Starting phenix.real_space_refine on Sun Apr 5 00:21:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s11_54430/04_2026/9s11_54430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s11_54430/04_2026/9s11_54430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s11_54430/04_2026/9s11_54430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s11_54430/04_2026/9s11_54430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s11_54430/04_2026/9s11_54430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s11_54430/04_2026/9s11_54430.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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 17 5.16 5 C 3934 2.51 5 N 1108 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6276 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6276 Classifications: {'peptide': 787} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 756} Time building chain proxies: 1.30, per 1000 atoms: 0.21 Number of scatterers: 6276 At special positions: 0 Unit cell: (93.22, 76.7, 90.86, 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 17 16.00 O 1217 8.00 N 1108 7.00 C 3934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 217.2 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 12.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.888A pdb=" N GLN A 479 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.521A pdb=" N VAL A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLY A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 584' Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.552A pdb=" N GLY A 588 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.574A pdb=" N ARG A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.619A pdb=" N LEU A 662 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 723 through 737 removed outlier: 3.876A pdb=" N ILE A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 774 removed outlier: 3.969A pdb=" N LYS A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.734A pdb=" N GLY A 6 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 105 removed outlier: 7.432A pdb=" N LEU A 111 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 162 removed outlier: 4.061A pdb=" N LEU A 157 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA8, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA9, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.831A pdb=" N THR A 231 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AB2, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AB3, first strand: chain 'A' and resid 447 through 449 removed outlier: 5.629A pdb=" N GLY A 520 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL A 513 " --> pdb=" O GLY A 520 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 481 through 483 Processing sheet with id=AB5, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.867A pdb=" N GLU A 533 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 556 through 558 removed outlier: 5.087A pdb=" N SER A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR A 706 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE A 712 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 684 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 652 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 688 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR A 650 " --> pdb=" O ARG A 688 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 315 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: 1.00 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1515 1.33 - 1.45: 1494 1.45 - 1.57: 3401 1.57 - 1.69: 0 1.69 - 1.82: 25 Bond restraints: 6435 Sorted by residual: bond pdb=" C PRO A 750 " pdb=" N PRO A 751 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.12e-02 7.97e+03 8.03e+00 bond pdb=" CB LYS A 600 " pdb=" CG LYS A 600 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CE2 PHE A 476 " pdb=" CZ PHE A 476 " ideal model delta sigma weight residual 1.382 1.337 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" SD MET A 388 " pdb=" CE MET A 388 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 1.98e+00 bond pdb=" CB MET A 388 " pdb=" CG MET A 388 