Starting phenix.real_space_refine on Fri Dec 27 21:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij3_60614/12_2024/9ij3_60614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij3_60614/12_2024/9ij3_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_60614/12_2024/9ij3_60614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij3_60614/12_2024/9ij3_60614.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij3_60614/12_2024/9ij3_60614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij3_60614/12_2024/9ij3_60614.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 4.36, per 1000 atoms: 0.62 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: 2.22 Conformation dependent library (CDL) restraints added in 737.7 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: 2.82 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: 3.35 Time building geometry restraints manager: 2.22 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- 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= 0.301 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (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 TRP 0.070 0.003 TRP A 358 HIS 0.009 0.001 HIS A 472 PHE 0.016 0.002 PHE A 758 TYR 0.031 0.003 TYR A 425 ARG 0.004 0.000 ARG A 570 *********************** 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 : 0.655 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: 1.0435 time to fit residues: 114.4739 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 : 0.580 ------------------------------------------------------------------------------- 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 65 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.1617 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= 0.293 Angle : 0.728 12.166 10079 Z= 0.367 Chirality : 0.047 0.283 1186 Planarity : 0.006 0.069 1085 Dihedral : 17.422 81.962 1568 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.49 % Favored : 91.37 % Rotamer: Outliers : 6.46 % Allowed : 28.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.30), residues: 730 helix: -0.06 (0.34), residues: 233 sheet: -1.41 (0.40), residues: 140 loop : -1.73 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 358 HIS 0.008 0.001 HIS A 472 PHE 0.014 0.002 PHE A 325 TYR 0.012 0.002 TYR A 241 ARG 0.005 0.001 ARG A 937 *********************** 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 131 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 88 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5557 (mp) REVERT: A 228 LEU cc_start: 0.2453 (OUTLIER) cc_final: 0.1812 (mt) REVERT: A 519 ILE cc_start: 0.5647 (mt) cc_final: 0.5282 (mt) REVERT: A 831 LEU cc_start: 0.5436 (tp) cc_final: 0.5191 (tp) outliers start: 43 outliers final: 17 residues processed: 110 average time/residue: 0.9435 time to fit residues: 111.5742 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 598 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 47 optimal weight: 0.0170 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.3824 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7262 Z= 0.309 Angle : 0.727 11.005 10079 Z= 0.368 Chirality : 0.047 0.242 1186 Planarity : 0.006 0.061 1085 Dihedral : 17.334 81.229 1564 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 6.01 % Allowed : 28.53 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.30), residues: 730 helix: 0.08 (0.34), residues: 232 sheet: -1.37 (0.38), residues: 147 loop : -1.79 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 358 HIS 0.008 0.001 HIS A 472 PHE 0.014 0.002 PHE A 325 TYR 0.010 0.002 TYR A 420 ARG 0.005 0.000 ARG A 937 *********************** 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 125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3041 (OUTLIER) cc_final: 0.2503 (mt) REVERT: A 329 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6484 (mpp) REVERT: A 519 ILE cc_start: 0.5465 (OUTLIER) cc_final: 0.5252 (mt) REVERT: A 671 ILE cc_start: 0.2772 (OUTLIER) cc_final: 0.2550 (tp) outliers start: 40 outliers final: 17 residues processed: 110 average time/residue: 0.8291 time to fit residues: 98.9033 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 : 0.680 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 624 GLU 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 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 69 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 655 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7262 Z= 0.324 Angle : 0.731 10.504 10079 Z= 0.370 Chirality : 0.047 0.249 1186 Planarity : 0.006 0.061 1085 Dihedral : 17.337 79.763 1564 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.77 % Favored : 91.10 % Rotamer: Outliers : 7.06 % Allowed : 28.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.30), residues: 730 helix: 0.08 (0.34), residues: 229 sheet: -1.63 (0.39), residues: 141 loop : -1.71 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 358 HIS 0.008 0.001 HIS A 472 PHE 0.013 0.002 PHE A 758 TYR 0.013 0.002 TYR A 321 ARG 0.004 0.000 ARG A 937 *********************** 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 133 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3222 (OUTLIER) cc_final: 0.2730 (mt) REVERT: A 329 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6390 (mpp) REVERT: A 470 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6699 (mp) REVERT: A 671 ILE cc_start: 0.3216 (OUTLIER) cc_final: 0.2994 (tp) outliers start: 47 outliers final: 22 residues processed: 120 average time/residue: 0.9805 time to fit residues: 125.7689 Evaluate side-chains 105 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 329 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 505 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 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 894 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 905 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0040 chunk 66 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 957 HIS A 958 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7262 Z= 0.181 Angle : 0.643 9.705 10079 Z= 0.324 Chirality : 0.044 0.211 1186 Planarity : 0.005 0.057 1085 Dihedral : 17.124 84.568 1564 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.90 % Favored : 90.96 % Rotamer: Outliers : 4.95 % Allowed : 31.