Starting phenix.real_space_refine on Fri Aug 22 18:14:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfx_33800/08_2025/7yfx_33800.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfx_33800/08_2025/7yfx_33800.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 { model { file = "/net/cci-nas-00/data/ceres_data/7yfx_33800/08_2025/7yfx_33800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfx_33800/08_2025/7yfx_33800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yfx_33800/08_2025/7yfx_33800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfx_33800/08_2025/7yfx_33800.map" } 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= -0.002 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 3989 2.51 5 N 1096 2.21 5 O 1170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 6319 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5999 Classifications: {'peptide': 746} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 707} Chain breaks: 1 Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna2p': 4, 'rna3p': 10} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" 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: 1.71, per 1000 atoms: 0.27 Number of scatterers: 6319 At special positions: 0 Unit cell: (84.0294, 115.271, 89.4159, 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 47 16.00 P 15 15.00 Mg 2 11.99 O 1170 8.00 N 1096 7.00 C 3989 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: 0.56 Conformation dependent library (CDL) restraints added in 316.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 9 sheets defined 37.1% alpha, 23.1% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.911A pdb=" N HIS A 264 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 318 through 334 removed outlier: 4.331A pdb=" N PHE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 524 through 542 Processing helix chain 'A' and resid 542 through 553 removed outlier: 4.741A pdb=" N TRP A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 4.010A pdb=" N THR A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.852A pdb=" N GLY A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 648 through 663 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 701 through 706 removed outlier: 4.062A pdb=" N GLN A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 725 Processing helix chain 'A' and resid 783 through 804 removed outlier: 4.150A pdb=" N SER A 787 " --> pdb=" O GLU A 783 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 790 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 828 through 835 removed outlier: 3.631A pdb=" N GLN A 832 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 835 " --> pdb=" O PRO A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 839 Processing helix chain 'A' and resid 916 through 928 removed outlier: 3.639A pdb=" N CYS A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 957 removed outlier: 3.523A pdb=" N ILE A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 removed outlier: 3.963A pdb=" N GLU A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 771 through 777 removed outlier: 3.955A pdb=" N SER A 763 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL A 741 " --> pdb=" O SER A 763 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET A 740 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A 813 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 742 " --> pdb=" O TYR A 813 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N MET A 847 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN A 911 " --> pdb=" O MET A 847 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 849 " --> pdb=" O VAL A 909 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 887 " --> pdb=" O CYS A 908 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER A 225 " --> pdb=" O ALA A 863 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.586A pdb=" N LEU A 357 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 344 removed outlier: 4.756A pdb=" N LEU A 374 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 555 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.592A pdb=" N LEU A 281 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 240 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE A 311 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN A 242 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 428 Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.723A pdb=" N LEU A 471 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 491 " --> pdb=" O HIS A 474 