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.97e+00 ... (remaining 6430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8417 1.88 - 3.77: 276 3.77 - 5.65: 47 5.65 - 7.53: 13 7.53 - 9.41: 5 Bond angle restraints: 8758 Sorted by residual: angle pdb=" CA LYS A 600 " pdb=" CB LYS A 600 " pdb=" CG LYS A 600 " ideal model delta sigma weight residual 114.10 123.51 -9.41 2.00e+00 2.50e-01 2.22e+01 angle pdb=" C GLY A 584 " pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta sigma weight residual 123.17 116.30 6.87 1.49e+00 4.50e-01 2.13e+01 angle pdb=" C LYS A 600 " pdb=" CA LYS A 600 " pdb=" CB LYS A 600 " ideal model delta sigma weight residual 111.97 121.13 -9.16 1.99e+00 2.53e-01 2.12e+01 angle pdb=" CA GLU A 208 " pdb=" CB GLU A 208 " pdb=" CG GLU A 208 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C ASP A 567 " pdb=" CA ASP A 567 " pdb=" CB ASP A 567 " ideal model delta sigma weight residual 109.53 115.13 -5.60 1.65e+00 3.67e-01 1.15e+01 ... (remaining 8753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 3059 15.96 - 31.93: 500 31.93 - 47.89: 137 47.89 - 63.86: 47 63.86 - 79.82: 12 Dihedral angle restraints: 3755 sinusoidal: 1497 harmonic: 2258 Sorted by residual: dihedral pdb=" CA LYS A 749 " pdb=" C LYS A 749 " pdb=" N PRO A 750 " pdb=" CA PRO A 750 " ideal model delta harmonic sigma weight residual -180.00 -146.46 -33.54 0 5.00e+00 4.00e-02 4.50e+01 dihedral pdb=" CA LYS A 517 " pdb=" C LYS A 517 " pdb=" N TYR A 518 " pdb=" CA TYR A 518 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLU A 658 " pdb=" C GLU A 658 " pdb=" N ALA A 659 " pdb=" CA ALA A 659 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 3752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 697 0.053 - 0.106: 186 0.106 - 0.159: 33 0.159 - 0.212: 4 0.212 - 0.265: 2 Chirality restraints: 922 Sorted by residual: chirality pdb=" CB VAL A 473 " pdb=" CA VAL A 473 " pdb=" CG1 VAL A 473 " pdb=" CG2 VAL A 473 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA LYS A 600 " pdb=" N LYS A 600 " pdb=" C LYS A 600 " pdb=" CB LYS A 600 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ASP A 585 " pdb=" N ASP A 585 " pdb=" C ASP A 585 " pdb=" CB ASP A 585 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 919 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 570 " 0.022 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR A 570 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 570 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 570 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 570 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 570 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 570 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 570 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 726 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLN A 726 " 0.062 2.00e-02 2.50e+03 pdb=" O GLN A 726 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE A 727 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 58 " 0.225 9.50e-02 1.11e+02 1.01e-01 6.56e+00 pdb=" NE ARG A 58 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 58 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 58 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 58 " 0.005 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 175 2.66 - 3.22: 6131 3.22 - 3.78: 9993 3.78 - 4.34: 14132 4.34 - 4.90: 23196 Nonbonded interactions: 53627 Sorted by model distance: nonbonded pdb=" O ASP A 106 " pdb=" OG1 THR A 109 " model vdw 2.095 3.040 nonbonded pdb=" NH1 ARG A 597 " pdb=" O SER A 738 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASN A 43 " pdb=" OG1 THR A 349 " model vdw 2.210 3.040 nonbonded pdb=" O PHE A 42 " pdb=" N GLU A 44 " model vdw 2.238 3.120 nonbonded pdb=" O ILE A 654 " pdb=" OH TYR A 675 " model vdw 2.263 3.040 ... (remaining 53622 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: 1.150 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.130 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6435 Z= 0.213 Angle : 0.836 9.414 8758 Z= 0.450 Chirality : 0.049 0.265 922 Planarity : 0.005 0.101 1148 Dihedral : 18.045 79.820 2317 