Starting phenix.real_space_refine on Thu Jul 24 07:03:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvv_37873/07_2025/8wvv_37873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvv_37873/07_2025/8wvv_37873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvv_37873/07_2025/8wvv_37873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvv_37873/07_2025/8wvv_37873.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvv_37873/07_2025/8wvv_37873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvv_37873/07_2025/8wvv_37873.cif" } resolution = 3.35 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= 0.006 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3643 2.51 5 N 918 2.21 5 O 1009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5596 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5596 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 682} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 4.13, per 1000 atoms: 0.74 Number of scatterers: 5596 At special positions: 0 Unit cell: (77.08, 93.48, 136.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1009 8.00 N 918 7.00 C 3643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=1.99 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.07 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: 1.41 Conformation dependent library (CDL) restraints added in 846.1 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 5 sheets defined 33.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.694A pdb=" N ALA A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 466 through 474 removed outlier: 4.158A pdb=" N CYS A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.665A pdb=" N ASN A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.837A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.915A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 644 removed outlier: 4.319A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 658 through 675 removed outlier: 3.560A pdb=" N PHE A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 4.214A pdb=" N LEU A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 729 removed outlier: 3.846A pdb=" N LEU A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 768 removed outlier: 3.564A pdb=" N ASN A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 780 through 789 Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.728A pdb=" N ASN A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 817 removed outlier: 3.715A pdb=" N LEU A 814 " --> pdb=" O GLU A 810 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 5.841A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 62 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 110 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 134 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 206 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 304 removed outlier: 7.578A pdb=" N LEU A 301 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR A 327 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE A 303 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 169 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 891 1.30 - 1.43: 1491 1.43 - 1.56: 3309 1.56 - 1.69: 1 1.69 - 1.82: 35 Bond restraints: 5727 Sorted by residual: bond pdb=" C ASN A 805 " pdb=" N PRO A 806 " ideal model delta sigma weight residual 1.335 1.507 -0.172 1.19e-02 7.06e+03 2.09e+02 bond pdb=" C TYR A 468 " pdb=" O TYR A 468 " ideal model delta sigma weight residual 1.236 1.341 -0.105 1.26e-02 6.30e+03 6.88e+01 bond pdb=" C PHE A 759 " pdb=" O PHE A 759 " ideal model delta sigma weight residual 1.236 1.308 -0.072 1.15e-02 7.56e+03 3.89e+01 bond pdb=" CA SER A 690 " pdb=" CB SER A 690 " ideal model delta sigma weight residual 1.538 1.459 0.079 1.38e-02 5.25e+03 3.32e+01 bond pdb=" C ILE A 758 " pdb=" O ILE A 758 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.12e-02 7.97e+03 3.31e+01 ... (remaining 5722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 7691 4.83 - 9.67: 81 9.67 - 14.50: 12 14.50 - 19.33: 3 19.33 - 24.17: 1 Bond angle restraints: 7788 Sorted by residual: angle pdb=" N ALA A 689 " pdb=" CA ALA A 689 " pdb=" C ALA A 689 " ideal model delta sigma weight residual 114.62 90.45 24.17 1.14e+00 7.69e-01 