Starting phenix.real_space_refine on Fri Dec 27 21:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfx_33800/12_2024/7yfx_33800.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfx_33800/12_2024/7yfx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfx_33800/12_2024/7yfx_33800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfx_33800/12_2024/7yfx_33800.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfx_33800/12_2024/7yfx_33800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfx_33800/12_2024/7yfx_33800.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 4.36, per 1000 atoms: 0.69 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: 1.91 Conformation dependent library (CDL) restraints added in 944.6 milliseconds 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: 2.18 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: 2.49 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.620 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- 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= 0.307 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 TRP 0.017 0.001 TRP A 552 HIS 0.003 0.001 HIS A 395 PHE 0.041 0.002 PHE A 580 TYR 0.034 0.002 TYR A 460 ARG 0.003 0.000 ARG A 295 *********************** 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 : 0.742 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: 0.2045 time to fit residues: 39.0113 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 : 0.655 ------------------------------------------------------------------------------- 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 63 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6487 Z= 0.353 Angle : 0.683 8.516 8851 Z= 0.361 Chirality : 0.047 0.156 1012 Planarity : 0.006 0.057 1068 Dihedral : 12.567 97.054 1013 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.45 % Allowed : 18.55 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.30), residues: 742 helix: 1.28 (0.32), residues: 238 sheet: -0.43 (0.36), residues: 190 loop : -0.59 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 588 HIS 0.007 0.001 HIS A 929 PHE 0.022 0.002 PHE A 322 TYR 0.023 0.002 TYR A 772 ARG 0.004 0.001 ARG A 295 *********************** 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 135 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.6748 (m-30) cc_final: 0.6333 (m-30) REVERT: A 308 MET cc_start: 0.7007 (pmm) cc_final: 0.6689 (pmm) REVERT: A 402 LYS cc_start: 0.8064 (mttt) cc_final: 0.7671 (ptpt) REVERT: A 507 MET cc_start: 0.4673 (tmt) cc_final: 0.4235 (tmt) REVERT: A 674 MET cc_start: 0.6981 (tpp) cc_final: 0.6752 (tpp) outliers start: 30 outliers final: 19 residues processed: 126 average time/residue: 0.1828 time to fit residues: 31.0329 Evaluate side-chains 116 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 385 ILE 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 721 ILE 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 37 optimal weight: 0.0000 chunk 21 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 542 ASN ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6487 Z= 0.167 Angle : 0.541 6.877 8851 Z= 0.286 Chirality : 0.043 0.156 1012 Planarity : 0.005 0.056 1068 Dihedral : 11.823 97.579 1013 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.26 % Allowed : 20.62 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 742 helix: 1.63 (0.33), residues: 248 sheet: -0.33 (0.36), residues: 186 loop : -0.72 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 606 HIS 0.003 0.000 HIS A 929 PHE 0.016 0.002 PHE A 322 TYR 0.013 0.001 TYR A 422 ARG 0.005 0.000 ARG A 551 *********************** 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 141 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 234 GLN cc_start: 0.6970 (tt0) cc_final: 0.6753 (tt0) REVERT: A 433 ASP cc_start: 0.3778 (p0) cc_final: 0.3547 (p0) REVERT: A 507 MET cc_start: 0.5029 (tmt) cc_final: 0.4687 (tmt) REVERT: A 815 ASP cc_start: 0.7300 (t0) cc_final: 0.6938 (t70) REVERT: A 821 GLN cc_start: 0.7699 (mp10) cc_final: 0.7331 (pm20) REVERT: A 860 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7386 (pp) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.1992 time to fit residues: 34.0149 Evaluate side-chains 114 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 271 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 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 67 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6487 Z= 0.298 Angle : 0.615 8.119 8851 Z= 0.320 Chirality : 0.045 0.150 1012 Planarity : 0.005 0.059 1068 Dihedral : 11.880 100.991 1012 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.34 % Allowed : 21.07 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.30), residues: 742 helix: 1.77 (0.33), residues: 236 sheet: -0.44 (0.35), residues: 189 loop : -0.83 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 588 HIS 0.006 0.001 HIS A 929 PHE 0.020 0.002 PHE A 760 TYR 0.019 0.002 TYR A 772 ARG 0.006 0.001 ARG A 329 *********************** 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 136 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 316 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.7851 (m) REVERT: A 436 LYS cc_start: 0.7552 (tptt) cc_final: 0.7268 (tptt) REVERT: A 439 LYS cc_start: 0.7917 (tppt) cc_final: 0.7704 (pttt) REVERT: A 471 LEU cc_start: 0.5169 (mp) cc_final: 0.4950 (mp) REVERT: A 507 MET cc_start: 0.5118 (tmt) cc_final: 0.4791 (tmt) REVERT: A 551 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7843 (mtm-85) REVERT: A 860 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7600 (pp) outliers start: 36 outliers final: 21 residues processed: 127 