Starting phenix.real_space_refine on Tue Jan 14 04:21:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvv_37873/01_2025/8wvv_37873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvv_37873/01_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_37873/01_2025/8wvv_37873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvv_37873/01_2025/8wvv_37873.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvv_37873/01_2025/8wvv_37873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvv_37873/01_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-5571/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: 3.64, per 1000 atoms: 0.65 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: 1.23 Conformation dependent library (CDL) restraints added in 744.1 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: 0.60 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: 1.79 Time building geometry restraints manager: 1.48 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: 1.690 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.980 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- 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 5727 Z= 0.443 Angle : 1.257 24.165 7788 Z= 0.813 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 *********************** 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 : 0.621 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: 0.1517 time to fit residues: 24.4130 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 : 0.618 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.126256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103659 restraints weight = 12184.492| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.78 r_work: 0.3551 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5727 Z= 0.252 Angle : 0.683 8.303 7788 Z= 0.343 Chirality : 0.045 0.161 920 Planarity : 0.006 0.077 981 Dihedral : 5.960 57.798 757 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.15 % Allowed : 24.40 % 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: -2.38 (0.30), residues: 704 helix: -0.93 (0.32), residues: 224 sheet: -3.14 (0.56), residues: 72 loop : -1.66 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.006 0.001 HIS A 748 PHE 0.035 0.002 PHE A 596 TYR 0.020 0.002 TYR A 280 ARG 0.003 0.000 ARG A 817 *********************** 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: 26 poor density : 115 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8059 (t80) cc_final: 0.7570 (t80) REVERT: A 204 VAL cc_start: 0.8278 (m) cc_final: 0.8053 (m) REVERT: A 231 ASP cc_start: 0.7248 (t0) cc_final: 0.7012 (t0) REVERT: A 245 LYS cc_start: 0.8880 (tttt) cc_final: 0.8390 (tppt) REVERT: A 252 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: A 273 LEU cc_start: 0.8876 (mm) cc_final: 0.8176 (tp) REVERT: A 279 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8262 (pp) REVERT: A 371 SER cc_start: 0.9125 (p) cc_final: 0.8756 (p) REVERT: A 395 ASP cc_start: 0.7797 (t70) cc_final: 0.7396 (t0) REVERT: A 442 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 520 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7716 (mp) REVERT: A 728 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7611 (mm) REVERT: A 731 ASN cc_start: 0.8059 (p0) cc_final: 0.7537 (t0) REVERT: A 783 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7314 (tptp) REVERT: A 808 PHE cc_start: 0.8275 (t80) cc_final: 0.7977 (t80) REVERT: A 814 LEU cc_start: 0.8135 (tt) cc_final: 0.7877 (mt) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.1236 time to fit residues: 23.9569 Evaluate side-chains 129 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 388 LEU 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 593 ILE Chi-restraints excluded: chain A residue 709 THR 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 796 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 0.0020 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 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 = 0.4029 r_free = 0.4029 target = 0.127031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104693 restraints weight = 12294.382| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.73 r_work: 0.3566 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5727 Z= 0.181 Angle : 0.617 8.689 7788 Z= 0.304 Chirality : 0.043 0.162 920 Planarity : 0.005 0.062 981 Dihedral : 5.068 49.770 748 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.78 % Allowed : 24.56 % 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: -2.08 (0.30), residues: 704 helix: -0.45 (0.33), residues: 226 sheet: -3.16 (0.56), residues: 72 loop : -1.59 (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 0.018 0.001 PHE A 808 TYR 0.015 0.002 TYR A 280 ARG 0.002 0.000 ARG A 135 *********************** 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 145 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8072 (t80) cc_final: 0.7785 (t80) REVERT: A 231 ASP cc_start: 0.7513 (t0) cc_final: 0.7100 (t0) REVERT: A 245 LYS cc_start: 0.8728 (tttt) cc_final: 0.8294 (tppt) REVERT: A 252 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: A 273 LEU cc_start: 0.8851 (mm) cc_final: 0.8146 (tp) REVERT: A 279 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8315 (pp) REVERT: A 371 SER cc_start: 0.9149 (p) cc_final: 0.8792 (p) REVERT: A 395 ASP cc_start: 0.7809 (t70) cc_final: 0.7357 (t0) REVERT: A 520 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 728 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7651 (mm) REVERT: A 731 ASN cc_start: 0.7982 (p0) cc_final: 0.7385 (t0) REVERT: A 783 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7413 (tptp) REVERT: A 814 LEU cc_start: 0.8229 (tt) cc_final: 0.8021 (mt) outliers start: 30 outliers final: 13 residues processed: 134 average time/residue: 0.1226 time to fit residues: 23.6727 Evaluate side-chains 123 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 595 THR 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: 2.