Starting phenix.real_space_refine on Thu Jul 2 02:08:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiy_60609/07_2026/9iiy_60609.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiy_60609/07_2026/9iiy_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_60609/07_2026/9iiy_60609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiy_60609/07_2026/9iiy_60609.map" model { file = "/net/cci-nas-00/data/ceres_data/9iiy_60609/07_2026/9iiy_60609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiy_60609/07_2026/9iiy_60609.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.52, per 1000 atoms: 0.26 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: 0.36 Conformation dependent library (CDL) restraints added in 400.1 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: 0.54 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: 0.73 Time building geometry restraints manager: 0.54 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=" C8 G B 14 " pdb=" N7 G B 14 " ideal model delta sigma weight residual 1.305 1.295 0.010 6.00e-03 2.78e+04 2.70e+00 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=" N9 A B 18 " pdb=" C4 A B 18 " ideal model delta sigma weight residual 1.374 1.382 -0.008 6.00e-03 2.78e+04 1.79e+00 bond pdb=" N9 G B 14 " pdb=" C4 G B 14 " ideal model delta sigma weight residual 1.375 1.385 -0.010 8.00e-03 1.56e+04 1.67e+00 bond pdb=" N7 G B 14 " pdb=" C5 G B 14 " ideal model delta sigma weight residual 1.388 1.381 0.007 6.00e-03 2.78e+04 1.49e+00 ... (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=" C1' G B 14 " pdb=" N9 G B 14 " pdb=" C4 G B 14 " ideal model delta sigma weight residual 126.50 133.35 -6.85 1.30e+00 5.92e-01 2.77e+01 angle pdb=" C1' G B 14 " pdb=" N9 G B 14 " pdb=" C8 G B 14 " ideal model delta sigma weight residual 127.00 120.82 6.18 1.30e+00 5.92e-01 2.26e+01 angle pdb=" N9 G B 14 " pdb=" C4 G B 14 " pdb=" N3 G B 14 " ideal model delta sigma weight residual 126.00 128.60 -2.60 6.00e-01 2.78e+00 1.87e+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=" C2' U C 21 " pdb=" C3' U C 21 " pdb=" O2' U C 21 " pdb=" C1' U C 21 " both_signs ideal model delta sigma weight residual False -2.62 -2.80 0.18 2.00e-01 2.50e+01 8.20e-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: 0.220 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4603 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= 0.149 Angle : 0.791 26.983 8526 Z= 0.446 Chirality : 0.076 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 : 19.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.010 0.001 ARG A 396 TYR 0.018 0.001 TYR A 946 PHE 0.005 0.001 PHE A 688 TRP 0.013 0.002 TRP A 447 HIS 0.003 0.000 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 ( 6154) covalent geometry : angle 0.79092 / 0.45 ( 8526) hydrogen bonds : bond 0.24119 / 15.08 ( 170) hydrogen bonds : angle 9.18357 / 6.08 ( 437) *********************** 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 : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 CYS cc_start: 0.0546 (OUTLIER) cc_final: -0.0269 (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: 0.5063 (pmt) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.3480 time to fit residues: 21.1950 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 : 0.165 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.282707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.258211 restraints weight = 8012.892| |-----------------------------------------------------------------------------| r_work (start): 0.4991 rms_B_bonded: 2.35 r_work: 0.4890 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5144 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6154 Z= 0.139 Angle : 0.773 27.164 8526 Z= 0.369 Chirality : 0.076 1.991 993 Planarity : 0.005 0.048 926 Dihedral : 19.395 149.753 1338 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 5.52 % Allowed : 32.74 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.31), residues: 608 helix: -1.01 (0.38), residues: 146 sheet: -2.13 (0.78), residues: 47 loop : -2.73 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 438 TYR 0.013 0.001 TYR A 435 PHE 0.009 0.001 PHE A 413 TRP 0.012 0.002 TRP A 447 HIS 0.002 0.000 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 6154) covalent geometry : angle 0.77309 / 0.37 ( 8526) hydrogen bonds : bond 0.09429 / 5.01 ( 170) hydrogen bonds : angle 7.41063 / 4.78 ( 437) *********************** 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 92 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.175 Fit side-chains REVERT: A 307 MET cc_start: 0.1870 (ptp) cc_final: 0.0687 (tmt) REVERT: A 458 HIS cc_start: 0.4995 (OUTLIER) cc_final: 0.3572 (m-70) REVERT: A 465 PHE cc_start: 0.4605 (OUTLIER) cc_final: 0.3468 (t80) REVERT: A 531 MET cc_start: 0.4144 (tpt) cc_final: 0.3696 (tpt) REVERT: A 736 MET cc_start: 0.5717 (mtp) cc_final: 0.5447 (mtp) REVERT: A 755 MET cc_start: 0.5547 (pmm) cc_final: 0.5274 (pmt) outliers start: 31 outliers final: 8 residues processed: 83 average time/residue: 0.3240 time to fit residues: 28.7482 Evaluate side-chains 62 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 CYS 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 892 ILE Chi-restraints excluded: chain A residue 910 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 0.0870 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 overall best weight: 3.