Starting phenix.real_space_refine on Fri Dec 27 15:43:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiy_60609/12_2024/9iiy_60609.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiy_60609/12_2024/9iiy_60609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iiy_60609/12_2024/9iiy_60609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiy_60609/12_2024/9iiy_60609.map" model { file = "/net/cci-nas-00/data/ceres_data/9iiy_60609/12_2024/9iiy_60609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiy_60609/12_2024/9iiy_60609.cif" } resolution = 3.0 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= 0.037 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: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 29 5.16 5 C 3611 2.51 5 N 1047 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5943 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5030 Classifications: {'peptide': 620} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 590} Chain breaks: 5 Chain: "B" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNA': 22} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 19} Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 19} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.79, per 1000 atoms: 0.64 Number of scatterers: 5943 At special positions: 0 Unit cell: (74.1, 82.08, 104.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 43 15.00 O 1213 8.00 N 1047 7.00 C 3611 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: 1.39 Conformation dependent library (CDL) restraints added in 716.8 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 10 sheets defined 31.3% alpha, 8.4% beta 17 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.786A pdb=" N ARG A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 Processing helix chain 'A' and resid 366 through 369 Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'A' and resid 415 through 426 Processing helix chain 'A' and resid 464 through 473 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.979A pdb=" N VAL A 536 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 559 removed outlier: 4.392A pdb=" N ILE A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.909A pdb=" N LEU A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 removed outlier: 3.968A pdb=" N GLN A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 removed outlier: 3.568A pdb=" N LYS A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.637A pdb=" N LEU A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 701 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 724 through 740 Processing helix chain 'A' and resid 798 through 803 Processing helix chain 'A' and resid 803 through 819 removed outlier: 3.740A pdb=" N LYS A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 943 removed outlier: 4.024A pdb=" N HIS A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.773A pdb=" N ASN A 381 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 247 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 306 through 309 removed outlier: 3.844A pdb=" N ILE A 317 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.667A pdb=" N ASP A 355 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.574A pdb=" N LEU A 363 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 372 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 365 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET A 370 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 398 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 456 removed outlier: 3.925A pdb=" N PHE A 455 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 463 " --> pdb=" O PHE A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 624 through 625 removed outlier: 7.342A pdb=" N ALA A 624 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL A 687 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 684 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU A 714 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 686 " --> pdb=" O LEU A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 758 through 759 removed outlier: 3.832A pdb=" N VAL A 776 " --> pdb=" O GLY A 758 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 904 through 905 128 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1780 1.34 - 1.46: 1541 1.46 - 1.58: 2701 1.58 - 1.70: 84 1.70 - 1.82: 48 Bond restraints: 6154 Sorted by residual: bond pdb=" CB ARG A 396 " pdb=" CG ARG A 396 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 1.506 1.542 -0.036 3.90e-02 6.57e+02 