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** A 379 GLN ** A 417 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 = 0.4019 r_free = 0.4019 target = 0.125425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102974 restraints weight = 12651.952| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.73 r_work: 0.3544 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5727 Z= 0.223 Angle : 0.629 8.243 7788 Z= 0.311 Chirality : 0.045 0.162 920 Planarity : 0.005 0.065 981 Dihedral : 4.935 45.011 746 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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: -2.08 (0.30), residues: 704 helix: -0.45 (0.33), residues: 234 sheet: -3.13 (0.57), residues: 72 loop : -1.61 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.016 0.001 PHE A 808 TYR 0.020 0.002 TYR A 801 ARG 0.002 0.000 ARG A 356 *********************** 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 142 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.674 Fit side-chains REVERT: A 113 GLN cc_start: 0.7676 (mp10) cc_final: 0.7429 (mp10) REVERT: A 231 ASP cc_start: 0.7526 (t0) cc_final: 0.7220 (t0) REVERT: A 245 LYS cc_start: 0.8763 (tttt) cc_final: 0.8504 (mmtm) REVERT: A 252 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: A 273 LEU cc_start: 0.8877 (mm) cc_final: 0.8198 (tp) REVERT: A 279 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8419 (pp) REVERT: A 371 SER cc_start: 0.9126 (p) cc_final: 0.8780 (p) REVERT: A 395 ASP cc_start: 0.7780 (t70) cc_final: 0.7383 (t0) REVERT: A 416 THR cc_start: 0.8842 (m) cc_final: 0.8542 (t) REVERT: A 442 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8420 (t) REVERT: A 473 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 728 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7646 (mm) REVERT: A 783 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7586 (tptp) REVERT: A 814 LEU cc_start: 0.8290 (tt) cc_final: 0.7970 (mt) outliers start: 31 outliers final: 15 residues processed: 128 average time/residue: 0.1269 time to fit residues: 23.2611 Evaluate side-chains 127 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 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 640 THR 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: 0.9990 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.125022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102767 restraints weight = 12443.978| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.70 r_work: 0.3541 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5727 Z= 0.215 Angle : 0.622 8.374 7788 Z= 0.304 Chirality : 0.044 0.151 920 Planarity : 0.005 0.063 981 Dihedral : 4.818 42.748 746 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.15 % Allowed : 25.36 % Favored : 70.49 % 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: -1.94 (0.30), residues: 704 helix: -0.24 (0.33), residues: 233 sheet: -3.03 (0.58), residues: 72 loop : -1.60 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.018 0.001 PHE A 808 TYR 0.016 0.002 TYR A 801 ARG 0.002 0.000 ARG A 392 *********************** 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 133 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.692 Fit side-chains REVERT: A 231 ASP cc_start: 0.7574 (t0) cc_final: 0.7315 (t0) REVERT: A 245 LYS cc_start: 0.8695 (tttt) cc_final: 0.8418 (mmtm) REVERT: A 252 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: A 273 LEU cc_start: 0.8902 (mm) cc_final: 0.8230 (tp) REVERT: A 279 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8459 (pp) REVERT: A 371 SER cc_start: 0.9125 (p) cc_final: 0.8765 (p) REVERT: A 395 ASP cc_start: 0.7760 (t70) cc_final: 0.7330 (t0) REVERT: A 416 THR cc_start: 0.8813 (m) cc_final: 0.8510 (t) REVERT: A 473 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.7100 (t80) REVERT: A 728 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7645 (mm) REVERT: A 814 LEU cc_start: 0.8228 (tt) cc_final: 0.7805 (mt) outliers start: 26 outliers final: 13 residues processed: 122 average time/residue: 0.1161 time to fit residues: 20.5451 Evaluate side-chains 117 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 293 HIS 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 593 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 187 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101356 restraints weight = 12352.881| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.69 r_work: 0.3516 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5727 Z= 0.246 Angle : 0.625 8.032 7788 Z= 0.312 Chirality : 0.045 0.151 920 Planarity : 0.005 0.065 981 Dihedral : 4.422 31.949 742 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.78 % Allowed : 24.24 % Favored : 70.97 % 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: -1.90 (0.31), residues: 704 helix: -0.29 (0.33), residues: 233 sheet: -2.99 (0.63), residues: 62 loop : -1.57 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.017 0.001 PHE A 808 TYR 0.015 0.002 TYR A 801 ARG 0.002 0.000 ARG A 356 *********************** 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 132 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.501 Fit side-chains REVERT: A 95 PHE cc_start: 0.8097 (t80) cc_final: 0.7742 (t80) REVERT: A 231 ASP cc_start: 