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.269635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.241233 restraints weight = 8035.342| |-----------------------------------------------------------------------------| r_work (start): 0.4859 rms_B_bonded: 2.41 r_work: 0.4755 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 6154 Z= 0.274 Angle : 0.956 27.216 8526 Z= 0.472 Chirality : 0.081 1.979 993 Planarity : 0.007 0.056 926 Dihedral : 19.645 148.924 1338 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 7.47 % Allowed : 32.03 % Favored : 60.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.31), residues: 608 helix: -1.23 (0.38), residues: 145 sheet: -1.86 (0.99), residues: 33 loop : -2.99 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 396 TYR 0.021 0.003 TYR A 357 PHE 0.033 0.003 PHE A 549 TRP 0.020 0.004 TRP A 447 HIS 0.009 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.27 ( 6154) covalent geometry : angle 0.95554 / 0.47 ( 8526) hydrogen bonds : bond 0.09672 / 5.32 ( 170) hydrogen bonds : angle 7.22932 / 4.68 ( 437) *********************** 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 100 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 58 time to evaluate : 0.205 Fit side-chains REVERT: A 294 TYR cc_start: 0.2512 (OUTLIER) cc_final: 0.1608 (m-80) REVERT: A 307 MET cc_start: 0.2287 (ptp) cc_final: 0.0956 (tmm) REVERT: A 356 TYR cc_start: 0.6989 (m-80) cc_final: 0.6701 (m-80) REVERT: A 458 HIS cc_start: 0.5067 (OUTLIER) cc_final: 0.4695 (t-90) REVERT: A 465 PHE cc_start: 0.4805 (OUTLIER) cc_final: 0.3315 (t80) REVERT: A 539 ARG cc_start: 0.4848 (OUTLIER) cc_final: 0.4542 (ptm160) REVERT: A 817 MET cc_start: 0.2408 (OUTLIER) cc_final: 0.2127 (ttt) REVERT: A 894 ASP cc_start: 0.4437 (OUTLIER) cc_final: 0.4233 (p0) outliers start: 42 outliers final: 15 residues processed: 91 average time/residue: 0.3323 time to fit residues: 32.3477 Evaluate side-chains 71 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 404 LEU 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 661 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 690 THR 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 817 MET Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 908 GLN Chi-restraints excluded: chain A residue 918 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.0040 chunk 57 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 737 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 = 0.5115 r_free = 0.5115 target = 0.276652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.249946 restraints weight = 8006.854| |-----------------------------------------------------------------------------| r_work (start): 0.4929 rms_B_bonded: 2.39 r_work: 0.4825 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.1921 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= 0.145 Angle : 0.826 27.142 8526 Z= 0.391 Chirality : 0.078 1.988 993 Planarity : 0.005 0.041 926 Dihedral : 19.555 150.870 1338 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.34 % Allowed : 35.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.31), residues: 608 helix: -1.06 (0.39), residues: 145 sheet: -2.36 (0.93), residues: 37 loop : -2.88 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 438 TYR 0.017 0.002 TYR A 919 PHE 0.011 0.001 PHE A 418 TRP 0.014 0.002 TRP A 447 HIS 0.003 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 6154) covalent geometry : angle 0.82565 / 0.39 ( 8526) hydrogen bonds : bond 0.07323 / 4.07 ( 170) hydrogen bonds : angle 6.72487 / 4.32 ( 437) *********************** 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 87 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 294 TYR cc_start: 0.2274 (OUTLIER) cc_final: 0.1771 (m-80) REVERT: A 307 MET cc_start: 0.2232 (ptp) cc_final: 0.1008 (tmm) REVERT: A 356 TYR cc_start: 0.6877 (m-80) cc_final: 0.6447 (m-80) REVERT: A 377 VAL cc_start: 0.6525 (t) cc_final: 0.6258 (m) REVERT: A 458 HIS cc_start: 0.5072 (OUTLIER) cc_final: 0.3670 (m-70) REVERT: A 465 PHE cc_start: 0.4857 (OUTLIER) cc_final: 0.3542 (t80) REVERT: A 539 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.4709 (ppp80) REVERT: A 817 MET cc_start: 0.2385 (OUTLIER) cc_final: 0.2129 (ttt) outliers start: 30 outliers final: 11 residues processed: 79 average time/residue: 