8.34e-01 bond pdb=" CB VAL A 397 " pdb=" CG1 VAL A 397 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.87e-01 bond pdb=" CG MET A 398 " pdb=" SD MET A 398 " ideal model delta sigma weight residual 1.803 1.823 -0.020 2.50e-02 1.60e+03 6.52e-01 bond pdb=" CA PRO A 949 " pdb=" C PRO A 949 " ideal model delta sigma weight residual 1.527 1.520 0.008 1.07e-02 8.73e+03 4.91e-01 ... (remaining 6149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 8507 5.40 - 10.79: 16 10.79 - 16.19: 1 16.19 - 21.59: 0 21.59 - 26.98: 2 Bond angle restraints: 8526 Sorted by residual: angle pdb=" O3' G B 11 " pdb=" P U B 12 " pdb=" OP1 U B 12 " ideal model delta sigma weight residual 108.00 81.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" O3' G B 11 " pdb=" P U B 12 " pdb=" OP2 U B 12 " ideal model delta sigma weight residual 108.00 84.26 23.74 3.00e+00 1.11e-01 6.26e+01 angle pdb=" O3' G B 11 " pdb=" P U B 12 " pdb=" O5' U B 12 " ideal model delta sigma weight residual 104.00 98.56 5.44 1.50e+00 4.44e-01 1.31e+01 angle pdb=" OP1 U B 12 " pdb=" P U B 12 " pdb=" OP2 U B 12 " ideal model delta sigma weight residual 119.60 130.30 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA LEU A 335 " pdb=" CB LEU A 335 " pdb=" CG LEU A 335 " ideal model delta sigma weight residual 116.30 128.76 -12.46 3.50e+00 8.16e-02 1.27e+01 ... (remaining 8521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 3393 29.44 - 58.87: 328 58.87 - 88.31: 60 88.31 - 117.74: 4 117.74 - 147.18: 2 Dihedral angle restraints: 3787 sinusoidal: 1957 harmonic: 1830 Sorted by residual: dihedral pdb=" CA ARG A 953 " pdb=" C ARG A 953 " pdb=" N THR A 954 " pdb=" CA THR A 954 " ideal model delta harmonic sigma weight residual 180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" C4' A C 8 " pdb=" C3' A C 8 " pdb=" O3' A C 8 " pdb=" P C C 9 " ideal model delta sinusoidal sigma weight residual 220.00 72.82 147.18 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' A B 5 " pdb=" C3' A B 5 " pdb=" O3' A B 5 " pdb=" P G B 6 " ideal model delta sinusoidal sigma weight residual 220.00 87.02 132.98 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 3784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 992 0.396 - 0.792: 0 0.792 - 1.187: 0 1.187 - 1.583: 0 1.583 - 1.979: 1 Chirality restraints: 993 Sorted by residual: chirality pdb=" P U B 12 " pdb=" OP1 U B 12 " pdb=" OP2 U B 12 " pdb=" O5' U B 12 " both_signs ideal model delta sigma weight residual True 2.41 0.43 1.98 2.00e-01 2.50e+01 9.79e+01 chirality pdb=" C3' A B 5 " pdb=" C4' A B 5 " pdb=" O3' A B 5 " pdb=" C2' A B 5 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' A C 8 " pdb=" C4' A C 8 " pdb=" O3' A C 8 " pdb=" C2' A C 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 990 not shown) Planarity restraints: 926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.030 2.00e-02 2.50e+03 1.28e-02 4.88e+00 pdb=" N9 G B 3 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B 3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 3 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 450 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO A 451 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 12 " -0.024 2.00e-02 2.50e+03 1.14e-02 2.91e+00 pdb=" N1 U B 12 " 0.019 2.00e-02 2.50e+03 pdb=" C2 U B 12 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U B 12 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 12 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B 12 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 12 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U B 12 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 12 " 0.009 2.00e-02 2.50e+03 ... (remaining 923 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 160 2.66 - 3.22: 5495 3.22 - 3.78: 9795 3.78 - 4.34: 12905 4.34 - 4.90: 19415 Nonbonded interactions: 47770 Sorted by model distance: nonbonded pdb=" OG SER A 916 " pdb=" OP2 G B 6 " model vdw 2.103 3.040 nonbonded pdb=" OG1 THR A 402 " pdb=" O CYS A 515 " model vdw 2.182 3.040 nonbonded pdb=" O TRP A 745 " pdb=" OH TYR A 946 " model vdw 2.186 3.040 nonbonded pdb=" O ARG A 555 " pdb=" OG1 THR A 559 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR A 244 " pdb=" O THR A 873 " model vdw 2.239 3.040 ... (remaining 47765 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: 0.210 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.620 Find NCS groups from input model: 0.050 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4514 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 : 0.003 0.043 6154 Z= 0.160 Angle : 0.789 26.983 8526 Z= 0.360 Chirality : 0.075 1.979 993 Planarity : 0.005 0.046 926 Dihedral : 21.548 147.176 2599 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.36 % Allowed : 35.05 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.11 (0.32), residues: 608 helix: -0.73 (0.42), residues: 143 sheet: -2.00 (0.79), residues: 47 loop : -2.77 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 447 HIS 0.003 0.000 HIS A 395 PHE 0.005 0.001 PHE A 688 TYR 0.018 0.001 TYR A 946 ARG 0.010 0.001 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 CYS cc_start: 0.0546 (OUTLIER) cc_final: -0.0270 (m) REVERT: A 307 MET cc_start: 0.1395 (ptp) cc_final: 0.0989 (tmt) REVERT: A 755 MET cc_start: 0.5264 (pmm) cc_final: 0.5049 (pmt) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.9217 time to fit residues: 56.2499 Evaluate side-chains 52 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 730 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN A 882 HIS A 909 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4682 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6154 Z= 0.228 Angle : 0.818 27.215 8526 Z= 0.381 Chirality : 0.077 1.970 993 Planarity : 0.005 0.045 926 Dihedral : 19.378 151.974 1338 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 6.76 % Allowed : 31.85 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.16 (0.31), residues: 608 helix: -1.00 (0.38), residues: 145 sheet: -1.68 (1.00), residues: 33 loop : -2.75 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 745 HIS 0.005 0.001 HIS A 909 PHE 0.018 0.002 PHE A 549 TYR 0.014 0.002 TYR A 919 ARG 0.009 0.001 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 58 time to evaluate : 0.606 Fit side-chains REVERT: A 307 MET cc_start: 0.1770 (ptp) cc_final: 0.1271 (tmm) REVERT: A 387 LEU cc_start: 0.6900 (mt) cc_final: 0.6694 (mt) REVERT: A 458 HIS cc_start: 0.4448 (OUTLIER) cc_final: 0.2968 (m-70) REVERT: A 465 PHE cc_start: 0.3783 (OUTLIER) cc_final: 0.2626 (t80) REVERT: A 531 MET cc_start: 0.3335 (tpt) cc_final: 0.2694 (tpt) REVERT: A 807 MET cc_start: 0.4500 (OUTLIER) cc_final: 0.1790 (ttm) outliers start: 38 outliers final: 10 residues processed: 88 average time/residue: 0.9113 time to fit residues: 85.4421 Evaluate side-chains 63 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 918 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4601 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6154 Z= 0.187 Angle : 0.805 27.019 8526 Z= 0.364 Chirality : 0.076 1.984 993 Planarity : 0.005 0.045 926 Dihedral : 19.327 153.231 1338 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.98 % Allowed : 35.59 % Favored : 59.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.08 (0.31), residues: 608 helix: -0.86 (0.39), residues: 146 sheet: -2.09 (0.87), residues: 44 loop : -2.68 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 447 HIS 0.002 0.000 HIS A 882 PHE 0.018 0.001 PHE A 418 TYR 0.011 0.001 TYR A 904 ARG 0.008 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.530 Fit side-chains REVERT: A 251 MET cc_start: 0.4855 (tpp) cc_final: 0.4155 (mmm) REVERT: A 307 MET cc_start: 0.1545 (ptp) cc_final: 0.1245 (tmm) REVERT: A 465 PHE cc_start: 0.3802 (OUTLIER) cc_final: 0.2555 (t80) REVERT: A 531 MET cc_start: 0.3369 (tpt) cc_final: 0.2929 (tpt) REVERT: A 807 MET cc_start: 0.4449 (OUTLIER) cc_final: 0.2331 (ttm) outliers start: 28 outliers final: 12 residues processed: 82 average time/residue: 0.8233 time to fit residues: 72.4075 Evaluate side-chains 65 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 948 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 31 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4639 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6154 Z= 0.184 Angle : 0.802 27.084 8526 Z= 0.361 Chirality : 0.076 1.978 993 Planarity : 0.005 0.043 926 Dihedral : 19.290 152.312 1338 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 6.23 % Allowed : 34.88 % Favored : 58.