Starting phenix.real_space_refine on Thu Jul 2 04:56:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij3_60614/07_2026/9ij3_60614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij3_60614/07_2026/9ij3_60614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij3_60614/07_2026/9ij3_60614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij3_60614/07_2026/9ij3_60614.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij3_60614/07_2026/9ij3_60614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij3_60614/07_2026/9ij3_60614.cif" } resolution = 2.6 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= -0.001 sd= 0.049 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 51 5.49 5 S 43 5.16 5 C 4284 2.51 5 N 1211 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7005 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5921 Classifications: {'peptide': 738} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 702} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 533 Classifications: {'RNA': 25} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 12} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.71, per 1000 atoms: 0.24 Number of scatterers: 7005 At special positions: 0 Unit cell: (75.24, 84.36, 107.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 43 16.00 P 51 15.00 O 1415 8.00 N 1211 7.00 C 4284 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 348.6 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 34.8% alpha, 15.9% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.763A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.505A pdb=" N SER A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 628 Processing helix chain 'A' and resid 646 through 661 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.948A pdb=" N GLY A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 703' Processing helix chain 'A' and resid 708 through 723 removed outlier: 3.691A pdb=" N LYS A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 833 through 837 Processing helix chain 'A' and resid 914 through 928 Processing helix chain 'A' and resid 939 through 955 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.772A pdb=" N TYR A 859 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 368 Processing sheet with id=AA7, first strand: chain 'A' and resid 423 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 564 through 565 removed outlier: 4.549A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AB3, first strand: chain 'A' and resid 667 through 671 258 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1099 1.32 - 1.45: 2147 1.45 - 1.57: 3849 1.57 - 1.70: 100 1.70 - 1.82: 67 Bond restraints: 7262 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" C SER A 816 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.23e-02 6.61e+03 2.02e+01 bond pdb=" C SER A 816 " pdb=" O SER A 816 " ideal model delta sigma weight residual 1.234 1.198 0.037 1.21e-02 6.83e+03 9.13e+00 bond pdb=" N GLN A 819 " pdb=" CA GLN A 819 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.06e-02 8.90e+03 9.09e+00 bond pdb=" C GLN A 819 " pdb=" O GLN A 819 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.39e-02 5.18e+03 8.50e+00 bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.66e-02 3.63e+03 7.14e+00 ... (remaining 7257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 9954 3.40 - 6.80: 101 6.80 - 10.20: 15 10.20 - 13.61: 6 13.61 - 17.01: 3 Bond angle restraints: 10079 Sorted by residual: angle pdb=" N GLY A 818 " pdb=" CA GLY A 818 " pdb=" C GLY A 818 " ideal model delta sigma weight residual 115.63 104.00 11.63 1.49e+00 4.50e-01 6.09e+01 angle pdb=" N GLN A 819 " pdb=" CA GLN A 819 " pdb=" C GLN A 819 " ideal model delta sigma weight residual 113.19 101.25 11.94 1.58e+00 4.01e-01 5.71e+01 angle pdb=" N1 C B 11 " pdb=" C6 C B 11 " pdb=" C5 C B 11 " ideal model delta sigma weight residual 121.00 124.07 -3.07 5.00e-01 4.00e+00 3.77e+01 angle pdb=" C1' C B 24 " pdb=" N1 C B 24 " pdb=" C2 C B 24 " ideal model delta sigma weight residual 118.80 125.14 -6.34 1.10e+00 8.26e-01 3.33e+01 angle pdb=" CB MET A 613 " pdb=" CG MET A 613 " pdb=" SD MET A 613 " ideal model delta sigma weight residual 112.70 129.71 -17.01 3.00e+00 1.11e-01 3.21e+01 ... (remaining 10074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3636 17.98 - 35.97: 503 35.97 - 53.95: 185 53.95 - 71.93: 82 71.93 - 89.92: 24 Dihedral angle restraints: 4430 sinusoidal: 2269 harmonic: 2161 Sorted by residual: dihedral pdb=" CA ILE A 415 " pdb=" C ILE A 415 " pdb=" N VAL A 416 " pdb=" CA VAL A 416 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C4' U B 7 " pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" C2' U B 7 " ideal model delta sinusoidal sigma weight residual 3.00 -30.45 33.45 1 8.00e+00 1.56e-02 2.49e+01 dihedral pdb=" CA TRP A 639 " pdb=" C TRP A 639 " pdb=" N VAL A 640 " pdb=" CA VAL A 640 " ideal model delta harmonic sigma weight