4.49e+02 angle pdb=" C ASN A 805 " pdb=" N PRO A 806 " pdb=" CA PRO A 806 " ideal model delta sigma weight residual 119.56 135.00 -15.44 1.02e+00 9.61e-01 2.29e+02 angle pdb=" C TYR A 801 " pdb=" CA TYR A 801 " pdb=" CB TYR A 801 " ideal model delta sigma weight residual 110.79 92.20 18.59 1.66e+00 3.63e-01 1.25e+02 angle pdb=" N SER A 573 " pdb=" CA SER A 573 " pdb=" C SER A 573 " ideal model delta sigma weight residual 113.18 101.03 12.15 1.21e+00 6.83e-01 1.01e+02 angle pdb=" C LEU A 575 " pdb=" N PHE A 576 " pdb=" CA PHE A 576 " ideal model delta sigma weight residual 120.54 108.55 11.99 1.35e+00 5.49e-01 7.88e+01 ... (remaining 7783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2845 16.90 - 33.80: 422 33.80 - 50.70: 106 50.70 - 67.59: 20 67.59 - 84.49: 9 Dihedral angle restraints: 3402 sinusoidal: 1318 harmonic: 2084 Sorted by residual: dihedral pdb=" C TYR A 801 " pdb=" N TYR A 801 " pdb=" CA TYR A 801 " pdb=" CB TYR A 801 " ideal model delta harmonic sigma weight residual -122.60 -98.42 -24.18 0 2.50e+00 1.60e-01 9.36e+01 dihedral pdb=" C PHE A 804 " pdb=" N PHE A 804 " pdb=" CA PHE A 804 " pdb=" CB PHE A 804 " ideal model delta harmonic sigma weight residual -122.60 -145.59 22.99 0 2.50e+00 1.60e-01 8.46e+01 dihedral pdb=" C SER A 688 " pdb=" N SER A 688 " pdb=" CA SER A 688 " pdb=" CB SER A 688 " ideal model delta harmonic sigma weight residual -122.60 -101.73 -20.87 0 2.50e+00 1.60e-01 6.97e+01 ... (remaining 3399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 901 0.178 - 0.357: 10 0.357 - 0.535: 7 0.535 - 0.713: 1 0.713 - 0.892: 1 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA PHE A 804 " pdb=" N PHE A 804 " pdb=" C PHE A 804 " pdb=" CB PHE A 804 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA PHE A 803 " pdb=" N PHE A 803 " pdb=" C PHE A 803 " pdb=" CB PHE A 803 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CA SER A 688 " pdb=" N SER A 688 " pdb=" C SER A 688 " pdb=" CB SER A 688 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 917 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 562 " -0.033 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C THR A 562 " 0.116 2.00e-02 2.50e+03 pdb=" O THR A 562 " -0.044 2.00e-02 2.50e+03 pdb=" N THR A 563 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 679 " -0.099 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO A 680 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO A 680 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 680 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 570 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO A 571 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " 0.063 5.00e-02 4.00e+02 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 15 2.33 - 2.98: 3001 2.98 - 3.62: 8782 3.62 - 4.26: 13457 4.26 - 4.90: 21703 Nonbonded interactions: 46958 Sorted by model distance: nonbonded pdb=" O GLY A 592 " pdb=" CD2 PHE A 596 " model vdw 1.693 3.340 nonbonded pdb=" CD2 PHE A 555 " pdb=" CG2 VAL A 799 " model vdw 1.729 3.760 nonbonded pdb=" CE2 PHE A 555 " pdb=" CG2 VAL A 799 " model vdw 2.171 3.760 nonbonded pdb=" O VAL A 153 " pdb=" OG1 THR A 178 " model vdw 2.174 3.040 nonbonded pdb=" O VAL A 711 " pdb=" OG SER A 715 " model vdw 2.179 3.040 ... (remaining 46953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.580 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.007 0.172 5732 Z= 0.482 Angle : 1.273 24.165 7798 Z= 0.819 Chirality : 0.077 0.892 920 Planarity : 0.010 0.142 981 Dihedral : 17.092 84.492 2025 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.28 % Allowed : 25.68 % Favored : 73.05 % Cbeta Deviations : 1.