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.07 (0.31), residues: 608 helix: -0.82 (0.40), residues: 147 sheet: -2.22 (0.85), residues: 44 loop : -2.67 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 447 HIS 0.004 0.001 HIS A 395 PHE 0.018 0.001 PHE A 418 TYR 0.010 0.002 TYR A 357 ARG 0.009 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.1553 (ptp) cc_final: 0.1325 (tmm) REVERT: A 313 ASP cc_start: 0.3215 (OUTLIER) cc_final: 0.3000 (p0) REVERT: A 465 PHE cc_start: 0.3785 (OUTLIER) cc_final: 0.2253 (t80) REVERT: A 539 ARG cc_start: 0.4930 (OUTLIER) cc_final: 0.4657 (ptp-110) REVERT: A 702 LEU cc_start: 0.4384 (OUTLIER) cc_final: 0.4085 (mt) REVERT: A 807 MET cc_start: 0.4097 (OUTLIER) cc_final: 0.1990 (ttm) outliers start: 35 outliers final: 15 residues processed: 85 average time/residue: 0.9152 time to fit residues: 83.1048 Evaluate side-chains 72 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4683 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6154 Z= 0.204 Angle : 0.829 27.133 8526 Z= 0.370 Chirality : 0.076 1.973 993 Planarity : 0.005 0.051 926 Dihedral : 19.296 154.301 1338 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 7.83 % Allowed : 33.10 % Favored : 59.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.04 (0.32), residues: 608 helix: -0.82 (0.40), residues: 148 sheet: -2.25 (0.82), residues: 44 loop : -2.64 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 447 HIS 0.003 0.001 HIS A 395 PHE 0.021 0.002 PHE A 418 TYR 0.010 0.002 TYR A 357 ARG 0.006 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 54 time to evaluate : 0.640 Fit side-chains REVERT: A 251 MET cc_start: 0.4741 (tpp) cc_final: 0.4032 (mmm) REVERT: A 458 HIS cc_start: 0.4419 (OUTLIER) cc_final: 0.2989 (m-70) REVERT: A 465 PHE cc_start: 0.3478 (OUTLIER) cc_final: 0.2005 (t80) REVERT: A 539 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4709 (ppp80) REVERT: A 702 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.4176 (mt) REVERT: A 807 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.2152 (ttm) outliers start: 44 outliers final: 18 residues processed: 87 average time/residue: 0.7934 time to fit residues: 74.4494 Evaluate side-chains 72 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 948 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 0.0030 chunk 7 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4825 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6154 Z= 0.262 Angle : 0.883 27.228 8526 Z= 0.406 Chirality : 0.078 1.962 993 Planarity : 0.005 0.041 926 Dihedral : 19.424 152.090 1338 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.32 % Favored : 86.68 % Rotamer: Outliers : 7.83 % Allowed : 32.92 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.20 (0.31), residues: 608 helix: -0.94 (0.39), residues: 146 sheet: -2.25 (0.85), residues: 43 loop : -2.76 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 447 HIS 0.006 0.001 HIS A 909 PHE 0.023 0.002 PHE A 418 TYR 0.013 0.002 TYR A 294 ARG 0.004 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 54 time to evaluate : 0.611 Fit side-chains REVERT: A 458 HIS cc_start: 0.4370 (OUTLIER) cc_final: 0.2938 (m-70) REVERT: A 465 PHE cc_start: 0.3410 (OUTLIER) cc_final: 0.2407 (t80) REVERT: A 539 ARG cc_start: 0.5349 (OUTLIER) cc_final: 0.4758 (mtm110) REVERT: A 807 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.2027 (ttm) outliers start: 44 outliers final: 23 residues processed: 90 average time/residue: 0.8663 time to fit residues: 83.3539 Evaluate side-chains 75 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 786 TRP Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 948 TRP Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 25 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4658 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6154 Z= 0.184 Angle : 0.845 27.154 8526 Z= 0.379 Chirality : 0.077 1.982 993 Planarity : 0.005 0.044 926 Dihedral : 19.430 154.175 1338 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 6.05 % Allowed : 35.59 % Favored : 58.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.05 (0.32), residues: 608 helix: -0.81 (0.40), residues: 148 sheet: -2.53 (0.78), residues: 46 loop : -2.60 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 447 HIS 0.001 0.000 HIS A 613 PHE 0.022 0.001 PHE A 418 TYR 0.012 0.001 TYR A 904 ARG 0.006 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 57 time to evaluate : 0.579 Fit side-chains REVERT: A 251 MET cc_start: 0.5038 (tpp) cc_final: 0.4031 (tpt) REVERT: A 539 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4731 (ppp80) REVERT: A 802 GLU cc_start: 0.3996 (pt0) cc_final: 0.3788 (pt0) REVERT: A 807 MET cc_start: 0.3917 (OUTLIER) cc_final: 0.2192 (ttt) REVERT: A 905 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5766 (mp) REVERT: A 944 MET cc_start: 0.6613 (mmp) cc_final: 0.6348 (mmm) outliers start: 34 outliers final: 20 residues processed: 85 average time/residue: 0.8578 time to fit residues: 78.1849 Evaluate side-chains 73 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4619 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6154 Z= 0.183 Angle : 0.845 27.154 8526 Z= 0.377 Chirality : 0.077 1.983 993 Planarity : 0.004 0.041 926 Dihedral : 19.332 153.614 1338 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 4.98 % Allowed : 37.90 % Favored : 57.