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 1.02 % Allowed : 14.01 % Favored : 84.97 % Rotamer: Outliers : 3.42 % Allowed : 33.28 % Favored : 63.30 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.26), residues: 785 helix: -3.60 (0.47), residues: 70 sheet: -2.80 (0.32), residues: 212 loop : -3.13 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.066 0.002 TYR A 570 PHE 0.030 0.002 PHE A 476 TRP 0.016 0.002 TRP A 441 HIS 0.005 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 6435) covalent geometry : angle 0.83604 ( 8758) hydrogen bonds : bond 0.21334 ( 136) hydrogen bonds : angle 9.95019 ( 315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 130 average time/residue: 0.0684 time to fit residues: 12.2953 Evaluate side-chains 84 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 763 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 425 ASN A 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052079 restraints weight = 25008.058| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 4.84 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6435 Z= 0.184 Angle : 0.709 9.315 8758 Z= 0.380 Chirality : 0.048 0.207 922 Planarity : 0.004 0.036 1148 Dihedral : 7.772 65.346 884 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.64 % Allowed : 12.48 % Favored : 86.88 % Rotamer: Outliers : 4.46 % Allowed : 29.27 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.27), residues: 785 helix: -3.46 (0.45), residues: 77 sheet: -2.57 (0.33), residues: 213 loop : -2.92 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 626 TYR 0.018 0.002 TYR A 757 PHE 0.020 0.002 PHE A 248 TRP 0.025 0.002 TRP A 772 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6435) covalent geometry : angle 0.70867 ( 8758) hydrogen bonds : bond 0.04649 ( 136) hydrogen bonds : angle 6.84470 ( 315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9557 (mt) cc_final: 0.9341 (mm) REVERT: A 169 LEU cc_start: 0.9246 (tp) cc_final: 0.8871 (tp) REVERT: A 208 GLU cc_start: 0.8777 (mp0) cc_final: 0.8317 (mp0) REVERT: A 256 ASP cc_start: 0.7361 (t0) cc_final: 0.6921 (t0) REVERT: A 269 MET cc_start: 0.8965 (tpp) cc_final: 0.8513 (mmt) REVERT: A 317 LEU cc_start: 0.9537 (tp) cc_final: 0.9244 (tp) REVERT: A 440 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7330 (t0) REVERT: A 568 LEU cc_start: 0.9387 (pt) cc_final: 0.9185 (pt) REVERT: A 571 MET cc_start: 0.8526 (mmp) cc_final: 0.8146 (mmp) REVERT: A 593 TYR cc_start: 0.8071 (t80) cc_final: 0.7664 (t80) REVERT: A 597 ARG cc_start: 0.7150 (ttp80) cc_final: 0.6530 (ttp80) REVERT: A 646 GLU cc_start: 0.4707 (OUTLIER) cc_final: 0.4264 (pp20) REVERT: A 670 ASP cc_start: 0.9248 (m-30) cc_final: 0.8912 (m-30) REVERT: A 687 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7482 (p0) REVERT: A 709 ASP cc_start: 0.8244 (p0) cc_final: 0.7993 (p0) REVERT: A 733 ASP cc_start: 0.8772 (m-30) cc_final: 0.8283 (t0) REVERT: A 772 TRP cc_start: 0.9004 (m-10) cc_final: 0.8019 (m-90) outliers start: 30 outliers final: 10 residues processed: 99 average time/residue: 0.0604 time to fit residues: 8.7343 Evaluate side-chains 79 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 687 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 0.0070 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 HIS A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054370 restraints weight = 24673.873| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.88 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6435 Z= 0.126 Angle : 0.640 7.642 8758 Z= 0.341 Chirality : 0.045 0.159 922 Planarity : 0.004 0.035 1148 Dihedral : 6.883 61.539 876 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.51 % Allowed : 12.10 % Favored : 87.39 % Rotamer: Outliers : 3.57 % Allowed : 30.01 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.28), residues: 785 helix: -3.21 (0.47), residues: 77 sheet: -2.43 (0.32), residues: 240 loop : -2.65 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 626 TYR 0.011 0.001 TYR A 518 PHE 0.011 0.002 PHE A 248 TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6435) covalent geometry : angle 0.64035 ( 8758) hydrogen bonds : bond 0.03799 ( 136) hydrogen bonds : angle 6.03496 ( 315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 4 ASN cc_start: 0.8643 (t0) cc_final: 0.8239 (t0) REVERT: A 5 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8652 (mm-30) REVERT: A 169 LEU cc_start: 0.9170 (tp) cc_final: 0.8915 (tp) REVERT: A 256 ASP cc_start: 0.7696 (t0) cc_final: 0.7085 (t0) REVERT: A 269 MET cc_start: 0.8986 (tpp) cc_final: 0.8631 (mpp) REVERT: A 317 LEU cc_start: 0.9528 (tp) cc_final: 0.9273 (tp) REVERT: A 380 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.9135 (p0) REVERT: A 440 ASP cc_start: 0.8512 (t0) cc_final: 0.8089 (t0) REVERT: A 540 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7590 (pp30) REVERT: A 568 LEU cc_start: 0.9306 (pt) cc_final: 0.9087 (pt) REVERT: A 574 ASP cc_start: 0.9236 (m-30) cc_final: 0.8720 (p0) REVERT: A 576 LEU cc_start: 0.9172 (mt) cc_final: 0.8946 (pp) REVERT: A 593 TYR cc_start: 0.8108 (t80) cc_final: 0.7807 (t80) REVERT: A 597 ARG cc_start: 0.7594 (ttp80) cc_final: 0.6958 (ttp80) REVERT: A 646 GLU cc_start: 0.4674 (OUTLIER) cc_final: 0.4236 (pp20) REVERT: A 670 ASP cc_start: 0.9236 (m-30) cc_final: 0.8857 (m-30) REVERT: A 687 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7569 (p0) REVERT: A 784 HIS cc_start: 0.7209 (m-70) cc_final: 0.6994 (m90) outliers start: 24 outliers final: 12 residues processed: 88 average time/residue: 0.0635 time to fit residues: 8.0730 Evaluate side-chains 74 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 710 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** 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 = 0.3324 r_free = 0.3324 target = 0.062995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053018 restraints weight = 25229.209| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.92 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6435 Z= 0.164 Angle : 0.623 7.461 8758 Z= 0.331 Chirality : 0.044 0.153 922 Planarity : 0.004 0.035 1148 Dihedral : 6.195 66.083 871 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.46 % Favored : 87.90 % Rotamer: Outliers : 3.57 % Allowed : 30.31 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.28), residues: 785 helix: -2.82 (0.52), residues: 77 sheet: -2.50 (0.32), residues: 236 loop : -2.48 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 737 TYR 0.010 0.001 TYR A 570 PHE 0.014 0.002 PHE A 42 TRP 0.009 0.001 TRP A 441 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6435) covalent geometry : angle 0.62328 ( 8758) hydrogen bonds : bond 0.03620 ( 136) hydrogen bonds : angle 5.67554 ( 315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.9682 (mmmt) cc_final: 0.9477 (tmtt) REVERT: A 169 LEU cc_start: 0.9208 (tp) cc_final: 0.8945 (tp) REVERT: A 256 ASP cc_start: 0.7697 (t0) cc_final: 0.7175 (t0) REVERT: A 317 LEU cc_start: 0.9513 (tp) cc_final: 0.9261 (tp) REVERT: A 440 ASP cc_start: 0.8722 (t0) cc_final: 0.8245 (t0) REVERT: A 540 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7743 (tm-30) REVERT: A 597 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7631 (ttp80) REVERT: A 621 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9055 (tmmt) REVERT: A 687 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7838 (p0) REVERT: A 733 ASP cc_start: 0.8727 (m-30) cc_final: 0.8173 (t0) outliers start: 24 outliers final: 16 residues processed: 82 average time/residue: 0.0637 time to fit residues: 7.5422 Evaluate side-chains 75 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 710 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 420 GLN A 784 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053141 restraints weight = 26040.913| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.73 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6435 Z= 0.159 Angle : 0.629 12.998 8758 Z= 0.327 Chirality : 0.044 0.166 922 Planarity : 0.004 0.034 1148 Dihedral : 6.057 65.465 871 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.08 % Favored : 88.28 % Rotamer: Outliers : 4.46 % Allowed : 29.12 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.28), residues: 785 helix: -2.96 (0.50), residues: 77 sheet: -2.52 (0.32), residues: 