residual 180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 4427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1016 0.077 - 0.154: 159 0.154 - 0.230: 9 0.230 - 0.307: 1 0.307 - 0.384: 1 Chirality restraints: 1186 Sorted by residual: chirality pdb=" CB ILE A 357 " pdb=" CA ILE A 357 " pdb=" CG1 ILE A 357 " pdb=" CG2 ILE A 357 " both_signs ideal model delta sigma weight residual False 2.64 3.03 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C3' A C 14 " pdb=" C4' A C 14 " pdb=" O3' A C 14 " pdb=" C2' A C 14 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB THR A 548 " pdb=" CA THR A 548 " pdb=" OG1 THR A 548 " pdb=" CG2 THR A 548 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1183 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 358 " 0.037 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP A 358 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A 358 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 358 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 358 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 358 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 358 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 358 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 358 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 358 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 628 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO A 629 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 629 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 629 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 472 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C HIS A 472 " -0.050 2.00e-02 2.50e+03 pdb=" O HIS A 472 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 473 " 0.017 2.00e-02 2.50e+03 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 52 2.55 - 3.14: 4985 3.14 - 3.73: 12225 3.73 - 4.31: 17046 4.31 - 4.90: 26182 Nonbonded interactions: 60490 Sorted by model distance: nonbonded pdb=" OD1 ASP A 743 " pdb="MN MN A1001 " model vdw 1.968 3.060 nonbonded pdb=" CE LYS A 252 " pdb=" OP1 U C 11 " model vdw 2.122 3.440 nonbonded pdb=" OD2 ASP A 369 " pdb=" OG1 THR A 880 " model vdw 2.298 3.040 nonbonded pdb=" O VAL A 249 " pdb=" NH1 ARG A 255 " model vdw 2.319 3.120 nonbonded pdb=" OH TYR A 904 " pdb=" O ARG A 937 " model vdw 2.322 3.040 ... (remaining 60485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.730 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 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 0.055 7262 Z= 0.257 Angle : 0.987 17.007 10079 Z= 0.586 Chirality : 0.053 0.384 1186 Planarity : 0.007 0.076 1085 Dihedral : 20.447 89.918 3030 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.77 % Favored : 91.10 % Rotamer: Outliers : 1.20 % Allowed : 31.38 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.04 (0.29), residues: 730 helix: -0.75 (0.32), residues: 226 sheet: -1.22 (0.40), residues: 159 loop : -1.77 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.031 0.003 TYR A 425 PHE 0.016 0.002 PHE A 758 TRP 0.070 0.003 TRP A 358 HIS 0.009 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.26 ( 7262) covalent geometry : angle 0.98661 / 0.59 (10079) hydrogen bonds : bond 0.14615 / 10.04 ( 312) hydrogen bonds : angle 7.07774 / 5.14 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 831 LEU cc_start: 0.5188 (tp) cc_final: 0.4924 (tp) outliers start: 8 outliers final: 4 residues processed: 103 average time/residue: 0.4675 time to fit residues: 51.4268 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 591 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS A 958 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.218621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180537 restraints weight = 7342.878| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 1.69 r_work: 0.4190 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7262 Z= 0.236 Angle : 0.749 9.502 10079 Z= 0.390 Chirality : 0.048 0.290 1186 Planarity : 0.006 0.066 1085 Dihedral : 17.541 83.010 1568 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 6.46 % Allowed : 28.98 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.83 (0.30), residues: 730 helix: -0.16 (0.34), residues: 232 sheet: -1.38 (0.40), residues: 146 loop : -1.84 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 937 TYR 0.012 0.003 TYR A 888 PHE 0.016 0.002 PHE A 758 TRP 0.039 0.003 TRP A 358 HIS 0.009 0.002 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 ( 7262) covalent geometry : angle 0.74925 / 0.39 (10079) hydrogen bonds : bond 0.05901 / 4.04 ( 312) hydrogen bonds : angle 5.69554 / 4.03 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5683 (mp) REVERT: A 228 LEU cc_start: 0.3352 (OUTLIER) cc_final: 0.2684 (mt) REVERT: A 276 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7023 (mt) REVERT: A 329 MET cc_start: 0.7568 (tpp) cc_final: 0.7178 (mpp) REVERT: A 