Starting phenix.real_space_refine on Fri Aug 22 17:35:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3z_18878/08_2025/8r3z_18878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3z_18878/08_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_18878/08_2025/8r3z_18878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3z_18878/08_2025/8r3z_18878.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3z_18878/08_2025/8r3z_18878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3z_18878/08_2025/8r3z_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.64, per 1000 atoms: 0.26 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: 0.58 Conformation dependent library (CDL) restraints added in 397.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.28 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: 0.80 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: 4.040 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.280 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.810 ------------------------------------------------------------------------------- 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= 0.177 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00361 ( 6541) covalent geometry : angle 0.65293 ( 8862) hydrogen bonds : bond 0.14283 ( 281) hydrogen bonds : angle 6.62200 ( 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 : 0.251 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: 0.0701 time to fit residues: 8.3685 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 : 0.203 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 234 HIS A 528 GLN A 551 GLN A 707 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.127133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097841 restraints weight = 15348.418| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 4.47 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6541 Z= 0.172 Angle : 0.557 7.114 8862 Z= 0.294 Chirality : 0.045 0.174 986 Planarity : 0.004 0.068 1098 Dihedral : 9.392 63.849 916 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.85 % Allowed : 24.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.30), residues: 743 helix: 1.19 (0.32), residues: 249 sheet: -0.18 (0.36), residues: 187 loop : -0.77 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.015 0.001 TYR A 816 PHE 0.015 0.001 PHE A 408 TRP 0.018 0.002 TRP A 568 HIS 0.007 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 6541) covalent geometry : angle 0.55683 ( 8862) hydrogen bonds : bond 0.03717 ( 281) hydrogen bonds : angle 5.40331 ( 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 106 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8986 (pttm) REVERT: A 84 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: A 85 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: A 206 GLU cc_start: 0.8481 (tt0) cc_final: 0.8263 (tt0) REVERT: A 224 MET cc_start: 0.9124 (mmm) cc_final: 0.8536 (mmm) REVERT: A 391 MET cc_start: 0.6748 (ttt) cc_final: 0.6413 (ttt) REVERT: A 417 TRP cc_start: 0.6935 (m100) cc_final: 0.6423 (m100) outliers start: 34 outliers final: 19 residues processed: 101 average time/residue: 0.0644 time to fit residues: 9.0992 Evaluate side-chains 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 246 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 544 ILE Chi-restraints excluded: chain A residue 574 SER 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 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 40 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 517 GLN A 551 GLN A 777 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.121913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090857 restraints weight = 16025.306| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.93 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6541 Z= 0.247 Angle : 0.601 6.746 8862 Z= 0.313 Chirality : 0.045 0.146 986 Planarity : 0.004 0.046 1098 Dihedral : 9.373 63.935 916 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.56 % Allowed : 25.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.30), residues: 743 helix: 1.02 (0.32), residues: 252 sheet: -0.30 (0.37), residues: 179 loop : -0.77 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 619 TYR 0.013 0.002 TYR A 816 PHE 0.028 0.002 PHE A 408 TRP 0.011 0.002 TRP A 568 HIS 0.010 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 6541) covalent geometry : angle 0.60091 ( 8862) hydrogen bonds : bond 0.03825 ( 281) hydrogen bonds : angle 5.37680 ( 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 105 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 66 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9249 (mmtt) cc_final: 0.8808 (mmmt) REVERT: A 224 MET cc_start: 0.9265 (mmm) cc_final: 0.8832 (mmm) REVERT: A 352 ASN cc_start: 0.8784 (m-40) cc_final: 0.8355 (m-40) REVERT: A 355 MET cc_start: 0.7899 (mpp) cc_final: 0.7286 (mpp) REVERT: A 416 ASN cc_start: 0.8591 (p0) cc_final: 0.8046 (p0) REVERT: A 417 TRP cc_start: 0.6785 (m100) cc_final: 0.6495 (m100) outliers start: 39 outliers final: 27 residues