233 loop : -2.26 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.009 0.001 TYR A 491 PHE 0.012 0.001 PHE A 42 TRP 0.009 0.001 TRP A 441 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6435) covalent geometry : angle 0.62932 ( 8758) hydrogen bonds : bond 0.03517 ( 136) hydrogen bonds : angle 5.60832 ( 315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4251 (ptp) cc_final: 0.3229 (ptp) REVERT: A 108 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9326 (tmtt) REVERT: A 169 LEU cc_start: 0.9251 (tp) cc_final: 0.8974 (tp) REVERT: A 256 ASP cc_start: 0.7795 (t0) cc_final: 0.7303 (t0) REVERT: A 269 MET cc_start: 0.9044 (mmt) cc_final: 0.8790 (mmt) REVERT: A 440 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8255 (t0) REVERT: A 540 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7690 (tm-30) REVERT: A 593 TYR cc_start: 0.8120 (t80) cc_final: 0.7909 (t80) REVERT: A 597 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7584 (ttp80) REVERT: A 621 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9037 (tmmt) REVERT: A 687 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7908 (p0) outliers start: 30 outliers final: 19 residues processed: 83 average time/residue: 0.0664 time to fit residues: 8.0472 Evaluate side-chains 79 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 710 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.0050 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.063096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.053265 restraints weight = 25666.862| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.83 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6435 Z= 0.130 Angle : 0.620 10.668 8758 Z= 0.320 Chirality : 0.044 0.174 922 Planarity : 0.004 0.034 1148 Dihedral : 5.877 62.883 871 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.57 % Favored : 88.79 % Rotamer: Outliers : 2.97 % Allowed : 30.76 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.29), residues: 785 helix: -2.91 (0.49), residues: 77 sheet: -2.38 (0.33), residues: 226 loop : -2.09 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 665 TYR 0.009 0.001 TYR A 491 PHE 0.013 0.001 PHE A 42 TRP 0.009 0.001 TRP A 441 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6435) covalent geometry : angle 0.62037 ( 8758) hydrogen bonds : bond 0.03404 ( 136) hydrogen bonds : angle 5.48693 ( 315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4019 (ptp) cc_final: 0.2946 (ptp) REVERT: A 169 LEU cc_start: 0.9212 (tp) cc_final: 0.8938 (tp) REVERT: A 256 ASP cc_start: 0.7814 (t0) cc_final: 0.7272 (t0) REVERT: A 269 MET cc_start: 0.9044 (mmt) cc_final: 0.8790 (mmt) REVERT: A 378 GLU cc_start: 0.8806 (tt0) cc_final: 0.8541 (tm-30) REVERT: A 440 ASP cc_start: 0.8613 (t0) cc_final: 0.8139 (t0) REVERT: A 466 ARG cc_start: 0.8413 (tpm170) cc_final: 0.8211 (tpm170) REVERT: A 494 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: A 540 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7718 (tm-30) REVERT: A 571 MET cc_start: 0.8000 (mmp) cc_final: 0.7704 (mmp) REVERT: A 597 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7377 (ttp80) REVERT: A 621 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9096 (tmmt) outliers start: 20 outliers final: 12 residues processed: 79 average time/residue: 0.0845 time to fit residues: 8.9440 Evaluate side-chains 72 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 710 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051198 restraints weight = 25751.301| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.78 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6435 Z= 0.153 Angle : 0.625 9.604 8758 Z= 0.325 Chirality : 0.044 0.162 922 Planarity : 0.004 0.034 1148 Dihedral : 5.806 63.432 871 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.96 % Favored : 88.41 % Rotamer: Outliers : 4.01 % Allowed : 30.76 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.29), residues: 785 helix: -2.69 (0.51), residues: 77 sheet: -2.28 (0.33), residues: 220 loop : -2.06 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 665 TYR 0.009 0.001 TYR A 335 PHE 0.014 0.001 PHE A 42 TRP 0.008 0.001 TRP A 