Starting phenix.real_space_refine on Fri Aug 22 18:20:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij3_60614/08_2025/9ij3_60614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij3_60614/08_2025/9ij3_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2025/9ij3_60614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2025/9ij3_60614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2025/9ij3_60614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2025/9ij3_60614.map" } 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-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.26 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: 0.44 Conformation dependent library (CDL) restraints added in 336.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.24 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: 1.72 Time building geometry restraints manager: 0.59 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=" 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 angle pdb=" N ILE A 879 " pdb=" CA ILE A 879 " pdb=" C ILE A 879 " ideal model delta sigma weight residual 113.20 107.86 5.34 9.60e-01 1.09e+00 3.09e+01 angle pdb=" C4' C B 8 " pdb=" C3' C B 8 " pdb=" O3' C B 8 " ideal model delta sigma weight residual 113.00 104.82 8.18 1.50e+00 4.44e-01 2.97e+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 2.320 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: 0.300 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.530 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 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= 0.240 Angle : 0.987 17.007 10079 Z= 0.512 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 aren 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 covalent geometry : bond 0.00459 ( 7262) covalent geometry : angle 0.98652 (10079) hydrogen bonds : bond 0.14615 ( 312) hydrogen bonds : angle 7.07774 ( 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 : 0.243 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: 0.5091 time to fit residues: 55.5952 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 : 0.244 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 954 GLN A 958 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.222786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.186044 restraints weight = 7346.288| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 1.59 r_work: 0.4268 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4177 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7262 Z= 0.248 Angle : 0.782 12.567 10079 Z= 0.393 Chirality : 0.049 0.286 1186 Planarity : 0.006 0.067 1085 Dihedral : 17.523 80.758 1568 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.36 % Favored : 91.51 % Rotamer: Outliers : 6.31 % Allowed : 29.28 % Favored : 64.41 % 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 aren not related in a simple way. whole: -1.82 (0.30), residues: 730 helix: -0.17 (0.34), residues: 232 sheet: -1.32 (0.40), residues: 145 loop : -1.84 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 937 TYR 0.012 0.002 TYR A 241 PHE 0.017 0.002 PHE A 325 TRP 0.037 0.003 TRP A 358 HIS 0.009 0.002 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 7262) covalent geometry : angle 0.78209 (10079) hydrogen bonds : bond 0.05850 ( 312) hydrogen bonds : angle 5.73086 ( 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 127 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.6039 (mp) REVERT: A 228 LEU cc_start: 0.2913 (OUTLIER) cc_final: 0.2196 (mt) REVERT: A 276 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7094 (mt) REVERT: A 519 ILE cc_start: 0.6555 (mt) cc_final: 0.6197 (mt) REVERT: A 623 LEU cc_start: 0.6533 (mm) cc_final: 0.6204 (mt) outliers start: 42 outliers final: 18 residues processed: 110 average time/residue: 0.4381 time to fit residues: 51.7650 Evaluate side-chains 110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 324 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 598 THR 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 954 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 655 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.217611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.180412 restraints weight = 7370.217| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 1.61 r_work: 0.4202 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7262 Z= 0.268 Angle : 0.783 11.489 10079 Z= 0.399 Chirality : 0.050 0.271 1186 Planarity : 0.006 0.067 1085 Dihedral : 17.509 78.976 1565 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 6.76 % Allowed : 27.63 % Favored : 65.62 % 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 aren not related in a simple way. whole: -1.81 (0.29), residues: 730 helix: -0.11 (0.34), residues: 231 sheet: -1.61 (0.39), residues: 132 loop : -1.75 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 937 TYR 0.012 0.002 TYR A 420 PHE 0.013 0.002 PHE A 272 TRP 0.028 0.003 TRP A 358 HIS 0.008 0.002 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 7262) covalent geometry : angle 0.78321 (10079) hydrogen bonds : bond 0.05797 ( 312) hydrogen bonds : angle 5.78969 ( 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 128 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 83 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6358 (mp) REVERT: A 228 LEU cc_start: 0.3504 (OUTLIER) cc_final: 0.2872 (mt) REVERT: A 