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.81 (0.32), residues: 608 helix: -0.60 (0.41), residues: 147 sheet: -2.08 (0.94), residues: 34 loop : -2.50 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 447 HIS 0.002 0.000 HIS A 909 PHE 0.025 0.001 PHE A 418 TYR 0.022 0.001 TYR A 435 ARG 0.006 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.599 Fit side-chains REVERT: A 539 ARG cc_start: 0.5218 (OUTLIER) cc_final: 0.4835 (ppp80) REVERT: A 807 MET cc_start: 0.3808 (OUTLIER) cc_final: 0.2073 (ttm) outliers start: 28 outliers final: 18 residues processed: 75 average time/residue: 0.8298 time to fit residues: 66.8633 Evaluate side-chains 67 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4743 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6154 Z= 0.229 Angle : 0.876 27.321 8526 Z= 0.397 Chirality : 0.077 1.965 993 Planarity : 0.005 0.042 926 Dihedral : 19.398 153.299 1338 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 4.63 % Allowed : 38.79 % Favored : 56.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.08 (0.32), residues: 608 helix: -0.59 (0.41), residues: 147 sheet: -2.62 (0.72), residues: 49 loop : -2.71 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 447 HIS 0.004 0.001 HIS A 613 PHE 0.023 0.002 PHE A 418 TYR 0.022 0.002 TYR A 435 ARG 0.007 0.001 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.594 Fit side-chains REVERT: A 303 ARG cc_start: 0.0725 (OUTLIER) cc_final: -0.1238 (tmt90) REVERT: A 539 ARG cc_start: 0.5340 (OUTLIER) cc_final: 0.4667 (mtm110) REVERT: A 807 MET cc_start: 0.4030 (OUTLIER) cc_final: 0.2135 (ttm) outliers start: 26 outliers final: 18 residues processed: 71 average time/residue: 0.9229 time to fit residues: 69.9693 Evaluate side-chains 68 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4705 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6154 Z= 0.205 Angle : 0.875 27.119 8526 Z= 0.395 Chirality : 0.078 1.973 993 Planarity : 0.005 0.041 926 Dihedral : 19.413 154.249 1338 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 4.27 % Allowed : 39.32 % Favored : 56.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.06 (0.32), residues: 608 helix: -0.65 (0.41), residues: 143 sheet: -2.60 (0.66), residues: 56 loop : -2.64 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 447 HIS 0.003 0.001 HIS A 613 PHE 0.023 0.001 PHE A 418 TYR 0.023 0.002 TYR A 435 ARG 0.007 0.000 ARG A 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.574 Fit side-chains REVERT: A 300 CYS cc_start: 0.0424 (OUTLIER) cc_final: -0.0434 (m) REVERT: A 303 ARG cc_start: 0.0686 (OUTLIER) cc_final: -0.1271 (tmt90) REVERT: A 539 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.4614 (mtm110) REVERT: A 807 MET cc_start: 0.3837 (OUTLIER) cc_final: 0.2115 (ttt) outliers start: 24 outliers final: 17 residues processed: 68 average time/residue: 0.8059 time to fit residues: 59.1088 Evaluate side-chains 66 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 786 TRP Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 980 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 0.0770 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 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 = 0.5108 r_free = 0.5108 target = 0.277241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.249967 restraints weight = 7978.689| |-----------------------------------------------------------------------------| r_work (start): 0.4917 rms_B_bonded: 2.35 r_work: 0.4813 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6154 Z= 0.206 Angle : 0.877 27.117 8526 Z= 0.396 Chirality : 0.077 1.969 993 Planarity : 0.005 0.042 926 Dihedral : 19.383 154.218 1338 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 4.27 % Allowed : 39.50 % Favored : 56.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.04 (0.32), residues: 608 helix: -0.57 (0.41), residues: 143 sheet: -2.59 (0.66), residues: 56 loop : -2.66 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 447 HIS 0.003 0.001 HIS A 613 PHE 0.023 0.001 PHE A 418 TYR 0.010 0.001 TYR A 919 ARG 0.006 0.001 ARG A 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.25 seconds wall clock time: 36 minutes 13.46 seconds (2173.46 seconds total)