.346 63.837 916 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.70 % Allowed : 23.54 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.30), residues: 743 helix: 1.09 (0.32), residues: 250 sheet: -0.27 (0.36), residues: 185 loop : -0.68 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 619 TYR 0.012 0.002 TYR A 512 PHE 0.015 0.001 PHE A 408 TRP 0.010 0.002 TRP A 417 HIS 0.004 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 6541) covalent geometry : angle 0.56158 / 0.29 ( 8862) hydrogen bonds : bond 0.03584 / 2.32 ( 281) hydrogen bonds : angle 5.31655 / 3.72 ( 819) *********************** 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 112 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 65 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 82 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8927 (mmmt) REVERT: A 85 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: A 352 ASN cc_start: 0.8739 (m-40) cc_final: 0.8247 (m-40) REVERT: A 416 ASN cc_start: 0.8554 (p0) cc_final: 0.8030 (p0) REVERT: A 417 TRP cc_start: 0.6800 (m100) cc_final: 0.6567 (m100) REVERT: A 436 MET cc_start: 0.7195 (tpp) cc_final: 0.6922 (tpp) REVERT: A 498 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: A 597 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7922 (mt) outliers start: 47 outliers final: 33 residues processed: 105 average time/residue: 0.0639 time to fit residues: 9.7263 Evaluate side-chains 101 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 82 LYS 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 306 TYR 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 461 GLN 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 531 VAL 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 597 ILE 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 660 THR Chi-restraints excluded: chain A residue 695 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.125501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.094928 restraints weight = 15934.604| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 5.00 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6541 Z= 0.127 Angle : 0.538 8.937 8862 Z= 0.278 Chirality : 0.044 0.148 986 Planarity : 0.003 0.031 1098 Dihedral : 9.269 63.838 916 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.30), residues: 743 helix: 1.21 (0.33), residues: 251 sheet: -0.21 (0.36), residues: 185 loop : -0.64 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 468 TYR 0.019 0.001 TYR A 84 PHE 0.013 0.001 PHE A 408 TRP 0.011 0.001 TRP A 417 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6541) covalent geometry : angle 0.53783 / 0.28 ( 8862) hydrogen bonds : bond 0.03312 / 2.14 ( 281) hydrogen bonds : angle 5.15880 / 3.60 ( 819) *********************** 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 106 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7604 (mp) REVERT: A 82 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8882 (pttm) REVERT: A 352 ASN cc_start: 0.8644 (m-40) cc_final: 0.8200 (m-40) REVERT: A 355 MET cc_start: 0.7946 (mpp) cc_final: 0.7232 (mpp) REVERT: A 416 ASN cc_start: 0.8501 (p0) cc_final: 0.8003 (p0) REVERT: A 417 TRP cc_start: 0.6777 (m100) cc_final: 0.6566 (m100) REVERT: A 436 MET cc_start: 0.7215 (tpp) cc_final: 0.6948 (tpp) REVERT: A 498 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: A 533 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8859 (tmtt) outliers start: 33 outliers final: 23 residues processed: 99 average time/residue: 0.0607 time to fit residues: 8.8557 Evaluate side-chains 94 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 82 LYS Chi-restraints excluded: chain A residue 222 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 533 LYS 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 660 THR Chi-restraints excluded: chain A residue 681 SER 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 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 37 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.121756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.090580 restraints weight = 16018.743| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.95 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6541 Z= 0.264 Angle : 0.621 9.688 8862 Z= 0.321 Chirality : 0.046 0.245 986 Planarity : 0.004 0.041 1098 Dihedral : 9.279 63.892 916 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.85 % Allowed : 25.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.30), residues: 743 helix: 1.08 (0.32), residues: 250 sheet: -0.33 (0.37), residues: 179 loop : -0.70 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.018 0.002 TYR A 512 PHE 0.017 0.001 PHE A 764 TRP 0.011 0.002 TRP A 417 HIS 0.008 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 ( 6541) covalent geometry : angle 0.62058 / 0.32 ( 8862) hydrogen bonds : bond 0.03716 / 2.39 ( 281) hydrogen bonds : angle 5.31316 / 3.72 ( 819) *********************** 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: 41 poor density : 63 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 286 TYR cc_start: 0.8380 (t80) cc_final: 0.8161 (t80) REVERT: A 352 ASN cc_start: 0.8740 (m-40) cc_final: 0.8420 (m-40) REVERT: A 416 ASN cc_start: 0.8536 (p0) cc_final: 0.8063 (p0) REVERT: A 417 TRP cc_start: 0.6840 (m100) cc_final: 0.6625 (m100) REVERT: A 436 MET cc_start: 0.7257 (tpp) cc_final: 0.6968 (tpp) REVERT: A 531 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7118 (m) REVERT: A 533 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8901 (tmtt) REVERT: A 776 TYR cc_start: 0.8479 (m-10) cc_final: 0.7986 (m-80) outliers start: 41 outliers final: 31 residues processed: 98 average time/residue: 0.0604 time to fit residues: 8.5476 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 : 0.251 ------------------------------------------------------------------------------- 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 82 LYS 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 266 THR 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 374 LEU 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 531 VAL 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 633 ILE Chi-restraints excluded: chain A residue 636 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 GLN A 711 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.123958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093400 restraints weight = 15823.351| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.96 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2025 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= 0.141 Angle : 0.567 8.851 8862 Z= 0.293 Chirality : 0.045 0.206 986 Planarity : 0.003 0.031 1098 Dihedral : 9.223 63.839 916 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.56 % Allowed : 27.