254 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6539 (ttm) REVERT: A 276 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7196 (mt) REVERT: A 329 MET cc_start: 0.7631 (tpp) cc_final: 0.7149 (mpp) REVERT: A 623 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6317 (mt) REVERT: A 671 ILE cc_start: 0.4322 (OUTLIER) cc_final: 0.3621 (tp) REVERT: A 672 MET cc_start: 0.5652 (mmp) cc_final: 0.5343 (mmt) outliers start: 45 outliers final: 18 residues processed: 116 average time/residue: 0.4652 time to fit residues: 57.7566 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 : 0.250 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 261 ASP 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 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 742 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.0050 chunk 18 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 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 = 0.4717 r_free = 0.4717 target = 0.225615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189293 restraints weight = 7441.890| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 1.59 r_work: 0.4289 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4199 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7262 Z= 0.136 Angle : 0.643 9.963 10079 Z= 0.325 Chirality : 0.044 0.210 1186 Planarity : 0.005 0.059 1085 Dihedral : 17.221 83.792 1565 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.77 % Favored : 91.10 % Rotamer: Outliers : 5.41 % Allowed : 30.03 % 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 aren not related in a simple way. whole: -1.57 (0.30), residues: 730 helix: 0.27 (0.34), residues: 229 sheet: -1.47 (0.38), residues: 134 loop : -1.73 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.014 0.002 TYR A 859 PHE 0.014 0.001 PHE A 950 TRP 0.017 0.002 TRP A 358 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7262) covalent geometry : angle 0.64292 (10079) hydrogen bonds : bond 0.04173 ( 312) hydrogen bonds : angle 5.33467 ( 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 122 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6563 (mp0) cc_final: 0.6347 (mp0) REVERT: A 276 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7298 (mt) REVERT: A 623 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6092 (mt) REVERT: A 671 ILE cc_start: 0.4284 (OUTLIER) cc_final: 0.3602 (tp) REVERT: A 672 MET cc_start: 0.5368 (mmp) cc_final: 0.4896 (mmm) REVERT: A 859 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6247 (m-80) outliers start: 36 outliers final: 13 residues processed: 109 average time/residue: 0.4819 time to fit residues: 55.9616 Evaluate side-chains 101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 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 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.0040 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 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 = 0.4692 r_free = 0.4692 target = 0.222477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.185930 restraints weight = 7389.967| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 1.60 r_work: 0.4256 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7262 Z= 0.170 Angle : 0.670 9.185 10079 Z= 0.338 Chirality : 0.045 0.201 1186 Planarity : 0.005 0.056 1085 Dihedral : 17.149 81.195 1565 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 5.11 % Allowed : 30.48 % Favored : 64.41 % 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 aren not related in a simple way. whole: -1.61 (0.30), residues: 730 helix: 0.32 (0.35), residues: 229 sheet: -1.67 (0.38), residues: 146 loop : -1.71 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.011 0.002 TYR A 420 PHE 0.012 0.002 PHE A 758 TRP 0.021 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7262) covalent geometry : angle 0.66989 (10079) hydrogen bonds : bond 0.04565 ( 312) hydrogen bonds : angle 5.32897 ( 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 118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7212 (mt) REVERT: A 329 MET cc_start: 0.7378 (tpp) cc_final: 0.7157 (mpp) REVERT: A 623 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6151 (mt) REVERT: A 671 ILE cc_start: 0.4281 (OUTLIER) cc_final: 0.3565 (tp) REVERT: A 672 MET cc_start: 0.5473 (mmp) cc_final: 0.4975 (mmp) REVERT: A 684 LYS cc_start: 0.6154 (tppt) cc_final: 0.5868 (mptt) outliers start: 34 outliers final: 16 residues processed: 106 average time/residue: 0.4697 time to fit residues: 53.2319 Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 495 LEU 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 742 MET 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 898 CYS Chi-restraints excluded: chain A residue 917 HIS 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: 10.0000 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.0270 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4709 r_free = 0.4709 target = 0.224275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.188018 restraints weight = 7435.683| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 1.60 r_work: 0.4275 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4189 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 0.052 7262 Z= 0.146 Angle : 0.632 8.777 10079 Z= 0.321 Chirality : 0.044 0.197 1186 Planarity : 0.005 0.054 1085 Dihedral : 17.042 81.792 1565 