processed: 101 average time/residue: 0.0537 time to fit residues: 7.9182 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 633 ILE Chi-restraints excluded: chain A residue 636 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.124149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093487 restraints weight = 15849.014| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.92 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1980 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= 0.137 Angle : 0.524 7.353 8862 Z= 0.272 Chirality : 0.044 0.144 986 Planarity : 0.003 0.034 1098 Dihedral : 9.307 63.909 916 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.14 % Allowed : 27.25 % Favored : 68.62 % 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 aren not related in a simple way. whole: 0.09 (0.30), residues: 743 helix: 1.25 (0.33), residues: 251 sheet: -0.20 (0.37), residues: 185 loop : -0.68 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 619 TYR 0.014 0.001 TYR A 46 PHE 0.019 0.001 PHE A 408 TRP 0.010 0.001 TRP A 417 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6541) covalent geometry : angle 0.52359 ( 8862) hydrogen bonds : bond 0.03219 ( 281) hydrogen bonds : angle 5.05357 ( 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 100 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 82 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8792 (mmmt) REVERT: A 224 MET cc_start: 0.9277 (mmm) cc_final: 0.8857 (mmm) REVERT: A 352 ASN cc_start: 0.8759 (m-40) cc_final: 0.8306 (m110) REVERT: A 355 MET cc_start: 0.7894 (mpp) cc_final: 0.7247 (mpp) REVERT: A 416 ASN cc_start: 0.8518 (p0) cc_final: 0.8064 (p0) REVERT: A 417 TRP cc_start: 0.6787 (m100) cc_final: 0.6553 (m100) REVERT: A 533 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8862 (tmtt) outliers start: 29 outliers final: 18 residues processed: 95 average time/residue: 0.0554 time to fit residues: 7.6172 Evaluate side-chains 85 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 533 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 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 = 0.4028 r_free = 0.4028 target = 0.122614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.091497 restraints weight = 16167.785| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 4.96 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2213 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= 0.189 Angle : 0.557 7.744 8862 Z= 0.288 Chirality : 0.044 0.155 986 Planarity : 0.003 0.029 1098 Dihedral : 9.243 64.058 916 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.85 % Allowed : 25.96 % 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 aren not related in a simple way. whole: 0.05 (0.30), residues: 743 helix: 1.28 (0.33), residues: 248 sheet: -0.27 (0.37), residues: 179 loop : -0.71 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 619 TYR 0.013 0.001 TYR A 249 PHE 0.019 0.001 PHE A 408 TRP 0.012 0.002 TRP A 417 HIS 0.008 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6541) covalent geometry : angle 0.55707 ( 8862) hydrogen bonds : bond 0.03349 ( 281) hydrogen bonds : angle 5.12660 ( 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 104 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 63 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 82 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8795 (mmmt) REVERT: A 84 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8192 (m-10) REVERT: A 206 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: A 224 MET cc_start: 0.9286 (mmm) cc_final: 0.8880 (mmm) REVERT: A 355 MET cc_start: 0.7966 (mpp) cc_final: 0.7289 (mpp) REVERT: A 416 ASN cc_start: 0.8477 (p0) cc_final: 0.8076 (p0) REVERT: A 417 TRP cc_start: 0.6826 (m100) cc_final: 0.6583 (m100) REVERT: A 431 GLU cc_start: 0.9053 (mp0) cc_final: 0.8804 (mp0) REVERT: A 533 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.8883 (tmtt) outliers start: 41 outliers final: 29 residues processed: 98 average time/residue: 0.0622 time to fit residues: 8.3468 Evaluate side-chains 92 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 84 TYR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 206 GLU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.119816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.088565 restraints weight = 16370.768| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.87 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 6541 Z= 0.317 Angle : 0.659 10.306 8862 Z= 0.341 Chirality : 0.047 0.171 986 Planarity : 0.004 0.038 1098 Dihedral : 9.449 64.191 916 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.28 % Allowed : 26.11 % Favored : 67.62 % 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 aren not related in a simple way. whole: -0.27 (0.30), residues: 743 helix: 0.95 (0.32), residues: 252 sheet: -0.56 (0.36), residues: 184 loop : -0.78 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 619 TYR 0.015 0.002 TYR A 754 PHE 0.019 0.002 PHE A 764 TRP 0.015 0.002 TRP A 417 HIS 0.016 0.002 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00724 ( 6541) covalent geometry : angle 0.65893 ( 8862) hydrogen bonds : bond 0.03872 ( 281) hydrogen bonds : angle 5.45023 ( 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 109 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 65 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7646 (mp) REVERT: A 82 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8795 (mmmt) REVERT: A 84 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: A 333 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 355 MET cc_start: 0.7980 (mpp) cc_final: 0.7295 (mpp) REVERT: A 416 ASN cc_start: 0.8386 (p0) cc_final: 0.8128 (p0) REVERT: A 417 TRP cc_start: 0.6882 (m100) cc_final: 0.6659 (m100) REVERT: A 533 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.8971 (tmtt) REVERT: A 776 TYR cc_start: 0.8573 (m-10) cc_final: 0.8075 (m-80) outliers start: 44 outliers final: 34 residues processed: 103 average time/residue: 0.0551 time to fit residues: 8.2338 Evaluate side-chains 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 84 TYR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 206 GLU 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 374 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 437 ILE 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 679 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN A 645 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.124555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093770 restraints weight = 16041.846| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.97 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6541 Z= 0.122 Angle : 0.549 8.516 8862 Z= 0.280 Chirality : 0.045 0.189 986 Planarity : 0.003 0.043 1098 Dihedral : 9.280 63.965 916 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.71 % Allowed : 27.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.30), residues: 743 helix: 1.32 (0.33), residues: 248 sheet: -0.39 (0.37), residues: 184 loop : -0.74 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 619 TYR 0.010 0.001 TYR A 46 PHE 0.012 0.001 PHE A 408 TRP 0.014 0.001 TRP A 417 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6541) covalent geometry : angle 0.54863 ( 8862) hydrogen bonds : bond 0.03121 ( 281) hydrogen bonds : angle 5.02684 ( 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 96 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7552 (mp) REVERT: A 84 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: A 355 MET cc_start: 0.7912 (mpp) cc_final: 0.7230 (mpp) REVERT: A 416 ASN cc_start: 0.8377 (p0) cc_final: 0.7653 (t0) REVERT: A 533 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8848 (tmtt) outliers start: 33 outliers final: 23 residues processed: 93 average time/residue: 0.0551 time to fit residues: 7.4003 Evaluate side-chains 84 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 84 TYR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 ASP 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 533 LYS 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 679 ASN 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 774 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.123037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.092221 restraints weight = 16077.666| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.94 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2590 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= 0.163 Angle : 0.572 10.397 8862 Z= 0.291 Chirality : 0.045 0.200 986 Planarity : 0.003 0.046 1098 Dihedral : 9.211 63.959 916 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.42 % Allowed : 28.10 % Favored : 67.48 % 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 aren not related in a simple way. whole: 0.07 (0.30), residues: 743 helix: 1.39 (0.33), residues: 248 sheet: -0.35 (0.37), residues: 184 loop : -0.72 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 619 TYR 0.013 0.001 TYR A 512 PHE 0.013 0.001 PHE A 408 TRP 0.007 0.001 TRP A 587 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6541) covalent geometry : angle 0.57215 ( 8862) hydrogen bonds : bond 0.03159 ( 281) hydrogen bonds : angle 5.02526 ( 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 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7533 (mp) REVERT: A 82 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8909 (mmmt) REVERT: A 84 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8126 (m-10) REVERT: A 355 MET cc_start: 0.7965 (mpp) cc_final: 0.7262 (mpp) REVERT: A 533 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8854 (tmtt) outliers start: 31 outliers final: 25 residues processed: 87 average time/residue: 0.0520 time to fit residues: 6.6039 Evaluate side-chains 84 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 84 TYR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 ASP 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 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 531 VAL Chi-restraints excluded: chain A residue 533 LYS 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 679 ASN 