average time/residue: 0.1777 time to fit residues: 30.5728 Evaluate side-chains 118 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 316 SER 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 417 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 570 MET 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 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 883 SER Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3413 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= 0.185 Angle : 0.542 6.834 8851 Z= 0.285 Chirality : 0.043 0.152 1012 Planarity : 0.005 0.057 1068 Dihedral : 11.643 100.898 1010 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.56 % Allowed : 23.44 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.30), residues: 742 helix: 1.90 (0.34), residues: 242 sheet: -0.18 (0.37), residues: 176 loop : -0.83 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 932 HIS 0.004 0.000 HIS A 929 PHE 0.017 0.002 PHE A 322 TYR 0.018 0.001 TYR A 931 ARG 0.005 0.000 ARG A 329 *********************** 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 130 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 436 LYS cc_start: 0.7839 (tptt) cc_final: 0.7571 (tptt) REVERT: A 439 LYS cc_start: 0.7879 (tppt) cc_final: 0.7576 (pttt) REVERT: A 507 MET cc_start: 0.5108 (tmt) cc_final: 0.4785 (tmt) REVERT: A 612 LYS cc_start: 0.8502 (tptp) cc_final: 0.8056 (tppt) REVERT: A 815 ASP cc_start: 0.7321 (t0) cc_final: 0.7109 (t0) REVERT: A 821 GLN cc_start: 0.7700 (mp10) cc_final: 0.7329 (pm20) REVERT: A 854 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8326 (mtmm) REVERT: A 860 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7472 (pp) outliers start: 24 outliers final: 18 residues processed: 121 average time/residue: 0.1957 time to fit residues: 31.2006 Evaluate side-chains 123 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 417 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 570 MET 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 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 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 65 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3716 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= 0.314 Angle : 0.604 8.343 8851 Z= 0.316 Chirality : 0.045 0.173 1012 Planarity : 0.005 0.058 1068 Dihedral : 11.714 102.635 1010 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.60 % Allowed : 22.40 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.30), residues: 742 helix: 1.77 (0.33), residues: 236 sheet: -0.39 (0.38), residues: 178 loop : -0.91 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 932 HIS 0.006 0.001 HIS A 929 PHE 0.021 0.002 PHE A 760 TYR 0.019 0.002 TYR A 772 ARG 0.009 0.001 ARG A 613 *********************** 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 130 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 LYS cc_start: 0.7759 (tptt) cc_final: 0.7490 (tptt) REVERT: A 439 LYS cc_start: 0.7878 (tppt) cc_final: 0.7632 (pttt) REVERT: A 507 MET cc_start: 0.5056 (tmt) cc_final: 0.4760 (tmt) REVERT: A 612 LYS cc_start: 0.8531 (tptp) cc_final: 0.8136 (tppt) REVERT: A 860 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7700 (pp) outliers start: 31 outliers final: 23 residues processed: 122 average time/residue: 0.2022 time to fit residues: 32.5214 Evaluate side-chains 122 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 ILE 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 433 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 570 MET 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 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 862 LEU Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.0370 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 61 optimal weight: 0.0040 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 28 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 1.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3854 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= 0.207 Angle : 0.554 6.439 8851 Z= 0.290 Chirality : 0.043 0.147 1012 Planarity : 0.005 0.057 1068 Dihedral : 11.564 102.673 1010 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.30 % Allowed : 23.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.30), residues: 742 helix: 1.79 (0.33), residues: 242 sheet: -0.39 (0.38), residues: 180 loop : -0.91 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.004 0.001 HIS A 929 PHE 0.016 0.002 PHE A 322 TYR 0.027 0.002 TYR A 460 ARG 0.007 0.000 ARG A 613 *********************** 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 130 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 436 LYS cc_start: 0.7777 (tptt) cc_final: 0.7519 (tptt) REVERT: A 507 MET cc_start: 0.5157 (tmt) cc_final: 0.4932 (tmt) REVERT: A 612 LYS cc_start: 0.8542 (tptp) cc_final: 0.8206 (tppt) REVERT: A 821 GLN cc_start: 0.7713 (mp10) cc_final: 0.7332 (pm20) REVERT: A 860 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7606 (pp) REVERT: A 884 CYS cc_start: 0.8141 (p) cc_final: 0.7668 (t) outliers start: 29 outliers final: 24 residues processed: 122 average time/residue: 0.2055 time to fit residues: 32.9764 Evaluate side-chains 121 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 315 CYS 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 570 MET 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 862 LEU Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6487 Z= 0.192 Angle : 0.550 6.467 8851 Z= 0.286 Chirality : 0.042 0.145 1012 Planarity : 0.005 0.054 1068 Dihedral : 11.414 101.507 1010 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.30 % Allowed : 23.74 