519 ILE cc_start: 0.6280 (OUTLIER) cc_final: 0.6018 (mt) REVERT: A 623 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5996 (mt) REVERT: A 684 LYS cc_start: 0.6125 (tppt) cc_final: 0.5768 (mptt) REVERT: A 831 LEU cc_start: 0.6088 (tp) cc_final: 0.5828 (tp) outliers start: 43 outliers final: 19 residues processed: 110 average time/residue: 0.4320 time to fit residues: 51.0351 Evaluate side-chains 111 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 905 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.213629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.175160 restraints weight = 7306.519| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.71 r_work: 0.4148 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7262 Z= 0.278 Angle : 0.796 11.166 10079 Z= 0.413 Chirality : 0.051 0.305 1186 Planarity : 0.006 0.062 1085 Dihedral : 17.579 79.531 1566 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 8.56 % Allowed : 28.23 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.79 (0.30), residues: 730 helix: -0.07 (0.34), residues: 231 sheet: -1.43 (0.40), residues: 137 loop : -1.83 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 423 TYR 0.013 0.003 TYR A 241 PHE 0.019 0.002 PHE A 325 TRP 0.028 0.003 TRP A 358 HIS 0.009 0.002 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.28 ( 7262) covalent geometry : angle 0.79568 / 0.41 (10079) hydrogen bonds : bond 0.06294 / 4.24 ( 312) hydrogen bonds : angle 5.78865 / 4.08 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 84 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6492 (ttm) REVERT: A 276 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 329 MET cc_start: 0.7716 (tpp) cc_final: 0.7174 (mpp) REVERT: A 623 LEU cc_start: 0.6462 (mm) cc_final: 0.6222 (mt) REVERT: A 671 ILE cc_start: 0.4537 (OUTLIER) cc_final: 0.3750 (tp) REVERT: A 672 MET cc_start: 0.5482 (mmp) cc_final: 0.5196 (mmt) REVERT: A 918 MET cc_start: 0.5899 (ptp) cc_final: 0.5592 (ptm) outliers start: 57 outliers final: 25 residues processed: 126 average time/residue: 0.3914 time to fit residues: 53.2738 Evaluate side-chains 109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 954 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.218325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180716 restraints weight = 7431.708| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 1.69 r_work: 0.4205 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4110 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7262 Z= 0.154 Angle : 0.662 10.214 10079 Z= 0.345 Chirality : 0.045 0.255 1186 Planarity : 0.005 0.060 1085 Dihedral : 17.415 82.273 1564 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 5.71 % Allowed : 30.18 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.70 (0.30), residues: 730 helix: 0.16 (0.34), residues: 232 sheet: -1.68 (0.38), residues: 142 loop : -1.74 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.012 0.002 TYR A 321 PHE 0.011 0.001 PHE A 758 TRP 0.026 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7262) covalent geometry : angle 0.66151 / 0.34 (10079) hydrogen bonds : bond 0.04642 / 3.12 ( 312) hydrogen bonds : angle 5.54446 / 3.93 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3483 (OUTLIER) cc_final: 0.3069 (mt) REVERT: A 254 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6348 (ttm) REVERT: A 276 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7026 (mt) REVERT: A 623 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6114 (mt) REVERT: A 671 ILE cc_start: 0.4144 (OUTLIER) cc_final: 0.3492 (tp) REVERT: A 753 ARG cc_start: 0.5836 (tpt170) cc_final: 0.5524 (tpt170) outliers start: 38 outliers final: 15 residues processed: 109 average time/residue: 0.4103 time to fit residues: 48.0913 Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 898 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.217845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.180025 restraints weight = 7348.260| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 1.68 r_work: 0.4201 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7262 Z= 0.166 Angle : 0.670 11.648 10079 Z= 0.345 Chirality : 0.045 0.231 1186 Planarity : 0.005 0.057 1085 Dihedral : 17.341 81.892 1564 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.14 % Rotamer: Outliers : 5.56 % Allowed : 29.58 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.67 (0.30), residues: 730 helix: 0.28 (0.35), residues: 229 sheet: -1.74 (0.39), residues: 138 loop : -1.76 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.017 0.002 TYR A 321 PHE 0.011 0.001 PHE A 758 TRP 0.025 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 7262) covalent geometry : angle 0.67007 / 0.34 (10079) hydrogen bonds : bond 0.04807 / 3.23 ( 312) hydrogen bonds : angle 5.45070 / 3.85 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6449 (ttm) REVERT: A 276 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.6992 (mt) REVERT: A 329 MET cc_start: 0.7409 (tpp) cc_final: 0.7167 (mpp) REVERT: A 623 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6113 (mt) REVERT: A 647 ILE cc_start: 0.3784 (OUTLIER) cc_final: 0.2145 (pt) REVERT: A 671 ILE cc_start: 0.4045 (OUTLIER) cc_final: 0.3181 (tp) REVERT: A 672 MET cc_start: 0.4743 (mmt) cc_final: 0.4540 (mmp) outliers start: 37 outliers final: 21 residues processed: 110 average time/residue: 0.4186 time to fit residues: 49.5848 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 898 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.218660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.181480 restraints weight = 7447.433| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 1.61 r_work: 0.4217 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7262 Z= 0.228 Angle : 0.733 13.000 10079 Z= 0.376 Chirality : 0.048 0.250 1186 Planarity : 0.006 0.060 1085 Dihedral : 17.321 79.446 1564 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.77 % Favored : 91.10 % Rotamer: Outliers : 6.76 % Allowed : 29.13 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.68 (0.30), residues: 730 helix: 0.17 (0.35), residues: 229 sheet: -1.44 (0.41), residues: 128 loop : -1.83 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 293 TYR 0.020 0.002 TYR A 321 PHE 0.014 0.002 PHE A 272 TRP 0.026 0.003 TRP A 358 HIS 0.007 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 ( 7262) covalent geometry : angle 0.73277 / 0.38 (10079) hydrogen bonds : bond 0.05596 / 3.77 ( 312) hydrogen bonds : angle 5.57724 / 3.91 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6542 (ttm) REVERT: A 276 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7174 (mt) REVERT: A 623 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6227 (mt) REVERT: A 647 ILE cc_start: 0.3286 (OUTLIER) cc_final: 0.1455 (pt) REVERT: A 671 ILE cc_start: 0.4478 (OUTLIER) cc_final: 0.3617 (tp) REVERT: A 684 LYS cc_start: 0.6211 (tppt) cc_final: 0.5948 (mptt) REVERT: A 918 MET cc_start: 0.5818 (ptp) cc_final: 0.5529 (ptm) outliers start: 45 outliers final: 28 residues processed: 110 average time/residue: 0.3854 time to fit residues: 45.8350 Evaluate side-chains 110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.221036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.184110 restraints weight = 7368.336| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 1.60 r_work: 0.4238 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7262 Z= 0.177 Angle : 0.689 12.408 10079 Z= 0.354 Chirality : 0.046 0.216 1186 Planarity : 0.005 0.057 1085 Dihedral : 17.264 80.941 1564 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 6.16 % Allowed : 30.33 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.67 (0.30), residues: 730 helix: 0.21 (0.34), residues: 229 sheet: -1.69 (0.39), residues: 136 loop : -1.72 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 293 TYR 0.025 0.002 TYR A 321 PHE 0.011 0.002 PHE A 758 TRP 0.025 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 7262) covalent geometry : angle 0.68881 / 0.35 (10079) hydrogen bonds : bond 0.04758 / 3.22 ( 312) hydrogen bonds : angle 5.51607 / 3.89 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6596 (ttm) REVERT: A 276 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7108 (mt) REVERT: A 329 MET cc_start: 0.7508 (tpp) cc_final: 0.7009 (mpp) REVERT: A 354 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.6172 (pmt-80) REVERT: A 623 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6253 (mt) REVERT: A 672 MET cc_start: 0.5572 (mmp) cc_final: 0.5141 (mmm) REVERT: A 918 MET cc_start: 0.5764 (ptp) cc_final: 0.5464 (ptm) outliers start: 41 outliers final: 27 residues processed: 110 average time/residue: 0.3865 time to fit residues: 45.7842 Evaluate side-chains 111 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 72 optimal weight: 0.0050 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.220630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.183727 restraints weight = 7431.470| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 1.65 r_work: 0.4223 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4127 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7262 Z= 0.134 Angle : 0.653 12.042 10079 Z= 0.331 Chirality : 0.045 0.326 1186 Planarity : 0.005 0.055 1085 Dihedral : 17.139 82.804 1564 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.86 % Favored : 90.00 % Rotamer: Outliers : 4.50 % Allowed : 32.28 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.50 (0.30), residues: 730 helix: 0.33 (0.34), residues: 229 sheet: -1.65 (0.40), residues: 136 loop : -1.58 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.027 0.002 TYR A 321 PHE 0.017 0.002 PHE A 950 TRP 0.021 0.001 TRP A 358 HIS 0.005 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7262) covalent geometry : angle 0.65267 / 0.33 (10079) hydrogen bonds : bond 0.04271 / 2.88 ( 