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.676A pdb=" N GLY A 731 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 644 removed outlier: 6.406A pdb=" N LEU A 608 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 644 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR A 610 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL A 669 " --> pdb=" O GLN A 697 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 699 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS A 671 " --> pdb=" O VAL A 699 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1465 1.33 - 1.45: 1327 1.45 - 1.57: 3595 1.57 - 1.69: 26 1.69 - 1.81: 74 Bond restraints: 6487 Sorted by residual: bond pdb=" O3' U B 2 " pdb=" P A B 3 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.50e-02 4.44e+03 1.81e+01 bond pdb=" P U B 2 " pdb=" OP2 U B 2 " ideal model delta sigma weight residual 1.485 1.418 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" P U B 2 " pdb=" OP1 U B 2 " ideal model delta sigma weight residual 1.485 1.427 0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" N ARG A 702 " pdb=" CA ARG A 702 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.21e-02 6.83e+03 6.35e+00 bond pdb=" N TYR A 681 " pdb=" CA TYR A 681 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.72e+00 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8510 1.83 - 3.66: 279 3.66 - 5.49: 51 5.49 - 7.32: 10 7.32 - 9.15: 1 Bond angle restraints: 8851 Sorted by residual: angle pdb=" C4' U B 2 " pdb=" C3' U B 2 " pdb=" O3' U B 2 " ideal model delta sigma weight residual 113.00 122.15 -9.15 1.50e+00 4.44e-01 3.72e+01 angle pdb=" C3' OMC B 26 " pdb=" C2' OMC B 26 " pdb=" C1' OMC B 26 " ideal model delta sigma weight residual 101.50 105.78 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" C3' U B 2 " pdb=" C2' U B 2 " pdb=" O2' U B 2 " ideal model delta sigma weight residual 110.70 104.81 5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" N THR A 880 " pdb=" CA THR A 880 " pdb=" CB THR A 880 " ideal model delta sigma weight residual 114.17 110.08 4.09 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C3' U B 2 " pdb=" C2' U B 2 " pdb=" C1' U B 2 " ideal model delta sigma weight residual 101.30 104.79 -3.49 1.00e+00 1.00e+00 1.22e+01 ... (remaining 8846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 3408 18.74 - 37.47: 414 37.47 - 56.21: 78 56.21 - 74.95: 25 74.95 - 93.68: 8 Dihedral angle restraints: 3933 sinusoidal: 1747 harmonic: 2186 Sorted by residual: dihedral pdb=" CA SER A 248 " pdb=" C SER A 248 " pdb=" N PRO A 249 " pdb=" CA PRO A 249 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ILE A 419 " pdb=" C ILE A 419 " pdb=" N THR A 420 " pdb=" CA THR A 420 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TRP A 588 " pdb=" C TRP A 588 " pdb=" N VAL A 589 " pdb=" CA VAL A 589 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 3930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 958 0.104 - 0.208: 51 0.208 - 0.311: 2 0.311 - 0.415: 0 0.415 - 0.519: 1 Chirality restraints: 1012 Sorted by residual: chirality pdb=" C3' U B 2 " pdb=" C4' U B 2 " pdb=" O3' U B 2 " pdb=" C2' U B 2 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.12 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ARG A 752 " pdb=" N ARG A 752 " pdb=" C ARG A 752 " pdb=" CB ARG A 752 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1009 not shown) Planarity restraints: 1068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " 0.039 2.00e-02 2.50e+03 2.45e-02 1.36e+01 pdb=" N1 U B 2 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U B 2 " -0.048 2.00e-02 2.50e+03 pdb=" O2 U B 2 " 0.016 2.00e-02 2.50e+03 pdb=" N3 U B 2 " 0.011 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U B 2 " 0.016 2.00e-02 2.50e+03 pdb=" C5 U B 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U B 2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 320 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO A 321 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 630 " -0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 631 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 631 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 631 " -0.035 5.00e-02 4.00e+02 ... (remaining 1065 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 63 2.56 - 3.14: 4880 3.14 - 3.73: 9395 3.73 - 4.31: 13160 4.31 - 4.90: 22133 Nonbonded interactions: 49631 Sorted by model distance: nonbonded pdb=" OP1 A B 3 " pdb="MG MG B1001 " model vdw 1.969 2.170 nonbonded pdb=" O LEU A 973 " pdb="MG MG B1001 " model vdw 