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.78 (0.30), residues: 704 helix: -1.61 (0.32), residues: 228 sheet: -3.17 (0.60), residues: 72 loop : -1.71 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 812 HIS 0.003 0.001 HIS A 171 PHE 0.045 0.002 PHE A 808 TYR 0.028 0.002 TYR A 801 ARG 0.003 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.27958 ( 169) hydrogen bonds : angle 9.96559 ( 498) SS BOND : bond 0.02651 ( 5) SS BOND : angle 5.91326 ( 10) covalent geometry : bond 0.00692 ( 5727) covalent geometry : angle 1.25654 ( 7788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 HIS cc_start: 0.7810 (t70) cc_final: 0.7363 (t70) REVERT: A 371 SER cc_start: 0.8914 (p) cc_final: 0.8545 (p) REVERT: A 762 PRO cc_start: 0.8048 (Cg_exo) cc_final: 0.7806 (Cg_endo) outliers start: 8 outliers final: 7 residues processed: 117 average time/residue: 0.1506 time to fit residues: 24.1438 Evaluate side-chains 109 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 571 PRO Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 783 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS A 171 HIS ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS A 417 ASN A 458 ASN A 584 ASN A 748 HIS A 797 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.126753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104348 restraints weight = 12119.669| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.76 r_work: 0.3566 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5732 Z= 0.167 Angle : 0.680 8.175 7798 Z= 0.343 Chirality : 0.045 0.171 920 Planarity : 0.006 0.076 981 Dihedral : 5.952 57.827 757 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.31 % Allowed : 24.24 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.37 (0.30), residues: 704 helix: -0.93 (0.32), residues: 224 sheet: -3.13 (0.57), residues: 72 loop : -1.66 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.005 0.001 HIS A 748 PHE 0.036 0.002 PHE A 596 TYR 0.021 0.002 TYR A 280 ARG 0.003 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 169) hydrogen bonds : angle 5.84780 ( 498) SS BOND : bond 0.00667 ( 5) SS BOND : angle 1.74621 ( 10) covalent geometry : bond 0.00370 ( 5727) covalent geometry : angle 0.67712 ( 7788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8026 (t80) cc_final: 0.7473 (t80) REVERT: A 204 VAL cc_start: 0.8233 (m) cc_final: 0.8014 (m) REVERT: A 231 ASP cc_start: 0.7201 (t0) cc_final: 0.6953 (t0) REVERT: A 245 LYS cc_start: 0.8798 (tttt) cc_final: 0.8335 (tppt) REVERT: A 252 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: A 273 LEU cc_start: 0.8854 (mm) cc_final: 0.8149 (tp) REVERT: A 279 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8257 (pp) REVERT: A 371 SER cc_start: 0.9123 (p) cc_final: 0.8770 (p) REVERT: A 442 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 520 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 728 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 731 ASN cc_start: 0.8039 (p0) cc_final: 0.7536 (t0) REVERT: A 754 PHE cc_start: 0.8224 (t80) cc_final: 0.8017 (t80) REVERT: A 759 PHE cc_start: 0.7679 (m-10) cc_final: 0.7438 (m-10) REVERT: A 783 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7261 (tptp) REVERT: A 808 PHE cc_start: 0.8238 (t80) cc_final: 0.7940 (t80) REVERT: A 814 LEU cc_start: 0.8125 (tt) cc_final: 0.7861 (mt) outliers start: 27 outliers final: 12 residues processed: 134 average time/residue: 0.1170 time to fit residues: 22.7639 Evaluate side-chains 125 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 0.0980 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 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 = 0.4026 r_free = 0.4026 target = 0.126787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104446 restraints weight = 12299.158| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.73 r_work: 0.3562 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5732 Z= 0.127 Angle : 0.623 8.805 7798 Z= 0.308 Chirality : 0.043 0.165 920 Planarity : 0.005 0.063 981 Dihedral : 5.094 50.288 749 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.47 % Allowed : 24.24 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.08 (0.30), residues: 704 helix: -0.43 (0.32), residues: 226 sheet: -3.18 (0.56), residues: 72 loop : -1.60 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 751 HIS 0.003 0.001 HIS A 97 PHE 0.017 0.001 PHE A 808 TYR 0.015 0.002 TYR A 280 ARG 0.002 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 169) hydrogen bonds : angle 5.27063 ( 498) SS BOND : bond 0.00439 ( 5) SS BOND : angle 1.55884 ( 10) covalent geometry : bond 0.00293 ( 5727) covalent geometry : angle 0.62139 ( 7788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8067 (t80) cc_final: 0.7767 (t80) REVERT: A 231 ASP cc_start: 0.7537 (t0) cc_final: 0.7287 (t0) REVERT: A 245 LYS cc_start: 0.8755 (tttt) cc_final: 0.8312 (tppt) REVERT: A 252 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: A 273 LEU cc_start: 0.8854 (mm) cc_final: 0.8150 (tp) REVERT: A 279 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8306 (pp) REVERT: A 371 SER cc_start: 0.9142 (p) cc_final: 0.8784 (p) REVERT: A 395 ASP cc_start: 0.7814 (t70) cc_final: 0.7350 (t0) REVERT: A 520 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 728 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7653 (mm) REVERT: A 731 ASN cc_start: 0.7965 (p0) cc_final: 0.7403 (t0) REVERT: A 783 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7373 (tptp) REVERT: A 814 LEU cc_start: 0.8230 (tt) cc_final: 0.8030 (mt) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 0.1249 time to fit residues: 23.5301 Evaluate side-chains 122 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 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 = 0.3989 r_free = 0.3989 target = 0.123352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100724 restraints weight = 12617.255| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.70 r_work: 0.3500 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5732 Z= 0.192 Angle : 0.681 8.331 7798 Z= 0.337 Chirality : 0.046 0.176 920 Planarity : 0.005 0.064 981 Dihedral : 5.272 47.282 746 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.42 % Allowed : 24.56 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.14 (0.30), residues: 704 helix: -0.54 (0.32), residues: 233 sheet: -3.19 (0.56), residues: 72 loop : -1.62 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 751 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.002 PHE A 808 TYR 0.019 0.002 TYR A 801 ARG 0.008 0.001 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 169) hydrogen bonds : angle 5.33779 ( 498) SS BOND : bond 0.00879 ( 5) SS BOND : angle 1.95896 ( 10) covalent geometry : bond 0.00449 ( 5727) covalent geometry : angle 0.67758 ( 7788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.594 Fit side-chains REVERT: A 113 GLN cc_start: 0.7832 (mp10) cc_final: 0.7534 (mp10) REVERT: A 231 ASP cc_start: 0.7578 (t0) cc_final: 0.7316 (t0) REVERT: A 245 LYS cc_start: 0.8799 (tttt) cc_final: 0.8543 (mmtm) REVERT: A 252 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: A 273 LEU cc_start: 0.8945 (mm) cc_final: 0.8258 (tp) REVERT: A 279 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8489 (pp) REVERT: A 300 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8546 (m) REVERT: A 371 SER cc_start: 0.9145 (p) cc_final: 0.8813 (p) REVERT: A 395 ASP cc_start: 0.7816 (t70) cc_final: 0.7413 (t0) REVERT: A 416 THR cc_start: 0.8849 (m) cc_final: 0.8575 (t) REVERT: A 442 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8474 (t) REVERT: A 473 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.7022 (t80) REVERT: A 728 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7704 (mm) REVERT: A 783 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7440 (tptp) REVERT: A 814 LEU cc_start: 0.8349 (tt) cc_final: 0.8013 (mt) outliers start: 34 outliers final: 18 residues processed: 132 average time/residue: 0.1173 time to fit residues: 22.3065 Evaluate side-chains 132 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 0.0870 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 GLN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.125560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103427 restraints weight = 12365.108| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.70 r_work: 0.3555 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5732 Z= 0.118 Angle : 0.604 8.118 7798 Z= 0.297 Chirality : 0.044 0.158 920 Planarity : 0.004 0.064 981 Dihedral : 4.863 43.577 746 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.99 % Allowed : 25.36 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.96 (0.30), residues: 704 helix: -0.26 (0.33), residues: 233 sheet: -3.14 (0.57), residues: 72 loop : -1.58 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 474 HIS 0.003 0.001 HIS A 97 PHE 0.019 0.001 PHE A 808 TYR 0.014 0.002 TYR A 801 ARG 0.003 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 169) hydrogen bonds : angle 5.00910 ( 498) SS BOND : bond 0.00365 ( 5) SS BOND : angle 1.52306 ( 