441 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6435) covalent geometry : angle 0.62464 ( 8758) hydrogen bonds : bond 0.03343 ( 136) hydrogen bonds : angle 5.37203 ( 315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.9204 (tp) cc_final: 0.8926 (tp) REVERT: A 256 ASP cc_start: 0.7793 (t0) cc_final: 0.7321 (t0) REVERT: A 269 MET cc_start: 0.9034 (mmt) cc_final: 0.8791 (mmt) REVERT: A 378 GLU cc_start: 0.8815 (tt0) cc_final: 0.8518 (tm-30) REVERT: A 440 ASP cc_start: 0.8672 (t0) cc_final: 0.8243 (t0) REVERT: A 445 PHE cc_start: 0.8921 (m-80) cc_final: 0.8548 (m-80) REVERT: A 466 ARG cc_start: 0.8458 (tpm170) cc_final: 0.8257 (tpm170) REVERT: A 494 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: A 540 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7783 (tm-30) REVERT: A 621 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9091 (tmmt) outliers start: 27 outliers final: 19 residues processed: 82 average time/residue: 0.0816 time to fit residues: 9.0872 Evaluate side-chains 76 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 710 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051078 restraints weight = 25575.551| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.81 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6435 Z= 0.183 Angle : 0.663 15.907 8758 Z= 0.338 Chirality : 0.044 0.167 922 Planarity : 0.004 0.036 1148 Dihedral : 5.950 63.909 871 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.45 % Favored : 89.04 % Rotamer: Outliers : 3.12 % Allowed : 31.65 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.29), residues: 785 helix: -2.60 (0.51), residues: 77 sheet: -2.25 (0.33), residues: 226 loop : -2.00 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 405 TYR 0.012 0.001 TYR A 112 PHE 0.015 0.001 PHE A 42 TRP 0.008 0.001 TRP A 406 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 6435) covalent geometry : angle 0.66323 ( 8758) hydrogen bonds : bond 0.03395 ( 136) hydrogen bonds : angle 5.31414 ( 315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3752 (ptp) cc_final: 0.2942 (ptp) REVERT: A 5 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8508 (mp0) REVERT: A 169 LEU cc_start: 0.9233 (tp) cc_final: 0.8938 (tp) REVERT: A 256 ASP cc_start: 0.8030 (t0) cc_final: 0.7666 (t0) REVERT: A 269 MET cc_start: 0.9028 (mmt) cc_final: 0.8804 (mpp) REVERT: A 378 GLU cc_start: 0.8808 (tt0) cc_final: 0.8516 (tm-30) REVERT: A 440 ASP cc_start: 0.8650 (t0) cc_final: 0.8233 (t0) REVERT: A 466 ARG cc_start: 0.8485 (tpm170) cc_final: 0.8280 (tpm170) REVERT: A 540 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7751 (tm-30) REVERT: A 589 ASP cc_start: 0.8491 (m-30) cc_final: 0.8247 (t0) REVERT: A 593 TYR cc_start: 0.8240 (t80) cc_final: 0.7923 (t80) REVERT: A 597 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7509 (ttp80) REVERT: A 621 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9105 (tmmt) REVERT: A 710 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8316 (t) outliers start: 21 outliers final: 16 residues processed: 73 average time/residue: 0.0782 time to fit residues: 7.8739 Evaluate side-chains 76 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 710 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.060873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050920 restraints weight = 25919.901| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.93 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6435 Z= 0.154 Angle : 0.657 15.220 8758 Z= 0.333 Chirality : 0.044 0.158 922 Planarity : 0.004 0.037 1148 Dihedral : 5.894 64.095 871 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.46 % Favored : 88.03 % Rotamer: Outliers : 3.12 % Allowed : 31.80 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.29), residues: 785 helix: -2.49 (0.51), residues: 77 sheet: -2.27 (0.33), residues: 220 loop : -1.98 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.009 0.001 TYR A 112 PHE 0.013 0.001 PHE A 42 TRP 0.008 0.001 TRP A 441 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6435) covalent geometry : angle 0.65683 ( 8758) hydrogen bonds : bond 0.03269 ( 136) hydrogen bonds : angle 