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.30), residues: 730 helix: 0.41 (0.34), residues: 229 sheet: -1.24 (0.39), residues: 145 loop : -1.76 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 358 HIS 0.006 0.001 HIS A 957 PHE 0.015 0.001 PHE A 758 TYR 0.019 0.001 TYR A 321 ARG 0.003 0.000 ARG A 570 *********************** 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 122 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 MET cc_start: 0.3096 (mmp) cc_final: 0.2842 (mmp) outliers start: 33 outliers final: 11 residues processed: 106 average time/residue: 0.9852 time to fit residues: 111.7489 Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 471 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 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 917 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 954 GLN A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 7262 Z= 0.504 Angle : 0.887 11.821 10079 Z= 0.446 Chirality : 0.053 0.271 1186 Planarity : 0.006 0.066 1085 Dihedral : 17.388 74.274 1564 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.86 % Favored : 89.86 % Rotamer: Outliers : 5.41 % Allowed : 30.33 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.29), residues: 730 helix: -0.01 (0.34), residues: 229 sheet: -1.77 (0.38), residues: 142 loop : -1.88 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 358 HIS 0.009 0.002 HIS A 472 PHE 0.018 0.003 PHE A 272 TYR 0.020 0.003 TYR A 859 ARG 0.007 0.001 ARG A 937 *********************** 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 119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3519 (OUTLIER) cc_final: 0.3111 (mt) REVERT: A 647 ILE cc_start: 0.2526 (OUTLIER) cc_final: 0.1598 (pt) outliers start: 36 outliers final: 24 residues processed: 109 average time/residue: 0.8275 time to fit residues: 97.3857 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 : 0.704 ------------------------------------------------------------------------------- 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 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 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 742 MET 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 860 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 954 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 54 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- 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 830 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7262 Z= 0.217 Angle : 0.691 13.033 10079 Z= 0.347 Chirality : 0.045 0.183 1186 Planarity : 0.005 0.053 1085 Dihedral : 17.113 81.948 1564 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.90 % Favored : 90.96 % Rotamer: Outliers : 4.05 % Allowed : 31.98 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.30), residues: 730 helix: 0.32 (0.34), residues: 229 sheet: -1.43 (0.38), residues: 146 loop : -1.80 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 358 HIS 0.005 0.001 HIS A 472 PHE 0.014 0.002 PHE A 950 TYR 0.020 0.002 TYR A 321 ARG 0.007 0.000 ARG A 570 *********************** 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 112 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 VAL cc_start: 0.6565 (OUTLIER) cc_final: 0.6340 (p) outliers start: 27 outliers final: 15 residues processed: 101 average time/residue: 0.9410 time to fit residues: 102.4143 Evaluate side-chains 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 349 VAL Chi-restraints excluded: chain A residue 495 LEU 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 624 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7262 Z= 0.253 Angle : 0.706 11.428 10079 Z= 0.354 Chirality : 0.046 0.232 1186 Planarity : 0.006 0.076 1085 Dihedral : 17.065 80.585 1564 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 3.75 % Allowed : 33.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.30), residues: 730 helix: 0.39 (0.34), residues: 229 sheet: -1.72 (0.37), residues: 156 loop : -1.71 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 PHE 0.012 0.002 PHE A 272 TYR 0.019 0.002 TYR A 321 ARG 0.004 0.000 ARG A 570 *********************** 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 108 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 MET cc_start: 0.1464 (ppp) cc_final: 0.1237 (mmt) outliers start: 25 outliers final: 18 residues processed: 99 average time/residue: 0.9797 time to fit residues: 104.5758 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 : 0.751 ------------------------------------------------------------------------------- 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 495 LEU 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 624 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.2718 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= 0.207 Angle : 0.651 8.999 10079 Z= 0.330 Chirality : 0.045 0.286 1186 Planarity : 0.005 0.068 1085 Dihedral : 16.993 82.183 1564 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.00 % Favored : 89.86 % Rotamer: Outliers : 3.15 % Allowed : 34.23 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.30), residues: 730 helix: 0.49 (0.35), residues: 229 sheet: -1.47 (0.38), residues: 150 loop : -1.67 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 358 HIS 0.006 0.001 HIS A 234 PHE 0.011 0.001 PHE A 758 TYR 0.051 0.002 TYR A 321 ARG 0.004 0.000 ARG A 570 *********************** 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 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 VAL cc_start: 0.6327 (OUTLIER) cc_final: 0.6116 (p) outliers start: 21 outliers final: 14 residues processed: 94 average time/residue: 0.9590 time to fit residues: 97.0064 Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 270 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 495 LEU 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 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 917 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7262 Z= 0.186 Angle : 0.647 8.622 10079 Z= 0.327 Chirality : 0.045 0.285 1186 Planarity : 0.005 0.067 1085 Dihedral : 16.962 83.499 1564 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 3.30 % Allowed : 34.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.31), residues: 730 helix: 0.57 (0.35), residues: 229 sheet: -1.36 (0.39), residues: 150 loop : -1.61 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 358 HIS 0.005 0.001 HIS A 472 PHE 0.025 0.002 PHE A 325 TYR 0.055 0.002 TYR A 321 ARG 0.004 0.000 ARG A 570 ********************** 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 114 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6101 (mp) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.9282 time to fit residues: 103.6600 Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 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 = 0.4564 r_free = 0.4564 target = 0.219115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.179460 restraints weight = 6777.410| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 1.69 r_work: 0.4072 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7262 Z= 0.289 Angle : 0.737 16.097 10079 Z= 0.369 Chirality : 0.049 0.405 1186 Planarity : 0.006 0.065 1085 Dihedral : 17.004 79.769 1564 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.14 % Rotamer: Outliers : 2.40 % Allowed : 35.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.30), residues: 730 helix: 0.44 (0.35), residues: 229 sheet: -1.39 (0.39), residues: 150 loop : -1.70 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 PHE 0.012 0.002 PHE A 272 TYR 0.074 0.003 TYR A 321 ARG 0.003 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.87 seconds wall clock time: 45 minutes 35.89 seconds (2735.89 seconds total)