312) hydrogen bonds : angle 5.34163 / 3.77 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7065 (mt) REVERT: A 623 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.6030 (mt) REVERT: A 666 MET cc_start: 0.7516 (mmt) cc_final: 0.7106 (mmt) REVERT: A 671 ILE cc_start: 0.3909 (OUTLIER) cc_final: 0.3246 (tp) REVERT: A 678 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5832 (tm) outliers start: 30 outliers final: 20 residues processed: 102 average time/residue: 0.4363 time to fit residues: 47.6961 Evaluate side-chains 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 22 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.236650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.201930 restraints weight = 7391.000| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 1.54 r_work: 0.4448 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4366 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7262 Z= 0.138 Angle : 0.675 11.952 10079 Z= 0.339 Chirality : 0.045 0.264 1186 Planarity : 0.005 0.055 1085 Dihedral : 17.131 83.010 1564 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.14 % Rotamer: Outliers : 4.20 % Allowed : 33.33 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.40 (0.30), residues: 730 helix: 0.45 (0.35), residues: 229 sheet: -1.51 (0.39), residues: 140 loop : -1.58 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 570 TYR 0.031 0.002 TYR A 321 PHE 0.013 0.001 PHE A 758 TRP 0.019 0.001 TRP A 358 HIS 0.004 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7262) covalent geometry : angle 0.67477 / 0.34 (10079) hydrogen bonds : bond 0.04288 / 2.90 ( 312) hydrogen bonds : angle 5.29596 / 3.74 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6531 (ttm) REVERT: A 276 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7146 (mt) REVERT: A 329 MET cc_start: 0.7433 (tpp) cc_final: 0.6996 (mpp) REVERT: A 666 MET cc_start: 0.7451 (mmt) cc_final: 0.7113 (mmt) REVERT: A 671 ILE cc_start: 0.4236 (OUTLIER) cc_final: 0.3601 (tp) REVERT: A 678 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6017 (tm) outliers start: 28 outliers final: 17 residues processed: 102 average time/residue: 0.4064 time to fit residues: 44.6180 Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.220029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.183388 restraints weight = 7420.521| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 1.61 r_work: 0.4232 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7262 Z= 0.208 Angle : 0.748 12.619 10079 Z= 0.376 Chirality : 0.049 0.323 1186 Planarity : 0.006 0.081 1085 Dihedral : 17.162 80.717 1564 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 3.30 % Allowed : 34.38 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.54 (0.30), residues: 730 helix: 0.34 (0.35), residues: 229 sheet: -1.49 (0.39), residues: 146 loop : -1.71 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 570 TYR 0.039 0.002 TYR A 321 PHE 0.013 0.002 PHE A 272 TRP 0.022 0.002 TRP A 358 HIS 0.007 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 7262) covalent geometry : angle 0.74755 / 0.38 (10079) hydrogen bonds : bond 0.05181 / 3.54 ( 312) hydrogen bonds : angle 5.48668 / 3.84 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7126 (mt) REVERT: A 329 MET cc_start: 0.7540 (tpp) cc_final: 0.7054 (mpp) REVERT: A 429 ASP cc_start: 0.6250 (t0) cc_final: 0.5941 (t0) REVERT: A 666 MET cc_start: 0.7439 (mmt) cc_final: 0.7045 (mmt) REVERT: A 671 ILE cc_start: 0.4309 (OUTLIER) cc_final: 0.3607 (tp) REVERT: A 672 MET cc_start: 0.5310 (mmp) cc_final: 0.4971 (mmp) REVERT: A 678 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6049 (tm) outliers start: 22 outliers final: 15 residues processed: 98 average time/residue: 0.3909 time to fit residues: 41.2780 Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.232334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.196814 restraints weight = 7239.677| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 1.53 r_work: 0.4402 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4320 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7262 Z= 0.188 Angle : 0.724 12.315 10079 Z= 0.367 Chirality : 0.048 0.387 1186 Planarity : 0.006 0.076 1085 Dihedral : 17.124 80.751 1562 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 3.60 % Allowed : 34.23 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.57 (0.30), residues: 730 helix: 0.31 (0.35), residues: 229 sheet: -1.57 (0.38), residues: 147 loop : -1.69 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 570 TYR 0.042 0.002 TYR A 321 PHE 0.012 0.002 PHE A 887 TRP 0.022 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 7262) covalent geometry : angle 0.72442 / 0.37 (10079) hydrogen bonds : bond 0.04832 / 3.31 ( 312) hydrogen bonds : angle 5.49876 / 3.86 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.82 seconds wall clock time: 45 minutes 34.21 seconds (2734.21 seconds total)