10) covalent geometry : bond 0.00274 ( 5727) covalent geometry : angle 0.60207 ( 7788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.586 Fit side-chains REVERT: A 231 ASP cc_start: 0.7634 (t0) cc_final: 0.7357 (t0) REVERT: A 245 LYS cc_start: 0.8722 (tttt) cc_final: 0.8424 (mmtm) REVERT: A 252 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: A 273 LEU cc_start: 0.8901 (mm) cc_final: 0.8233 (tp) REVERT: A 279 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8382 (pp) REVERT: A 371 SER cc_start: 0.9044 (p) cc_final: 0.8701 (p) REVERT: A 395 ASP cc_start: 0.7776 (t70) cc_final: 0.7384 (t0) REVERT: A 416 THR cc_start: 0.8770 (m) cc_final: 0.8476 (t) REVERT: A 473 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 728 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 814 LEU cc_start: 0.8213 (tt) cc_final: 0.7825 (mt) outliers start: 25 outliers final: 11 residues processed: 126 average time/residue: 0.1193 time to fit residues: 21.9125 Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 4 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 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 = 0.4023 r_free = 0.4023 target = 0.125590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103432 restraints weight = 12351.055| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.69 r_work: 0.3552 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5732 Z= 0.126 Angle : 0.598 7.698 7798 Z= 0.296 Chirality : 0.044 0.144 920 Planarity : 0.004 0.064 981 Dihedral : 4.300 30.103 742 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.83 % Allowed : 25.36 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.89 (0.31), residues: 704 helix: -0.17 (0.33), residues: 231 sheet: -3.09 (0.58), residues: 72 loop : -1.57 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.016 0.001 PHE A 808 TYR 0.015 0.002 TYR A 801 ARG 0.002 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 169) hydrogen bonds : angle 4.90884 ( 498) SS BOND : bond 0.00410 ( 5) SS BOND : angle 1.42246 ( 10) covalent geometry : bond 0.00296 ( 5727) covalent geometry : angle 0.59579 ( 7788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.635 Fit side-chains REVERT: A 95 PHE cc_start: 0.8038 (t80) cc_final: 0.7663 (t80) REVERT: A 231 ASP cc_start: 0.7626 (t0) cc_final: 0.7336 (t0) REVERT: A 245 LYS cc_start: 0.8637 (tttt) cc_final: 0.8356 (mmtm) REVERT: A 252 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: A 273 LEU cc_start: 0.8893 (mm) cc_final: 0.8240 (tp) REVERT: A 279 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8464 (pp) REVERT: A 371 SER cc_start: 0.9040 (p) cc_final: 0.8672 (p) REVERT: A 395 ASP cc_start: 0.7800 (t70) cc_final: 0.7374 (t0) REVERT: A 416 THR cc_start: 0.8755 (m) cc_final: 0.8448 (t) REVERT: A 473 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7095 (t80) REVERT: A 728 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7551 (mm) REVERT: A 814 LEU cc_start: 0.8223 (tt) cc_final: 0.7777 (mt) outliers start: 24 outliers final: 16 residues processed: 119 average time/residue: 0.1373 time to fit residues: 23.4758 Evaluate side-chains 117 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.0040 chunk 46 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 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 = 0.4028 r_free = 0.4028 target = 0.125654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103355 restraints weight = 12381.100| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.71 r_work: 0.3554 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5732 Z= 0.123 Angle : 0.597 7.447 7798 Z= 0.297 Chirality : 0.043 0.142 920 Planarity : 0.004 0.063 981 Dihedral : 4.225 29.556 742 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.83 % Allowed : 26.32 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.31), residues: 704 helix: -0.04 (0.34), residues: 232 sheet: -2.54 (0.71), residues: 51 loop : -1.64 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 474 HIS 0.002 0.001 HIS A 256 PHE 0.015 0.001 PHE A 808 TYR 0.014 0.002 TYR A 801 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 169) hydrogen bonds : angle 4.86387 ( 498) SS BOND : bond 0.00409 ( 5) SS BOND : angle 1.36938 ( 10) covalent geometry : bond 0.00290 ( 