0.4468 time to fit residues: 37.4261 Evaluate side-chains 65 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 450 ASN 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 572 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 948 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5081 r_free = 0.5081 target = 0.272039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.244234 restraints weight = 8123.291| |-----------------------------------------------------------------------------| r_work (start): 0.4881 rms_B_bonded: 2.42 r_work: 0.4776 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6154 Z= 0.203 Angle : 0.873 27.247 8526 Z= 0.415 Chirality : 0.078 1.970 993 Planarity : 0.005 0.047 926 Dihedral : 19.493 151.039 1338 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.32 % Favored : 86.68 % Rotamer: Outliers : 8.90 % Allowed : 32.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.31), residues: 608 helix: -1.11 (0.39), residues: 145 sheet: -3.09 (0.76), residues: 53 loop : -2.84 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 438 TYR 0.017 0.002 TYR A 356 PHE 0.020 0.002 PHE A 418 TRP 0.019 0.003 TRP A 447 HIS 0.005 0.001 HIS A 978 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 6154) covalent geometry : angle 0.87294 / 0.42 ( 8526) hydrogen bonds : bond 0.06868 / 4.01 ( 170) hydrogen bonds : angle 6.73019 / 4.34 ( 437) *********************** 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 99 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 49 time to evaluate : 0.134 Fit side-chains REVERT: A 294 TYR cc_start: 0.2040 (OUTLIER) cc_final: 0.1473 (m-80) REVERT: A 307 MET cc_start: 0.2396 (ptp) cc_final: 0.1122 (tmm) REVERT: A 356 TYR cc_start: 0.6789 (m-80) cc_final: 0.6501 (m-80) REVERT: A 458 HIS cc_start: 0.5048 (OUTLIER) cc_final: 0.3679 (m-70) REVERT: A 465 PHE cc_start: 0.4947 (OUTLIER) cc_final: 0.3368 (t80) REVERT: A 807 MET cc_start: 0.4030 (tpp) cc_final: 0.1795 (ttm) REVERT: A 817 MET cc_start: 0.2295 (OUTLIER) cc_final: 0.2006 (ttt) outliers start: 50 outliers final: 19 residues processed: 90 average time/residue: 0.3138 time to fit residues: 30.3021 Evaluate side-chains 70 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 300 CYS 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 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 641 MET 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 801 HIS Chi-restraints excluded: chain A residue 817 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5095 r_free = 0.5095 target = 0.273199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.246462 restraints weight = 8139.560| |-----------------------------------------------------------------------------| r_work (start): 0.4906 rms_B_bonded: 2.37 r_work: 0.4804 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5419 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6154 Z= 0.177 Angle : 0.847 27.227 8526 Z= 0.402 Chirality : 0.078 1.973 993 Planarity : 0.005 0.041 926 Dihedral : 19.518 151.805 1338 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 8.19 % Allowed : 32.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.31), residues: 608 helix: -1.11 (0.39), residues: 145 sheet: -2.51 (0.95), residues: 37 loop : -2.88 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 438 TYR 0.014 0.002 TYR A 919 PHE 0.018 0.002 PHE A 418 TRP 0.018 0.002 TRP A 447 HIS 0.005 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 ( 6154) covalent geometry : angle 0.84672 / 0.40 ( 8526) hydrogen bonds : bond 0.06165 / 3.64 ( 170) hydrogen bonds : angle 6.58892 / 4.25 ( 437) *********************** 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 99 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 53 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 294 TYR cc_start: 0.2248 (OUTLIER) cc_final: 0.1511 (m-80) REVERT: A 303 ARG cc_start: 0.0102 (OUTLIER) cc_final: -0.0130 (ttt180) REVERT: A 307 MET cc_start: 0.2392 (ptp) cc_final: 0.1127 (tmm) REVERT: A 377 VAL cc_start: 0.6790 (t) cc_final: 0.6529 (m) REVERT: A 458 HIS cc_start: 0.5055 (OUTLIER) cc_final: 0.3689 (m-70) REVERT: A 465 PHE cc_start: 0.4729 (OUTLIER) cc_final: 0.3013 (t80) REVERT: A 807 MET cc_start: 0.4087 (tpp) cc_final: 0.1788 (ttm) REVERT: A 817 MET cc_start: 0.2161 (OUTLIER) cc_final: 0.1868 (ttt) outliers start: 46 outliers final: 22 residues processed: 89 average time/residue: 0.3539 time to fit residues: 33.8283 Evaluate side-chains 76 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 312 THR 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 450 ASN 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 558 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 641 MET 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 801 HIS Chi-restraints excluded: chain A residue 817 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 978 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5098 r_free = 0.5098 target = 0.273321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.246467 restraints weight = 8095.581| |-----------------------------------------------------------------------------| r_work (start): 0.4904 rms_B_bonded: 2.35 r_work: 0.4803 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6154 Z= 0.176 Angle : 0.857 27.294 8526 Z= 0.403 Chirality : 0.078 1.973 993 Planarity : 0.005 0.044 926 Dihedral : 19.538 151.383 1338 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 7.12 % Allowed : 33.