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 774 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.124758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094192 restraints weight = 16121.597| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.95 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6541 Z= 0.127 Angle : 0.560 10.810 8862 Z= 0.282 Chirality : 0.044 0.206 986 Planarity : 0.003 0.042 1098 Dihedral : 9.148 63.897 916 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.85 % Allowed : 28.67 % Favored : 67.48 % 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 aren not related in a simple way. whole: 0.24 (0.30), residues: 743 helix: 1.58 (0.33), residues: 248 sheet: -0.22 (0.38), residues: 184 loop : -0.71 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 619 TYR 0.013 0.001 TYR A 249 PHE 0.011 0.001 PHE A 408 TRP 0.008 0.001 TRP A 568 HIS 0.007 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6541) covalent geometry : angle 0.56000 ( 8862) hydrogen bonds : bond 0.02928 ( 281) hydrogen bonds : angle 4.87149 ( 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 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 82 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8907 (mmmt) REVERT: A 84 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: A 224 MET cc_start: 0.9142 (mmm) cc_final: 0.8528 (mmm) REVERT: A 417 TRP cc_start: 0.6454 (m100) cc_final: 0.6178 (m100) REVERT: A 533 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8853 (tmtt) outliers start: 27 outliers final: 22 residues processed: 84 average time/residue: 0.0588 time to fit residues: 7.0828 Evaluate side-chains 83 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 84 TYR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 ASP 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 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 533 LYS 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 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 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.123661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093008 restraints weight = 15924.758| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.93 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6541 Z= 0.152 Angle : 0.574 10.427 8862 Z= 0.288 Chirality : 0.045 0.206 986 Planarity : 0.003 0.039 1098 Dihedral : 9.119 63.945 916 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.71 % Allowed : 28.25 % 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 aren not related in a simple way. whole: 0.25 (0.30), residues: 743 helix: 1.62 (0.33), residues: 248 sheet: -0.23 (0.37), residues: 184 loop : -0.71 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 619 TYR 0.014 0.001 TYR A 249 PHE 0.012 0.001 PHE A 408 TRP 0.007 0.001 TRP A 587 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6541) covalent geometry : angle 0.57448 ( 8862) hydrogen bonds : bond 0.03053 ( 281) hydrogen bonds : angle 4.91592 ( 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 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 82 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8911 (mmmt) REVERT: A 84 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.8137 (m-10) REVERT: A 224 MET cc_start: 0.9167 (mmm) cc_final: 0.8566 (mmm) REVERT: A 355 MET cc_start: 0.7937 (mpp) cc_final: 0.7258 (mpp) REVERT: A 417 TRP cc_start: 0.6477 (m100) cc_final: 0.6198 (m100) REVERT: A 533 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8875 (tmtt) outliers start: 26 outliers final: 23 residues processed: 85 average time/residue: 0.0622 time to fit residues: 7.5985 Evaluate side-chains 84 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 84 TYR 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 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 533 LYS 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 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 64 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.125558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.095135 restraints weight = 15858.440| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 4.94 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6541 Z= 0.116 Angle : 0.571 10.432 8862 Z= 0.283 Chirality : 0.044 0.209 986 Planarity : 0.003 0.038 1098 Dihedral : 9.098 63.887 916 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.85 % Allowed : 28.53 % Favored : 67.62 % 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 aren not related in a simple way. whole: 0.33 (0.30), residues: 743 helix: 1.74 (0.33), residues: 248 sheet: -0.21 (0.38), residues: 177 loop : -0.69 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 619 TYR 0.012 0.001 TYR A 249 PHE 0.010 0.001 PHE A 408 TRP 0.008 0.001 TRP A 568 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6541) covalent geometry : angle 0.57087 ( 8862) hydrogen bonds : bond 0.02849 ( 281) hydrogen bonds : angle 4.83000 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.20 seconds wall clock time: 21 minutes 26.18 seconds (1286.18 seconds total)