5727) covalent geometry : angle 0.59578 ( 7788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.607 Fit side-chains REVERT: A 95 PHE cc_start: 0.8030 (t80) cc_final: 0.7799 (t80) REVERT: A 182 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8214 (tp) REVERT: A 231 ASP cc_start: 0.7596 (t0) cc_final: 0.7313 (t0) REVERT: A 245 LYS cc_start: 0.8596 (tttt) cc_final: 0.8324 (mmtm) REVERT: A 252 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: A 273 LEU cc_start: 0.8888 (mm) cc_final: 0.8273 (tp) REVERT: A 279 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8455 (pp) REVERT: A 371 SER cc_start: 0.9004 (p) cc_final: 0.8628 (p) REVERT: A 388 LEU cc_start: 0.7485 (mm) cc_final: 0.7217 (mp) REVERT: A 395 ASP cc_start: 0.7797 (t70) cc_final: 0.7349 (t0) REVERT: A 416 THR cc_start: 0.8692 (m) cc_final: 0.8373 (t) REVERT: A 473 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 728 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7551 (mm) REVERT: A 745 MET cc_start: 0.7633 (mmp) cc_final: 0.7416 (tpp) outliers start: 24 outliers final: 15 residues processed: 115 average time/residue: 0.1155 time to fit residues: 19.4460 Evaluate side-chains 114 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 67 optimal weight: 5.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 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 = 0.3909 r_free = 0.3909 target = 0.118593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095486 restraints weight = 12414.431| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.75 r_work: 0.3404 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 5732 Z= 0.292 Angle : 0.757 11.049 7798 Z= 0.376 Chirality : 0.049 0.163 920 Planarity : 0.005 0.057 981 Dihedral : 4.928 33.858 742 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.94 % Allowed : 25.04 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.00 (0.31), residues: 704 helix: -0.42 (0.33), residues: 233 sheet: -2.96 (0.63), residues: 60 loop : -1.64 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 546 HIS 0.005 0.001 HIS A 209 PHE 0.021 0.002 PHE A 473 TYR 0.017 0.002 TYR A 801 ARG 0.005 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 169) hydrogen bonds : angle 5.46368 ( 498) SS BOND : bond 0.00791 ( 5) SS BOND : angle 2.23402 ( 10) covalent geometry : bond 0.00683 ( 5727) covalent geometry : angle 0.75285 ( 7788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.597 Fit side-chains REVERT: A 95 PHE cc_start: 0.8344 (t80) cc_final: 0.8050 (t80) REVERT: A 182 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 231 ASP cc_start: 0.7665 (t0) cc_final: 0.7302 (t0) REVERT: A 245 LYS cc_start: 0.8761 (tttt) cc_final: 0.8437 (mmtm) REVERT: A 252 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: A 273 LEU cc_start: 0.8998 (mm) cc_final: 0.8303 (tp) REVERT: A 371 SER cc_start: 0.9131 (p) cc_final: 0.8772 (p) REVERT: A 395 ASP cc_start: 0.7946 (t70) cc_final: 0.7449 (t0) REVERT: A 473 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7165 (t80) REVERT: A 517 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.6036 (tp-100) REVERT: A 728 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 731 ASN cc_start: 0.7780 (p0) cc_final: 0.7315 (p0) outliers start: 31 outliers final: 20 residues processed: 122 average time/residue: 0.1265 time to fit residues: 22.2499 Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 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 = 0.3958 r_free = 0.3958 target = 0.121819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099026 restraints weight = 12336.599| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.79 r_work: 0.3470 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5732 Z= 0.152 Angle : 0.681 11.395 7798 Z= 0.330 Chirality : 0.045 0.149 920 Planarity : 0.005 0.064 981 Dihedral : 4.633 32.281 742 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.99 % Allowed : 26.48 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.87 (0.31), residues: 704 helix: -0.27 (0.34), residues: 233 sheet: -2.89 (0.64), residues: 59 loop : -1.59 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 474 HIS 0.003 0.001 HIS A 256 PHE 0.021 0.001 PHE A 759 TYR 0.015 0.002 TYR A 234 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 