1.974 2.170 nonbonded pdb=" OD2 ASP A 745 " pdb="MG MG A1001 " model vdw 2.111 2.170 nonbonded pdb=" NZ LYS A 949 " pdb=" OP1 C B 4 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR A 422 " pdb=" OP1 OMC B 26 " model vdw 2.231 3.040 ... (remaining 49626 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.300 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 : 0.005 0.067 6487 Z= 0.220 Angle : 0.794 9.147 8851 Z= 0.436 Chirality : 0.051 0.519 1012 Planarity : 0.007 0.081 1068 Dihedral : 16.956 93.682 2517 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.45 % Allowed : 20.47 % Favored : 79.08 % 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: -0.16 (0.29), residues: 742 helix: 0.80 (0.32), residues: 240 sheet: -0.21 (0.37), residues: 179 loop : -0.62 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.034 0.002 TYR A 460 PHE 0.041 0.002 PHE A 580 TRP 0.017 0.001 TRP A 552 HIS 0.003 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6487) covalent geometry : angle 0.79431 ( 8851) hydrogen bonds : bond 0.17908 ( 272) hydrogen bonds : angle 7.24935 ( 774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.6699 (m-30) cc_final: 0.6162 (m-30) REVERT: A 317 ASP cc_start: 0.6378 (m-30) cc_final: 0.6115 (m-30) REVERT: A 402 LYS cc_start: 0.7798 (mttt) cc_final: 0.7492 (ptpt) REVERT: A 434 TRP cc_start: 0.7166 (m100) cc_final: 0.6944 (m100) REVERT: A 507 MET cc_start: 0.4827 (tmt) cc_final: 0.4317 (tmt) REVERT: A 617 GLN cc_start: 0.7234 (mp10) cc_final: 0.7018 (mp10) REVERT: A 674 MET cc_start: 0.7032 (tpp) cc_final: 0.6824 (tpp) outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.0900 time to fit residues: 17.2708 Evaluate side-chains 110 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 401 ASN A 561 HIS ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.191403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149222 restraints weight = 8375.914| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.63 r_work: 0.3747 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6487 Z= 0.179 Angle : 0.636 7.879 8851 Z= 0.338 Chirality : 0.046 0.162 1012 Planarity : 0.006 0.057 1068 Dihedral : 12.515 95.700 1013 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.45 % Allowed : 17.95 % Favored : 77.60 % 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: 0.04 (0.29), residues: 742 helix: 1.40 (0.32), residues: 243 sheet: -0.44 (0.35), residues: 191 loop : -0.69 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 386 TYR 0.020 0.002 TYR A 772 PHE 0.020 0.002 PHE A 322 TRP 0.018 0.002 TRP A 588 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6487) covalent geometry : angle 0.63625 ( 8851) hydrogen bonds : bond 0.04466 ( 272) hydrogen bonds : angle 5.59623 ( 774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.6986 (m-30) cc_final: 0.6672 (m-30) REVERT: A 402 LYS cc_start: 0.7908 (mttt) cc_final: 0.7459 (ptpt) REVERT: A 507 MET cc_start: 0.5615 (tmt) cc_final: 0.4947 (tmt) outliers start: 30 outliers final: 18 residues processed: 131 average time/residue: 0.0881 time to fit residues: 15.2716 Evaluate side-chains 117 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN ** A 722 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 = 0.4333 r_free = 0.4333 target = 0.194362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153199 restraints weight = 8286.948| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.60 r_work: 0.3783 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6487 Z= 0.119 Angle : 0.548 6.991 8851 Z= 0.289 Chirality : 0.043 0.153 1012 Planarity : 0.005 0.055 1068 Dihedral : 11.836 96.356 1013 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.41 % Allowed : 19.73 % Favored : 76.85 % 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: 0.26 (0.30), residues: 742 helix: 1.65 (0.32), residues: 249 sheet: -0.30 (0.36), residues: 186 loop : -0.70 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 551 TYR 0.012 0.001 TYR A 772 PHE 0.017 0.002 PHE A 322 TRP 0.010 0.001 TRP A 606 HIS 0.003 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6487) covalent geometry : angle 0.54776 ( 8851) hydrogen bonds : bond 0.03566 ( 272) hydrogen bonds : angle 5.07623 ( 774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 436 LYS cc_start: 0.7786 (tptt) cc_final: 0.7493 (tptt) REVERT: A 507 MET cc_start: 0.5699 (tmt) cc_final: 0.5169 (tmt) REVERT: A 612 LYS cc_start: 0.8531 (tptp) cc_final: 0.8020 (tppt) REVERT: A 815 ASP cc_start: 0.7717 (t0) cc_final: 0.7477 (t70) REVERT: A 821 GLN cc_start: 0.7982 (mp10) cc_final: 