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.31), residues: 608 helix: -1.11 (0.39), residues: 145 sheet: -2.52 (0.94), residues: 37 loop : -2.88 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 351 TYR 0.014 0.002 TYR A 919 PHE 0.016 0.002 PHE A 418 TRP 0.018 0.002 TRP A 447 HIS 0.005 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 ( 6154) covalent geometry : angle 0.85662 / 0.40 ( 8526) hydrogen bonds : bond 0.05856 / 3.54 ( 170) hydrogen bonds : angle 6.56022 / 4.23 ( 437) *********************** 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 93 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 53 time to evaluate : 0.254 Fit side-chains REVERT: A 294 TYR cc_start: 0.2115 (OUTLIER) cc_final: 0.1354 (m-80) REVERT: A 303 ARG cc_start: -0.0057 (OUTLIER) cc_final: -0.2166 (tmt90) REVERT: A 307 MET cc_start: 0.2340 (ptp) cc_final: 0.1080 (tmm) REVERT: A 377 VAL cc_start: 0.6859 (t) cc_final: 0.6590 (m) REVERT: A 458 HIS cc_start: 0.5059 (OUTLIER) cc_final: 0.3700 (m-70) REVERT: A 465 PHE cc_start: 0.4665 (OUTLIER) cc_final: 0.2922 (t80) outliers start: 40 outliers final: 24 residues processed: 83 average time/residue: 0.4164 time to fit residues: 36.8032 Evaluate side-chains 76 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TYR 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 450 ASN 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 558 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 641 MET 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 801 HIS 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 978 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 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN ** A 737 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 = 0.5129 r_free = 0.5129 target = 0.277955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.252563 restraints weight = 8133.654| |-----------------------------------------------------------------------------| r_work (start): 0.4952 rms_B_bonded: 2.33 r_work: 0.4852 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5298 moved from start: 0.2619 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= 0.134 Angle : 0.829 27.181 8526 Z= 0.385 Chirality : 0.078 1.987 993 Planarity : 0.005 0.045 926 Dihedral : 19.483 152.267 1338 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 5.69 % Allowed : 35.77 % Favored : 58.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.31), residues: 608 helix: -1.08 (0.39), residues: 146 sheet: -2.24 (1.09), residues: 27 loop : -2.78 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 438 TYR 0.014 0.002 TYR A 904 PHE 0.016 0.001 PHE A 418 TRP 0.019 0.002 TRP A 447 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 6154) covalent geometry : angle 0.82916 / 0.38 ( 8526) hydrogen bonds : bond 0.05186 / 3.22 ( 170) hydrogen bonds : angle 6.29152 / 4.06 ( 437) *********************** 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 84 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 303 ARG cc_start: -0.0040 (OUTLIER) cc_final: -0.2145 (tmt90) REVERT: A 307 MET cc_start: 0.2278 (ptp) cc_final: 0.1070 (tmm) REVERT: A 465 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.3482 (t80) REVERT: A 807 MET cc_start: 0.3623 (tpp) cc_final: 0.1691 (ttm) outliers start: 32 outliers final: 17 residues processed: 79 average time/residue: 0.3505 time to fit residues: 29.7269 Evaluate side-chains 68 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 563 SER 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 690 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 801 HIS 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 6 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5123 r_free = 0.5123 target = 0.277474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.251723 restraints weight = 8141.573| |-----------------------------------------------------------------------------| r_work (start): 0.4946 rms_B_bonded: 2.33 r_work: 0.4846 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6154 Z= 0.139 Angle : 0.830 27.236 8526 Z= 0.386 Chirality : 0.077 1.984 993 Planarity : 0.005 0.047 926 Dihedral : 19.432 150.800 1338 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 5.16 % Allowed : 36.