169) hydrogen bonds : angle 5.15765 ( 498) SS BOND : bond 0.00461 ( 5) SS BOND : angle 1.46708 ( 10) covalent geometry : bond 0.00364 ( 5727) covalent geometry : angle 0.67985 ( 7788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8392 (t80) cc_final: 0.8046 (t80) REVERT: A 182 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8142 (tp) REVERT: A 231 ASP cc_start: 0.7620 (t0) cc_final: 0.7283 (t0) REVERT: A 245 LYS cc_start: 0.8619 (tttt) cc_final: 0.8307 (mmtm) REVERT: A 252 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: A 273 LEU cc_start: 0.8947 (mm) cc_final: 0.8287 (tp) REVERT: A 371 SER cc_start: 0.9068 (p) cc_final: 0.8690 (p) REVERT: A 395 ASP cc_start: 0.7942 (t70) cc_final: 0.7494 (t0) REVERT: A 416 THR cc_start: 0.8752 (m) cc_final: 0.8524 (t) REVERT: A 473 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7252 (t80) REVERT: A 728 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7736 (mm) REVERT: A 745 MET cc_start: 0.7735 (mmp) cc_final: 0.7508 (tpp) outliers start: 25 outliers final: 15 residues processed: 112 average time/residue: 0.1380 time to fit residues: 21.7683 Evaluate side-chains 116 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100763 restraints weight = 12487.678| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.71 r_work: 0.3505 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5732 Z= 0.141 Angle : 0.672 11.594 7798 Z= 0.324 Chirality : 0.045 0.154 920 Planarity : 0.005 0.068 981 Dihedral : 4.469 30.635 742 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.67 % Allowed : 26.95 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.80 (0.31), residues: 704 helix: -0.22 (0.34), residues: 234 sheet: -2.60 (0.72), residues: 47 loop : -1.64 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 474 HIS 0.004 0.001 HIS A 521 PHE 0.016 0.001 PHE A 759 TYR 0.016 0.002 TYR A 234 ARG 0.004 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 169) hydrogen bonds : angle 5.05511 ( 498) SS BOND : bond 0.00410 ( 5) SS BOND : angle 1.42191 ( 10) covalent geometry : bond 0.00332 ( 5727) covalent geometry : angle 0.67064 ( 7788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8379 (t80) cc_final: 0.8048 (t80) REVERT: A 182 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8165 (tp) REVERT: A 231 ASP cc_start: 0.7625 (t0) cc_final: 0.7326 (t0) REVERT: A 245 LYS cc_start: 0.8595 (tttt) cc_final: 0.8289 (mmtm) REVERT: A 252 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 273 LEU cc_start: 0.8946 (mm) cc_final: 0.8311 (tp) REVERT: A 371 SER cc_start: 0.8972 (p) cc_final: 0.8595 (p) REVERT: A 395 ASP cc_start: 0.7825 (t70) cc_final: 0.7394 (t0) REVERT: A 728 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 745 MET cc_start: 0.7664 (mmp) cc_final: 0.7456 (tpp) outliers start: 23 outliers final: 16 residues processed: 116 average time/residue: 0.1392 time to fit residues: 22.7285 Evaluate side-chains 117 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 64 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 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 = 0.3977 r_free = 0.3977 target = 0.122369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099825 restraints weight = 12374.451| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.70 r_work: 0.3491 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5732 Z= 0.152 Angle : 0.685 11.471 7798 Z= 0.330 Chirality : 0.046 0.189 920 Planarity : 0.005 0.068 981 Dihedral : 4.508 30.463 742 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.19 % Allowed : 28.71 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.82 (0.31), residues: 704 helix: -0.21 (0.34), residues: 233 sheet: -2.63 (0.71), residues: 47 loop : -1.66 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 474 HIS 0.002 0.001 HIS A 256 PHE 0.022 0.001 PHE A 706 TYR 0.016 0.002 TYR A 234 ARG 0.005 0.001 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 169) hydrogen bonds : angle 5.08666 ( 498) SS BOND : bond 0.00460 ( 5) SS BOND : angle 1.46597 ( 10) covalent geometry : bond 0.00360 ( 5727) covalent geometry : angle 0.68367 ( 7788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3201.09 seconds wall clock time: 55 minutes 33.75 seconds (3333.75 seconds total)