0.7427 (pm20) REVERT: A 860 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7627 (pp) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 0.0939 time to fit residues: 15.1494 Evaluate side-chains 114 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 722 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 = 0.4268 r_free = 0.4268 target = 0.187209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.146723 restraints weight = 8521.740| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.69 r_work: 0.3688 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6487 Z= 0.242 Angle : 0.677 10.230 8851 Z= 0.351 Chirality : 0.048 0.158 1012 Planarity : 0.006 0.062 1068 Dihedral : 12.026 101.518 1012 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.49 % Allowed : 21.96 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.30), residues: 742 helix: 1.42 (0.33), residues: 236 sheet: -0.52 (0.36), residues: 178 loop : -0.80 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 295 TYR 0.024 0.002 TYR A 772 PHE 0.021 0.002 PHE A 760 TRP 0.017 0.002 TRP A 588 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 6487) covalent geometry : angle 0.67703 ( 8851) hydrogen bonds : bond 0.04503 ( 272) hydrogen bonds : angle 5.48961 ( 774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 350 MET cc_start: 0.8016 (tpp) cc_final: 0.7796 (tpt) REVERT: A 436 LYS cc_start: 0.7718 (tptt) cc_final: 0.7514 (tptt) REVERT: A 439 LYS cc_start: 0.8142 (tppt) cc_final: 0.7777 (pttt) REVERT: A 507 MET cc_start: 0.5653 (tmt) cc_final: 0.5129 (tmt) REVERT: A 738 GLN cc_start: 0.8626 (mp10) cc_final: 0.8294 (mp10) REVERT: A 860 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7825 (pp) REVERT: A 930 MET cc_start: 0.7862 (mtt) cc_final: 0.7660 (mtt) outliers start: 37 outliers final: 25 residues processed: 131 average time/residue: 0.0839 time to fit residues: 14.6540 Evaluate side-chains 118 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 73 optimal weight: 0.0040 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.192604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150706 restraints weight = 8481.290| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.57 r_work: 0.3758 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6487 Z= 0.122 Angle : 0.549 5.843 8851 Z= 0.289 Chirality : 0.043 0.151 1012 Planarity : 0.005 0.060 1068 Dihedral : 11.680 101.512 1010 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.01 % Allowed : 23.74 % Favored : 72.26 % 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: 0.22 (0.31), residues: 742 helix: 1.74 (0.33), residues: 242 sheet: -0.34 (0.37), residues: 176 loop : -0.75 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 613 TYR 0.016 0.001 TYR A 243 PHE 0.017 0.002 PHE A 322 TRP 0.016 0.001 TRP A 588 HIS 0.004 0.000 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6487) covalent geometry : angle 0.54890 ( 8851) hydrogen bonds : bond 0.03386 ( 272) hydrogen bonds : angle 5.03467 ( 774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 SER cc_start: 0.7333 (OUTLIER) cc_final: 0.7133 (p) REVERT: A 436 LYS cc_start: 0.7785 (tptt) cc_final: 0.7529 (tptt) REVERT: A 439 LYS cc_start: 0.8099 (tppt) cc_final: 0.7767 (pttt) REVERT: A 507 MET cc_start: 0.5780 (tmt) cc_final: 0.5275 (tmt) REVERT: A 612 LYS cc_start: 0.8677 (tptp) cc_final: 0.8148 (tppt) REVERT: A 738 GLN cc_start: 0.8474 (mp10) cc_final: 0.8263 (mp10) REVERT: A 821 GLN cc_start: 0.7928 (mp10) cc_final: 0.7400 (pm20) REVERT: A 860 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7610 (pp) outliers start: 27 outliers final: 18 residues processed: 121 average time/residue: 0.0853 time to fit residues: 13.7751 Evaluate side-chains 119 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 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 = 0.4288 r_free = 0.4288 target = 0.188860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.149039 restraints weight = 8498.363| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.62 r_work: 0.3719 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6487 Z= 0.197 Angle : 0.602 7.935 8851 Z= 0.314 Chirality : 0.045 0.150 1012 Planarity : 0.005 0.058 1068 Dihedral : 11.723 102.875 1010 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.45 % Allowed : 22.40 % Favored : 73.15 % 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: -0.06 (0.30), residues: 742 helix: 1.60 (0.33), residues: 236 sheet: -0.56 (0.37), residues: 178 loop : -0.90 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 613 TYR 