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.32), residues: 608 helix: -0.96 (0.39), residues: 146 sheet: -2.15 (0.95), residues: 34 loop : -2.67 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 438 TYR 0.021 0.002 TYR A 435 PHE 0.015 0.001 PHE A 418 TRP 0.020 0.002 TRP A 447 HIS 0.001 0.000 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 6154) covalent geometry : angle 0.83006 / 0.39 ( 8526) hydrogen bonds : bond 0.04991 / 3.10 ( 170) hydrogen bonds : angle 6.22036 / 4.03 ( 437) *********************** 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 84 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 55 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 303 ARG cc_start: -0.0238 (OUTLIER) cc_final: -0.2159 (tmt90) REVERT: A 307 MET cc_start: 0.2337 (ptp) cc_final: 0.1151 (tmm) REVERT: A 465 PHE cc_start: 0.4266 (OUTLIER) cc_final: 0.3398 (t80) REVERT: A 807 MET cc_start: 0.3934 (tpp) cc_final: 0.1620 (ttm) outliers start: 29 outliers final: 19 residues processed: 81 average time/residue: 0.3587 time to fit residues: 31.0604 Evaluate side-chains 71 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 563 SER 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 690 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 892 ILE Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 940 LYS 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 39 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5117 r_free = 0.5117 target = 0.276658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.250565 restraints weight = 8148.491| |-----------------------------------------------------------------------------| r_work (start): 0.4940 rms_B_bonded: 2.32 r_work: 0.4836 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.2821 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= 0.153 Angle : 0.856 27.314 8526 Z= 0.398 Chirality : 0.078 1.977 993 Planarity : 0.005 0.050 926 Dihedral : 19.426 149.857 1338 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 4.98 % Allowed : 37.01 % Favored : 58.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.32), residues: 608 helix: -0.76 (0.40), residues: 146 sheet: -2.69 (0.91), residues: 37 loop : -2.75 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 438 TYR 0.013 0.002 TYR A 919 PHE 0.015 0.002 PHE A 418 TRP 0.023 0.002 TRP A 447 HIS 0.003 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6154) covalent geometry : angle 0.85636 / 0.40 ( 8526) hydrogen bonds : bond 0.05106 / 3.13 ( 170) hydrogen bonds : angle 6.20632 / 4.03 ( 437) ********************** 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 78 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 251 MET cc_start: 0.6833 (tpp) cc_final: 0.4560 (tpp) REVERT: A 303 ARG cc_start: -0.0124 (OUTLIER) cc_final: -0.2162 (tmt90) REVERT: A 307 MET cc_start: 0.2199 (ptp) cc_final: 0.1075 (tmm) REVERT: A 465 PHE cc_start: 0.4266 (OUTLIER) cc_final: 0.3406 (t80) REVERT: A 807 MET cc_start: 0.3817 (tpp) cc_final: 0.1476 (ttm) outliers start: 28 outliers final: 23 residues processed: 74 average time/residue: 0.3497 time to fit residues: 27.9572 Evaluate side-chains 75 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 312 THR 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 450 ASN Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 563 SER 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 690 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 802 GLU 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 940 LYS 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 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5089 r_free = 0.5089 target = 0.273003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.246028 restraints weight = 8091.331| |-----------------------------------------------------------------------------| r_work (start): 0.4902 rms_B_bonded: 2.34 r_work: 0.4797 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5439 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6154 Z= 0.184 Angle : 0.881 27.532 8526 Z= 0.414 Chirality : 0.078 1.961 993 Planarity : 0.005 0.047 926 Dihedral : 19.534 148.983 1338 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 5.87 % Allowed : 36.48 % Favored : 57.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.31), residues: 608 helix: -0.81 (0.40), residues: 146 sheet: -3.49 (0.76), residues: 47 loop : -2.77 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 438 TYR 0.014 0.002 TYR A 919 PHE 0.015 0.002 PHE A 418 TRP 0.028 0.003 TRP A 447 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 6154) covalent geometry : angle 0.88133 / 0.41 ( 8526) hydrogen bonds : bond 0.05556 / 3.39 ( 170) hydrogen bonds : angle 6.31456 / 4.11 ( 437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.99 seconds wall clock time: 28 minutes 23.45 seconds (1703.45 seconds total)