5.34950 ( 315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3591 (ptp) cc_final: 0.3037 (ptp) REVERT: A 169 LEU cc_start: 0.9198 (tp) cc_final: 0.8911 (tp) REVERT: A 256 ASP cc_start: 0.8033 (t0) cc_final: 0.7630 (t0) REVERT: A 269 MET cc_start: 0.9065 (mmt) cc_final: 0.8837 (mpp) REVERT: A 378 GLU cc_start: 0.8844 (tt0) cc_final: 0.8554 (tm-30) REVERT: A 440 ASP cc_start: 0.8620 (t0) cc_final: 0.8111 (t0) REVERT: A 494 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: A 540 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7673 (tm-30) REVERT: A 589 ASP cc_start: 0.8579 (m-30) cc_final: 0.8312 (t0) REVERT: A 593 TYR cc_start: 0.8295 (t80) cc_final: 0.7938 (t80) REVERT: A 597 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7482 (ttp80) REVERT: A 621 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9092 (tmmt) REVERT: A 710 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 736 ASP cc_start: 0.8159 (t0) cc_final: 0.7662 (t0) outliers start: 21 outliers final: 16 residues processed: 76 average time/residue: 0.0793 time to fit residues: 8.1301 Evaluate side-chains 77 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 710 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051518 restraints weight = 25181.327| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.81 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6435 Z= 0.154 Angle : 0.677 14.944 8758 Z= 0.340 Chirality : 0.044 0.161 922 Planarity : 0.004 0.037 1148 Dihedral : 5.887 64.084 871 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.83 % Favored : 88.66 % Rotamer: Outliers : 2.97 % Allowed : 31.65 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.29), residues: 785 helix: -2.38 (0.52), residues: 77 sheet: -2.24 (0.33), residues: 218 loop : -1.96 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.009 0.001 TYR A 112 PHE 0.013 0.001 PHE A 42 TRP 0.008 0.001 TRP A 441 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6435) covalent geometry : angle 0.67670 ( 8758) hydrogen bonds : bond 0.03241 ( 136) hydrogen bonds : angle 5.30597 ( 315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3863 (ptp) cc_final: 0.2873 (ptp) REVERT: A 169 LEU cc_start: 0.9184 (tp) cc_final: 0.8903 (tp) REVERT: A 256 ASP cc_start: 0.7711 (t0) cc_final: 0.7318 (t0) REVERT: A 269 MET cc_start: 0.9026 (mmt) cc_final: 0.8804 (mpp) REVERT: A 378 GLU cc_start: 0.8840 (tt0) cc_final: 0.8484 (tm-30) REVERT: A 440 ASP cc_start: 0.8599 (t0) cc_final: 0.8123 (t0) REVERT: A 494 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: A 540 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7770 (tm-30) REVERT: A 589 ASP cc_start: 0.8595 (m-30) cc_final: 0.8338 (t0) REVERT: A 593 TYR cc_start: 0.8332 (t80) cc_final: 0.7932 (t80) REVERT: A 597 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7317 (ttp80) REVERT: A 621 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9099 (tmmt) outliers start: 20 outliers final: 16 residues processed: 79 average time/residue: 0.0793 time to fit residues: 8.5911 Evaluate side-chains 76 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 642 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051382 restraints weight = 25892.369| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.83 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6435 Z= 0.138 Angle : 0.668 14.484 8758 Z= 0.335 Chirality : 0.044 0.157 922 Planarity : 0.004 0.038 1148 Dihedral : 5.826 64.687 871 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.08 % Favored : 88.41 % Rotamer: Outliers : 2.67 % Allowed : 31.50 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.29), residues: 785 helix: -2.22 (0.53), residues: 77 sheet: -2.21 (0.33), residues: 220 loop : -1.90 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.009 0.001 TYR A 570 PHE 0.013 0.001 PHE A 684 TRP 0.010 0.001 TRP A 441 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6435) covalent geometry : angle 0.66807 ( 8758) hydrogen bonds : bond 0.03161 ( 136) hydrogen bonds : angle 5.25838 ( 315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.82 seconds wall clock time: 20 minutes 50.65 seconds (1250.65 seconds total)