0.7538 (t0) cc_final: 0.7279 (t0) REVERT: A 245 LYS cc_start: 0.8632 (tttt) cc_final: 0.8364 (mmtm) REVERT: A 252 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: A 273 LEU cc_start: 0.8914 (mm) cc_final: 0.8255 (tp) REVERT: A 279 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8469 (pp) REVERT: A 371 SER cc_start: 0.9063 (p) cc_final: 0.8715 (p) REVERT: A 395 ASP cc_start: 0.7789 (t70) cc_final: 0.7392 (t0) REVERT: A 416 THR cc_start: 0.8772 (m) cc_final: 0.8497 (t) REVERT: A 473 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7074 (t80) REVERT: A 728 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7556 (mm) REVERT: A 731 ASN cc_start: 0.7672 (p0) cc_final: 0.7348 (p0) REVERT: A 783 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7589 (tptp) REVERT: A 814 LEU cc_start: 0.8274 (tt) cc_final: 0.7761 (mt) outliers start: 30 outliers final: 17 residues processed: 122 average time/residue: 0.1309 time to fit residues: 22.8872 Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 386 GLN 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 573 SER 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 728 LEU 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 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: 6.9990 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 187 ASN ** 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 = 0.3989 r_free = 0.3989 target = 0.123130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100689 restraints weight = 12334.959| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.69 r_work: 0.3511 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5727 Z= 0.260 Angle : 0.642 10.089 7788 Z= 0.318 Chirality : 0.045 0.147 920 Planarity : 0.005 0.064 981 Dihedral : 4.446 31.668 742 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.63 % Allowed : 25.20 % Favored : 70.18 % 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: -0.32 (0.34), residues: 233 sheet: -2.69 (0.68), residues: 52 loop : -1.62 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 751 HIS 0.003 0.001 HIS A 209 PHE 0.016 0.001 PHE A 808 TYR 0.014 0.002 TYR A 801 ARG 0.002 0.000 ARG A 135 *********************** 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 132 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.7562 (t0) cc_final: 0.7306 (t0) REVERT: A 245 LYS cc_start: 0.8615 (tttt) cc_final: 0.8340 (mmtm) REVERT: A 252 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 273 LEU cc_start: 0.8941 (mm) cc_final: 0.8258 (tp) REVERT: A 279 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8467 (pp) REVERT: A 371 SER cc_start: 0.9053 (p) cc_final: 0.8689 (p) REVERT: A 395 ASP cc_start: 0.7806 (t70) cc_final: 0.7402 (t0) REVERT: A 416 THR cc_start: 0.8804 (m) cc_final: 0.8525 (t) REVERT: A 473 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.7128 (t80) REVERT: A 728 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7577 (mm) REVERT: A 731 ASN cc_start: 0.7708 (p0) cc_final: 0.7425 (p0) REVERT: A 814 LEU cc_start: 0.8307 (tt) cc_final: 0.8103 (tt) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 0.1304 time to fit residues: 22.9508 Evaluate side-chains 118 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 213 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 442 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 67 optimal weight: 0.5980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 187 ASN ** 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 = 0.4009 r_free = 0.4009 target = 0.124522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102343 restraints weight = 12382.005| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.69 r_work: 0.3537 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5727 Z= 0.193 Angle : 0.633 9.865 7788 Z= 0.306 Chirality : 0.043 0.142 920 Planarity : 0.005 0.066 981 Dihedral : 4.337 29.975 742 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.99 % Allowed : 26.00 % Favored : 70.02 % 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: -1.77 (0.31), residues: 704 helix: -0.13 (0.34), residues: 233 sheet: -2.96 (0.63), residues: 62 loop : -1.52 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.002 0.001 HIS A 521 PHE 0.016 0.001 PHE A 808 TYR 0.015 0.002 TYR A 234 ARG 0.005 0.000 ARG A 643 *********************** 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 123 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.7563 (t0) cc_final: 0.7329 (t0) REVERT: A 245 LYS cc_start: 0.8580 (tttt) cc_final: 0.8279 (mmtm) REVERT: A 252 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: A 273 LEU cc_start: 0.8935 (mm) cc_final: 0.8244 (tp) REVERT: A 279 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8441 (pp) REVERT: A 371 SER cc_start: 0.8994 (p) cc_final: 0.8618 (p) REVERT: A 395 ASP cc_start: 0.7797 (t70) cc_final: 0.7384 (t0) REVERT: A 416 THR cc_start: 0.8769 (m) cc_final: 0.8487 (t) REVERT: A 473 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7177 (t80) REVERT: A 728 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7586 (mm) REVERT: A 731 ASN cc_start: 0.7660 (p0) cc_final: 0.7393 (p0) REVERT: A 745 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7430 (tpp) REVERT: A 783 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7611 (tptp) outliers start: 25 outliers final: 17 residues processed: 114 average time/residue: 0.1252 time to fit residues: 20.6365 Evaluate side-chains 117 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 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 279 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE 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 745 MET 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 Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** 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 = 0.3989 r_free = 0.3989 target = 0.123292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100818 restraints weight = 12407.304| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.69 r_work: 0.3510 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5727 Z= 0.223 Angle : 0.652 9.712 7788 Z= 0.315 Chirality : 0.044 0.150 920 Planarity : 0.005 0.067 981 Dihedral : 4.373 30.278 742 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.99 % Allowed : 27.11 % Favored : 68.90 % 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: -1.74 (0.31), residues: 704 helix: -0.12 (0.34), residues: 233 sheet: -2.52 (0.79), residues: 42 loop : -1.66 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 751 HIS 0.002 0.001 HIS A 521 PHE 0.027 0.001 PHE A 95 TYR 0.016 0.002 TYR A 234 ARG 0.004 0.000 ARG A 643 *********************** 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 128 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8468 (tp30) cc_final: 0.8249 (tp30) REVERT: A 87 GLN cc_start: 0.7989 (tp40) cc_final: 0.7710 (mm-40) REVERT: A 231 ASP cc_start: 0.7572 (t0) cc_final: 0.7339 (t0) REVERT: A 245 LYS cc_start: 0.8590 (tttt) cc_final: 0.8293 (mmtm) REVERT: A 252 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: A 273 LEU cc_start: 0.8940 (mm) cc_final: 0.8303 (tp) REVERT: A 388 LEU cc_start: 0.7657 (mm) cc_final: 0.7425 (mt) REVERT: A 395 ASP cc_start: 0.7802 (t70) cc_final: 0.7426 (t0) REVERT: A 473 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7237 (t80) REVERT: A 728 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7673 (mm) REVERT: A 731 ASN cc_start: 0.7661 (p0) cc_final: 0.7382 (p0) REVERT: A 783 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7601 (tptp) outliers start: 25 outliers final: 17 residues processed: 118 average time/residue: 0.1404 time to fit residues: 23.1780 Evaluate side-chains 115 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 386 GLN 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 681 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 154 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS A 226 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.122661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.100079 restraints weight = 12484.178| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.70 r_work: 0.3495 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5727 Z= 0.252 Angle : 0.675 9.848 7788 Z= 0.325 Chirality : 0.045 0.151 920 Planarity : 0.005 0.067 981 Dihedral : 4.475 30.685 742 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.15 % Allowed : 27.43 % Favored : 68.42 % 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: -1.76 (0.31), residues: 704 helix: -0.19 (0.33), residues: 232 sheet: -2.44 (0.73), residues: 47 loop : -1.63 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 751 HIS 0.002 0.001 HIS A 521 PHE 0.015 0.001 PHE A 808 TYR 0.017 0.002 TYR A 234 ARG 0.005 0.000 ARG A 643 ********************** 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 123 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8470 (tp30) cc_final: 0.8186 (tp30) REVERT: A 87 GLN cc_start: 0.7969 (tp40) cc_final: 0.7614 (mm-40) REVERT: A 182 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 231 ASP cc_start: 0.7588 (t0) cc_final: 0.7356 (t0) REVERT: A 245 LYS cc_start: 0.8596 (tttt) cc_final: 0.8258 (mmtm) REVERT: A 252 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: A 273 LEU cc_start: 0.8949 (mm) cc_final: 0.8310 (tp) REVERT: A 371 SER cc_start: 0.9128 (m) cc_final: 0.8486 (t) REVERT: A 388 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7469 (mt) REVERT: A 395 ASP cc_start: 0.7827 (t70) cc_final: 0.7457 (t0) REVERT: A 473 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7228 (t80) REVERT: A 728 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7678 (mm) REVERT: A 783 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7558 (tptp) outliers start: 26 outliers final: 17 residues processed: 114 average time/residue: 0.1526 time to fit residues: 24.5339 Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 386 GLN Chi-restraints excluded: chain A residue 388 LEU 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 681 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 4 optimal weight: 0.0000 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4502 ------------------------------------------------------------------------------- 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 163 ASN A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.125555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.103448 restraints weight = 12480.731| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.60 r_work: 0.3568 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5727 Z= 0.180 Angle : 0.643 9.899 7788 Z= 0.308 Chirality : 0.043 0.144 920 Planarity : 0.005 0.069 981 Dihedral : 4.277 29.240 742 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.67 % Allowed : 28.07 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.62 (0.31), residues: 704 helix: 0.01 (0.34), residues: 231 sheet: -2.39 (0.74), residues: 47 loop : -1.60 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 474 HIS 0.002 0.001 HIS A 256 PHE 0.028 0.001 PHE A 95 TYR 0.015 0.002 TYR A 234 ARG 0.005 0.000 ARG A 643 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.01 seconds wall clock time: 56 minutes 12.47 seconds (3372.47 seconds total)