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.18 % Favored : 90.68 % Rotamer: Outliers : 4.50 % Allowed : 30.78 % Favored : 64.71 % 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 aren not related in a simple way. whole: -1.48 (0.30), residues: 730 helix: 0.39 (0.35), residues: 229 sheet: -1.43 (0.39), residues: 138 loop : -1.70 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.023 0.002 TYR A 321 PHE 0.013 0.001 PHE A 758 TRP 0.018 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7262) covalent geometry : angle 0.63191 (10079) hydrogen bonds : bond 0.04229 ( 312) hydrogen bonds : angle 5.25647 ( 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 117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6487 (mp0) cc_final: 0.6260 (mp0) REVERT: A 276 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7228 (mt) REVERT: A 329 MET cc_start: 0.7287 (tpp) cc_final: 0.7084 (mpp) REVERT: A 671 ILE cc_start: 0.4219 (OUTLIER) cc_final: 0.3475 (tp) REVERT: A 672 MET cc_start: 0.5450 (mmp) cc_final: 0.5053 (mmp) outliers start: 30 outliers final: 17 residues processed: 106 average time/residue: 0.4660 time to fit residues: 52.7722 Evaluate side-chains 101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 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 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 868 THR Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 0.0570 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.0020 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4765 r_free = 0.4765 target = 0.228641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.193081 restraints weight = 7292.849| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 1.54 r_work: 0.4337 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4249 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7262 Z= 0.134 Angle : 0.619 11.143 10079 Z= 0.312 Chirality : 0.044 0.197 1186 Planarity : 0.005 0.054 1085 Dihedral : 16.923 82.098 1565 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.18 % Favored : 90.68 % Rotamer: Outliers : 3.90 % Allowed : 31.98 % 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 aren not related in a simple way. whole: -1.37 (0.30), residues: 730 helix: 0.51 (0.35), residues: 229 sheet: -1.42 (0.39), residues: 142 loop : -1.63 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.030 0.002 TYR A 321 PHE 0.013 0.001 PHE A 758 TRP 0.016 0.001 TRP A 358 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7262) covalent geometry : angle 0.61859 (10079) hydrogen bonds : bond 0.04031 ( 312) hydrogen bonds : angle 5.13610 ( 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 111 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7373 (mt) REVERT: A 329 MET cc_start: 0.7414 (tpp) cc_final: 0.7031 (mpp) REVERT: A 671 ILE cc_start: 0.4169 (OUTLIER) cc_final: 0.3439 (tp) REVERT: A 672 MET cc_start: 0.5445 (mmp) cc_final: 0.4994 (mmp) REVERT: A 726 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6747 (pt0) outliers start: 26 outliers final: 19 residues processed: 101 average time/residue: 0.4433 time to fit residues: 48.0484 Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 358 TRP Chi-restraints excluded: chain A residue 505 MET 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 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 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: 3.9990 chunk 4 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 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 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 = 0.4759 r_free = 0.4759 target = 0.228034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.192256 restraints weight = 7327.392| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 1.54 r_work: 0.4332 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4244 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7262 Z= 0.141 Angle : 0.633 11.070 10079 Z= 0.320 Chirality : 0.045 0.223 1186 Planarity : 0.004 0.046 1085 Dihedral : 16.938 81.770 1565 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 4.35 % Allowed : 32.73 % Favored : 62.91 % 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 aren not related in a simple way. whole: -1.38 (0.30), residues: 730 helix: 0.51 (0.35), residues: 229 sheet: -1.62 (0.38), residues: 148 loop : -1.53 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.035 0.002 TYR A 321 PHE 0.013 0.001 PHE A 758 TRP 0.019 0.001 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7262) covalent geometry : angle 0.63257 (10079) hydrogen bonds : bond 0.04103 ( 312) hydrogen bonds : angle 5.14842 ( 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 113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 671 ILE cc_start: 0.4026 (OUTLIER) cc_final: 0.3317 (tp) REVERT: A 672 MET cc_start: 0.5537 (mmp) cc_final: 0.5017 (mmp) REVERT: A 726 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6759 (pt0) outliers start: 29 outliers final: 22 residues processed: 104 average time/residue: 0.4543 time to fit residues: 50.6226 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 : 0.246 ------------------------------------------------------------------------------- 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 238 VAL 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 358 TRP Chi-restraints excluded: chain A residue 505 MET 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 