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.30), residues: 742 helix: 1.91 (0.34), residues: 242 sheet: -0.30 (0.38), residues: 177 loop : -0.97 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 932 HIS 0.004 0.000 HIS A 929 PHE 0.016 0.002 PHE A 760 TYR 0.016 0.001 TYR A 931 ARG 0.006 0.000 ARG A 613 *********************** 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 130 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.4929 (tmt) cc_final: 0.4686 (tmt) REVERT: A 603 MET cc_start: 0.7219 (mmm) cc_final: 0.6983 (mmm) REVERT: A 612 LYS cc_start: 0.8515 (tptp) cc_final: 0.8206 (tppt) REVERT: A 648 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7203 (mtp-110) REVERT: A 716 LYS cc_start: 0.7531 (mmtm) cc_final: 0.7164 (mmtm) REVERT: A 821 GLN cc_start: 0.7737 (mp10) cc_final: 0.7342 (pm20) REVERT: A 860 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7640 (pp) REVERT: A 884 CYS cc_start: 0.8173 (p) cc_final: 0.7713 (t) outliers start: 29 outliers final: 19 residues processed: 118 average time/residue: 0.1907 time to fit residues: 29.5716 Evaluate side-chains 120 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 306 ILE 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 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 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 964 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6487 Z= 0.201 Angle : 0.564 6.855 8851 Z= 0.292 Chirality : 0.043 0.142 1012 Planarity : 0.005 0.053 1068 Dihedral : 11.371 101.268 1010 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.01 % Allowed : 24.04 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.30), residues: 742 helix: 1.82 (0.33), residues: 242 sheet: -0.36 (0.38), residues: 177 loop : -0.91 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 932 HIS 0.004 0.000 HIS A 929 PHE 0.017 0.001 PHE A 322 TYR 0.016 0.001 TYR A 931 ARG 0.005 0.000 ARG A 613 *********************** 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 131 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.5146 (tmt) cc_final: 0.4895 (tmt) REVERT: A 522 ASN cc_start: 0.7267 (m110) cc_final: 0.7043 (m-40) REVERT: A 603 MET cc_start: 0.7287 (mmm) cc_final: 0.7035 (mmm) REVERT: A 612 LYS cc_start: 0.8484 (tptp) cc_final: 0.8220 (tppt) REVERT: A 648 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7313 (mtp180) REVERT: A 716 LYS cc_start: 0.7519 (mmtm) cc_final: 0.7165 (mmtm) REVERT: A 821 GLN cc_start: 0.7736 (mp10) cc_final: 0.7340 (pm20) REVERT: A 860 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7638 (pp) REVERT: A 884 CYS cc_start: 0.8156 (p) cc_final: 0.7705 (t) outliers start: 27 outliers final: 22 residues processed: 120 average time/residue: 0.1945 time to fit residues: 30.8127 Evaluate side-chains 126 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 315 CYS 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 437 THR 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 862 LEU Chi-restraints excluded: chain A residue 891 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 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 68 optimal weight: 0.0980 chunk 59 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6487 Z= 0.183 Angle : 0.567 12.975 8851 Z= 0.288 Chirality : 0.042 0.139 1012 Planarity : 0.005 0.051 1068 Dihedral : 11.280 100.340 1010 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.56 % Allowed : 24.33 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 742 helix: 2.01 (0.34), residues: 237 sheet: -0.27 (0.38), residues: 177 loop : -0.81 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 932 HIS 0.003 0.000 HIS A 929 PHE 0.016 0.001 PHE A 322 TYR 0.010 0.001 TYR A 772 ARG 0.005 0.000 ARG A 386 ********************** 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 130 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: A 603 MET cc_start: 0.7314 (mmm) cc_final: 0.7018 (mmm) REVERT: A 612 LYS cc_start: 0.8530 (tptp) cc_final: 0.8278 (tppt) REVERT: A 648 ARG cc_start: 0.7509 (mtm180) cc_final: 0.7207 (mtp-110) REVERT: A 821 GLN cc_start: 0.7644 (mp10) cc_final: 0.7248 (pm20) REVERT: A 860 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 884 CYS cc_start: 0.8151 (p) cc_final: 0.7696 (t) outliers start: 24 outliers final: 18 residues processed: 123 average time/residue: 0.1960 time to fit residues: 31.7981 Evaluate side-chains 124 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 315 CYS 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 419 ILE Chi-restraints excluded: chain A residue 437 THR 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 964 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 0.0980 chunk 61 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 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 = 0.4333 r_free = 0.4333 target = 0.193398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151973 restraints weight = 8284.717| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.63 r_work: 0.3780 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6487 Z= 0.181 Angle : 0.555 6.921 8851 Z= 0.286 Chirality : 0.042 0.154 1012 Planarity : 0.005 0.050 1068 Dihedral : 11.227 100.101 1010 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.56 % Allowed : 24.48 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 742 helix: 2.07 (0.34), residues: 237 sheet: -0.21 (0.38), residues: 177 loop : -0.81 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 932 HIS 0.003 0.000 HIS A 929 PHE 0.017 0.001 PHE A 322 TYR 0.011 0.001 TYR A 772 ARG 0.005 0.000 ARG A 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.34 seconds wall clock time: 29 minutes 57.04 seconds (1797.04 seconds total)