0.025 0.002 TYR A 422 PHE 0.020 0.002 PHE A 760 TRP 0.019 0.002 TRP A 932 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6487) covalent geometry : angle 0.60160 ( 8851) hydrogen bonds : bond 0.03904 ( 272) hydrogen bonds : angle 5.30852 ( 774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 LYS cc_start: 0.7746 (tptt) cc_final: 0.7510 (tptt) REVERT: A 439 LYS cc_start: 0.8115 (tppt) cc_final: 0.7759 (pttt) REVERT: A 507 MET cc_start: 0.5716 (tmt) cc_final: 0.5249 (tmt) REVERT: A 612 LYS cc_start: 0.8720 (tptp) cc_final: 0.8229 (tppt) REVERT: A 860 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7779 (pp) REVERT: A 884 CYS cc_start: 0.8614 (p) cc_final: 0.7964 (t) outliers start: 30 outliers final: 25 residues processed: 120 average time/residue: 0.0870 time to fit residues: 13.9359 Evaluate side-chains 120 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.0570 chunk 36 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.194072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152542 restraints weight = 8409.434| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.57 r_work: 0.3781 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6487 Z= 0.110 Angle : 0.542 7.244 8851 Z= 0.281 Chirality : 0.042 0.145 1012 Planarity : 0.005 0.056 1068 Dihedral : 11.467 101.841 1010 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.15 % Allowed : 23.15 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 742 helix: 1.97 (0.34), residues: 236 sheet: -0.43 (0.37), residues: 178 loop : -0.87 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 613 TYR 0.020 0.001 TYR A 243 PHE 0.016 0.002 PHE A 322 TRP 0.014 0.001 TRP A 932 HIS 0.004 0.000 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6487) covalent geometry : angle 0.54151 ( 8851) hydrogen bonds : bond 0.03170 ( 272) hydrogen bonds : angle 5.00043 ( 774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8030 (tppt) cc_final: 0.7794 (pttt) REVERT: A 507 MET cc_start: 0.5660 (tmt) cc_final: 0.5282 (tmt) REVERT: A 522 ASN cc_start: 0.7220 (t0) cc_final: 0.6956 (m-40) REVERT: A 570 MET cc_start: 0.7620 (mmp) cc_final: 0.7087 (mtp) REVERT: A 612 LYS cc_start: 0.8597 (tptp) cc_final: 0.8216 (tppt) REVERT: A 634 MET cc_start: 0.7012 (mmm) cc_final: 0.6792 (mmt) REVERT: A 648 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7212 (mtp180) REVERT: A 821 GLN cc_start: 0.7861 (mp10) cc_final: 0.7341 (pm20) REVERT: A 860 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7670 (pp) outliers start: 28 outliers final: 19 residues processed: 130 average time/residue: 0.0877 time to fit residues: 15.0326 Evaluate side-chains 121 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A 969 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.191534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149385 restraints weight = 8276.149| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.69 r_work: 0.3706 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6487 Z= 0.103 Angle : 0.528 5.322 8851 Z= 0.277 Chirality : 0.041 0.143 1012 Planarity : 0.005 0.054 1068 Dihedral : 11.318 99.870 1010 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.26 % Allowed : 24.93 % Favored : 71.81 % 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 (0.31), residues: 742 helix: 2.05 (0.34), residues: 236 sheet: -0.31 (0.38), residues: 177 loop : -0.80 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.015 0.001 TYR A 243 PHE 0.015 0.001 PHE A 760 TRP 0.019 0.001 TRP A 932 HIS 0.003 0.000 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6487) covalent geometry : angle 0.52824 ( 8851) hydrogen bonds : bond 0.03087 ( 272) hydrogen bonds : angle 4.90683 ( 774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.5768 (tmt) cc_final: 0.5323 (tmt) REVERT: A 522 ASN cc_start: 0.7323 (t0) cc_final: 0.7047 (m-40) REVERT: A 570 MET cc_start: 0.7832 (mmp) cc_final: 0.7142 (mtp) REVERT: A 612 LYS cc_start: 0.8590 (tptp) cc_final: 0.8214 (tppt) REVERT: A 648 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7274 (mtp180) REVERT: A 821 GLN cc_start: 0.7988 (mp10) cc_final: 0.7360 (pm20) REVERT: A 854 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8302 (mtmm) REVERT: A 860 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7716 (pp) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.1013 time to fit residues: 16.0994 Evaluate side-chains 124 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 0.0270 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 GLN ** A 722 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 = 0.4283 r_free = 0.4283 target = 0.188515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146479 restraints weight = 8466.979| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.65 r_work: 0.3709 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6487 Z= 0.181 Angle : 0.613 8.040 8851 Z= 0.317 Chirality : 0.044 0.172 1012 Planarity : 0.005 0.056 1068 Dihedral : 11.456 101.283 1010 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.56 % Allowed : 25.07 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 742 helix: 1.89 (0.34), residues: 230 sheet: -0.50 (0.38), residues: 179 loop : -0.83 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 295 TYR 0.021 0.002 TYR A 931 PHE 0.021 0.002 PHE A 850 TRP 0.017 0.002 TRP A 932 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6487) covalent geometry : angle 0.61313 ( 8851) hydrogen bonds : bond 0.03739 ( 272) hydrogen bonds : angle 5.21897 ( 774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.5655 (tmt) cc_final: 0.5215 (tmt) REVERT: A 612 LYS cc_start: 0.8634 (tptp) cc_final: 0.8266 (tppt) REVERT: A 648 ARG cc_start: 0.7628 (mtm180) cc_final: 0.7346 (mtp180) REVERT: A 738 GLN cc_start: 0.8578 (mp10) cc_final: 0.8349 (mp10) REVERT: A 860 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7833 (pp) REVERT: A 884 CYS cc_start: 0.8670 (p) cc_final: 0.8034 (t) outliers start: 24 outliers final: 17 residues processed: 122 average time/residue: 0.0896 time to fit residues: 14.4014 Evaluate side-chains 120 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 0.0270 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 ASN A 697 GLN ** A 722 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 = 0.4313 r_free = 0.4313 target = 0.191471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.149995 restraints weight = 8309.213| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.63 r_work: 0.3754 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6487 Z= 0.132 Angle : 0.573 6.062 8851 Z= 0.299 Chirality : 0.043 0.163 1012 Planarity : 0.005 0.056 1068 Dihedral : 11.411 101.556 1010 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.41 % Allowed : 24.78 % Favored : 71.81 % 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: 0.17 (0.30), residues: 742 helix: 1.87 (0.34), residues: 236 sheet: -0.39 (0.38), residues: 177 loop : -0.88 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 386 TYR 0.016 0.001 TYR A 813 PHE 0.019 0.002 PHE A 850 TRP 0.015 0.001 TRP A 932 HIS 0.003 0.000 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6487) covalent geometry : angle 0.57310 ( 8851) hydrogen bonds : bond 0.03406 ( 272) hydrogen bonds : angle 5.03631 ( 774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.5664 (tmt) cc_final: 0.5276 (tmt) REVERT: A 522 ASN cc_start: 0.7538 (m110) cc_final: 0.7308 (m-40) REVERT: A 612 LYS cc_start: 0.8580 (tptp) cc_final: 0.8239 (tppt) REVERT: A 648 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7373 (mtp180) REVERT: A 738 GLN cc_start: 0.8504 (mp10) cc_final: 0.8250 (mp10) REVERT: A 821 GLN cc_start: 0.7911 (mp10) cc_final: 0.7349 (pm20) REVERT: A 860 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7824 (pp) REVERT: A 884 CYS cc_start: 0.8640 (p) cc_final: 0.7993 (t) outliers start: 23 outliers final: 20 residues processed: 119 average time/residue: 0.0771 time to fit residues: 12.1963 Evaluate side-chains 123 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 70 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.192516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151277 restraints weight = 8357.784| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.58 r_work: 0.3773 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6487 Z= 0.126 Angle : 0.562 5.693 8851 Z= 0.294 Chirality : 0.043 0.150 1012 Planarity : 0.005 0.055 1068 Dihedral : 11.361 101.584 1010 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.41 % Allowed : 25.22 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.30), residues: 742 helix: 1.97 (0.34), residues: 236 sheet: -0.37 (0.38), residues: 177 loop : -0.88 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 551 TYR 0.016 0.001 TYR A 813 PHE 0.019 0.002 PHE A 850 TRP 0.016 0.001 TRP A 932 HIS 0.003 0.000 HIS A 929 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6487) covalent geometry : angle 0.56236 ( 8851) hydrogen bonds : bond 0.03284 ( 272) hydrogen bonds : angle 4.98402 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.81 seconds wall clock time: 27 minutes 53.50 seconds (1673.50 seconds total)