599 ILE Chi-restraints excluded: chain A residue 671 ILE 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 868 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 898 CYS 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: 6.9990 chunk 75 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4820 r_free = 0.4820 target = 0.232215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.196416 restraints weight = 7296.340| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 1.51 r_work: 0.4395 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4311 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7262 Z= 0.189 Angle : 0.691 10.684 10079 Z= 0.349 Chirality : 0.048 0.344 1186 Planarity : 0.005 0.051 1085 Dihedral : 17.019 79.181 1565 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 3.90 % Allowed : 33.03 % Favored : 63.06 % 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 aren not related in a simple way. whole: -1.53 (0.30), residues: 730 helix: 0.35 (0.35), residues: 229 sheet: -1.64 (0.38), residues: 147 loop : -1.62 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.043 0.002 TYR A 321 PHE 0.012 0.002 PHE A 758 TRP 0.024 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7262) covalent geometry : angle 0.69147 (10079) hydrogen bonds : bond 0.04746 ( 312) hydrogen bonds : angle 5.37373 ( 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 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7341 (mt) REVERT: A 329 MET cc_start: 0.7383 (tpp) cc_final: 0.7154 (mpp) REVERT: A 671 ILE cc_start: 0.4126 (OUTLIER) cc_final: 0.3417 (tp) REVERT: A 672 MET cc_start: 0.5353 (mmp) cc_final: 0.4857 (mmp) REVERT: A 726 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6729 (pt0) REVERT: A 918 MET cc_start: 0.5323 (ptp) cc_final: 0.5077 (ptm) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.4362 time to fit residues: 45.4847 Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 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 742 MET Chi-restraints excluded: chain A residue 755 VAL 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 860 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 873 THR 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 62 optimal weight: 0.2980 chunk 60 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4614 r_free = 0.4614 target = 0.225004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.186359 restraints weight = 6843.868| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.68 r_work: 0.4143 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7262 Z= 0.130 Angle : 0.630 11.109 10079 Z= 0.318 Chirality : 0.045 0.297 1186 Planarity : 0.004 0.045 1085 Dihedral : 16.880 82.216 1565 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 2.85 % Allowed : 34.23 % Favored : 62.91 % 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 aren not related in a simple way. whole: -1.38 (0.30), residues: 730 helix: 0.50 (0.34), residues: 230 sheet: -1.61 (0.38), residues: 148 loop : -1.53 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.043 0.002 TYR A 321 PHE 0.014 0.001 PHE A 758 TRP 0.013 0.001 TRP A 358 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7262) covalent geometry : angle 0.62988 (10079) hydrogen bonds : bond 0.04051 ( 312) hydrogen bonds : angle 5.17072 ( 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 110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.7112 (tpp) cc_final: 0.6822 (mpp) REVERT: A 633 ARG cc_start: 0.7352 (mpp80) cc_final: 0.7140 (mpp80) REVERT: A 671 ILE cc_start: 0.4012 (OUTLIER) cc_final: 0.3200 (tp) REVERT: A 672 MET cc_start: 0.5485 (mmp) cc_final: 0.4951 (mmp) REVERT: A 726 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6726 (pt0) REVERT: A 904 TYR cc_start: 0.6599 (m-80) cc_final: 0.6289 (m-80) REVERT: A 917 HIS cc_start: 0.6643 (m-70) cc_final: 0.6428 (m90) outliers start: 19 outliers final: 15 residues processed: 104 average time/residue: 0.4374 time to fit residues: 48.8687 Evaluate side-chains 101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 291 SER 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 755 VAL 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 860 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4581 r_free = 0.4581 target = 0.221210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.181681 restraints weight = 6781.895| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.68 r_work: 0.4093 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.2664 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= 0.163 Angle : 0.665 10.607 10079 Z= 0.338 Chirality : 0.047 0.329 1186 Planarity : 0.005 0.048 1085 Dihedral : 16.871 80.289 1565 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 3.15 % Allowed : 34.53 % 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 aren not related in a simple way. whole: -1.42 (0.30), residues: 730 helix: 0.48 (0.34), residues: 230 sheet: -1.68 (0.38), residues: 149 loop : -1.53 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.050 0.002 TYR A 321 PHE 0.013 0.002 PHE A 758 TRP 0.020 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7262) covalent geometry : angle 0.66479 (10079) hydrogen bonds : bond 0.04424 ( 312) hydrogen bonds : angle 5.26584 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2923.23 seconds wall clock time: 51 minutes 1.50 seconds (3061.50 seconds total)