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.30), residues: 743 helix: 1.19 (0.33), residues: 251 sheet: -0.29 (0.36), residues: 185 loop : -0.63 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.014 0.001 TYR A 84 PHE 0.012 0.001 PHE A 476 TRP 0.013 0.001 TRP A 417 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6541) covalent geometry : angle 0.56746 / 0.29 ( 8862) hydrogen bonds : bond 0.03332 / 2.15 ( 281) hydrogen bonds : angle 5.15628 / 3.60 ( 819) *********************** 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 101 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7599 (mp) REVERT: A 352 ASN cc_start: 0.8690 (m-40) cc_final: 0.8250 (m110) REVERT: A 355 MET cc_start: 0.7936 (mpp) cc_final: 0.7268 (mpp) REVERT: A 416 ASN cc_start: 0.8506 (p0) cc_final: 0.8155 (p0) REVERT: A 436 MET cc_start: 0.7274 (tpp) cc_final: 0.7003 (tpp) REVERT: A 531 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.7075 (m) REVERT: A 533 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8874 (tmtt) outliers start: 32 outliers final: 26 residues processed: 95 average time/residue: 0.0620 time to fit residues: 8.6613 Evaluate side-chains 94 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 82 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 266 THR 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 531 VAL Chi-restraints excluded: chain A residue 533 LYS 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 632 ILE 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 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 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 17 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 801 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 = 0.4060 r_free = 0.4060 target = 0.124360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093643 restraints weight = 16073.053| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 5.01 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2045 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= 0.148 Angle : 0.577 10.858 8862 Z= 0.295 Chirality : 0.045 0.196 986 Planarity : 0.003 0.031 1098 Dihedral : 9.231 63.835 916 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.28 % Allowed : 27.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.30), residues: 743 helix: 1.20 (0.33), residues: 251 sheet: -0.27 (0.36), residues: 185 loop : -0.68 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 619 TYR 0.013 0.001 TYR A 84 PHE 0.010 0.001 PHE A 408 TRP 0.007 0.001 TRP A 417 HIS 0.007 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6541) covalent geometry : angle 0.57740 / 0.29 ( 8862) hydrogen bonds : bond 0.03296 / 2.13 ( 281) hydrogen bonds : angle 5.08871 / 3.56 ( 819) *********************** 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 95 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 352 ASN cc_start: 0.8687 (m-40) cc_final: 0.8236 (m110) REVERT: A 355 MET cc_start: 0.7882 (mpp) cc_final: 0.7219 (mpp) REVERT: A 416 ASN cc_start: 0.8397 (p0) cc_final: 0.7957 (p0) REVERT: A 436 MET cc_start: 0.7261 (tpp) cc_final: 0.6978 (tpp) REVERT: A 531 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7095 (m) REVERT: A 533 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8875 (tmtt) outliers start: 30 outliers final: 27 residues processed: 90 average time/residue: 0.0596 time to fit residues: 7.9357 Evaluate side-chains 91 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 82 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 266 THR 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 374 LEU 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 531 VAL Chi-restraints excluded: chain A residue 533 LYS 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 632 ILE 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 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 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 801 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 = 0.4071 r_free = 0.4071 target = 0.124960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094600 restraints weight = 15801.497| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.98 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2115 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= 0.127 Angle : 0.582 11.249 8862 Z= 0.296 Chirality : 0.045 0.197 986 Planarity : 0.003 0.031 1098 Dihedral : 9.186 63.834 916 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.28 % Allowed : 27.39 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.30), residues: 743 helix: 1.29 (0.33), residues: 251 sheet: -0.21 (0.36), residues: 185 loop : -0.69 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 619 TYR 0.011 0.001 TYR A 84 PHE 0.014 0.001 PHE A 476 TRP 0.007 0.001 TRP A 568 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6541) covalent geometry : angle 0.58160 / 0.30 ( 8862) hydrogen bonds : bond 0.03167 / 2.04 ( 281) hydrogen bonds : angle 5.02574 / 3.51 ( 819) ********************** 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 95 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7541 (mp) REVERT: A 352 ASN cc_start: 0.8650 (m-40) cc_final: 0.8216 (m110) REVERT: A 355 MET cc_start: 0.7879 (mpp) cc_final: 0.7223 (mpp) REVERT: A 417 TRP cc_start: 0.6321 (m100) cc_final: 0.6098 (m100) REVERT: A 436 MET cc_start: 0.7219 (tpp) cc_final: 0.6946 (tpp) REVERT: A 531 VAL cc_start: 0.7235 (OUTLIER) cc_final: 0.7028 (m) REVERT: A 533 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8866 (tmtt) outliers start: 30 outliers final: 27 residues processed: 90 average time/residue: 0.0607 time to fit residues: 8.2098 Evaluate side-chains 92 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 82 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 266 THR 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 374 LEU 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 531 VAL Chi-restraints excluded: chain A residue 533 LYS 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 632 ILE 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 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 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 0.0870 chunk 49 optimal weight: 0.0570 chunk 3 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 801 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 = 0.4065 r_free = 0.4065 target = 0.124729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094173 restraints weight = 15860.171| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.97 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6541 Z= 0.136 Angle : 0.578 11.015 8862 Z= 0.295 Chirality : 0.044 0.190 986 Planarity : 0.003 0.031 1098 Dihedral : 9.165 63.833 916 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.14 % Allowed : 27.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.30), residues: 743 helix: 1.33 (0.33), residues: 251 sheet: -0.19 (0.36), residues: 185 loop : -0.67 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 619 TYR 0.012 0.001 TYR A 249 PHE 0.010 0.001 PHE A 408 TRP 0.006 0.001 TRP A 568 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6541) covalent geometry : angle 0.57783 / 0.29 ( 8862) hydrogen bonds : bond 0.03125 / 2.01 ( 281) hydrogen bonds : angle 4.99031 / 3.49 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.04 seconds wall clock time: 22 minutes 47.46 seconds (1367.46 seconds total)