Starting phenix.real_space_refine on Fri Aug 22 18:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhk_61485/08_2025/9jhk_61485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhk_61485/08_2025/9jhk_61485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2025/9jhk_61485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2025/9jhk_61485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2025/9jhk_61485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhk_61485/08_2025/9jhk_61485.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 42 5.49 5 S 20 5.16 5 C 4313 2.51 5 N 1139 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 6898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'DNA': 21} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 419 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" 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: 2.10, per 1000 atoms: 0.30 Number of scatterers: 6898 At special positions: 0 Unit cell: (72.16, 85.28, 104.14, 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 20 16.00 P 42 15.00 O 1383 8.00 N 1139 7.00 C 4313 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: 0.67 Conformation dependent library (CDL) restraints added in 368.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 12 sheets defined 31.1% alpha, 17.4% beta 6 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.242A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.158A pdb=" N ASP A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.538A pdb=" N GLN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.831A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.516A pdb=" N ASN A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.846A pdb=" N TYR A 175 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.795A pdb=" N LEU A 67 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 27 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.671A pdb=" N VAL A 262 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.731A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.697A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.277A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLU A 433 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.277A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.536A pdb=" N GLU A 411 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 462 through 463 229 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 0.89 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: 1269 1.32 - 1.44: 1927 1.44 - 1.56: 3814 1.56 - 1.69: 78 1.69 - 1.81: 35 Bond restraints: 7123 Sorted by residual: bond pdb=" CG1 ILE A 515 " pdb=" CD1 ILE A 515 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.27e+01 bond pdb=" CG LEU A 520 " pdb=" CD2 LEU A 520 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.36e+00 bond pdb=" C VAL A 21 " pdb=" N ASN A 22 " ideal model delta sigma weight residual 1.331 1.271 0.060 2.07e-02 2.33e+03 8.42e+00 bond pdb=" O5' DG C 8 " pdb=" C5' DG C 8 " ideal model delta sigma weight residual 1.423 1.336 0.087 3.00e-02 1.11e+03 8.40e+00 bond pdb=" C5' DG C 2 " pdb=" C4' DG C 2 " ideal model delta sigma weight residual 1.518 1.461 0.057 2.00e-02 2.50e+03 8.26e+00 ... (remaining 7118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 8941 1.95 - 3.90: 724 3.90 - 5.85: 88 5.85 - 7.80: 23 7.80 - 9.75: 7 Bond angle restraints: 9783 Sorted by residual: angle pdb=" C ASN A 288 " pdb=" N ASP A 289 " pdb=" CA ASP A 289 " ideal model delta sigma weight residual 122.00 117.35 4.65 1.08e+00 8.57e-01 1.85e+01 angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C LYS A 631 " pdb=" N ASN A 632 " pdb=" CA ASN A 632 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" CG1 VAL A 594 " pdb=" CB VAL A 594 " pdb=" CG2 VAL A 594 " ideal model delta sigma weight residual 110.80 102.70 8.10 2.20e+00 2.07e-01 1.36e+01 angle pdb=" N GLY A 381 " pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 113.18 104.45 8.73 2.37e+00 1.78e-01 1.36e+01 ... (remaining 9778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 3928 25.30 - 50.59: 236 50.59 - 75.89: 40 75.89 - 101.18: 5 101.18 - 126.48: 1 Dihedral angle restraints: 4210 sinusoidal: 2023 harmonic: 2187 Sorted by residual: dihedral pdb=" CA ILE A 471 " pdb=" C ILE A 471 " pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta harmonic sigma weight residual -180.00 -139.34 -40.66 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA LYS A 63 " pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta harmonic sigma weight residual -180.00 -144.17 -35.83 0 5.00e+00 4.00e-02 5.14e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 660 0.054 - 0.108: 296 0.108 - 0.162: 82 0.162 - 0.216: 29 0.216 - 0.269: 5 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CB THR A 725 " pdb=" CA THR A 725 " pdb=" OG1 THR A 725 " pdb=" CG2 THR A 725 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 431 " pdb=" CA ILE A 431 " pdb=" CG1 ILE A 431 " pdb=" CG2 ILE A 431 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASN A 632 " pdb=" N ASN A 632 " pdb=" C ASN A 632 " pdb=" CB ASN A 632 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1069 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 470 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C GLU A 470 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 470 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 471 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " 0.017 2.00e-02 2.50e+03 1.56e-02 6.12e+00 pdb=" CG TRP A 623 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 154 " -0.016 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 154 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 154 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 154 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 154 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 154 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 154 " -0.003 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 29 2.44 - 3.06: 4273 3.06 - 3.67: 10867 3.67 - 4.29: 16318 4.29 - 4.90: 26642 Nonbonded interactions: 58129 Sorted by model distance: nonbonded pdb=" OD1 ASN A 451 " pdb=" CZ3 TRP A 482 " model vdw 1.829 3.340 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.846 2.320 nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.858 2.320 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.874 2.320 nonbonded pdb=" ND2 ASN A 451 " pdb=" CZ3 TRP A 482 " model vdw 2.005 3.420 ... (remaining 58124 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: 1.190 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 : 0.014 0.139 7123 Z= 0.582 Angle : 1.155 9.751 9783 Z= 0.631 Chirality : 0.069 0.269 1072 Planarity : 0.007 0.053 1097 Dihedral : 16.103 126.480 2816 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.78 (0.24), residues: 743 helix: -2.90 (0.23), residues: 224 sheet: -2.50 (0.42), residues: 122 loop : -2.24 (0.25), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 721 TYR 0.034 0.004 TYR A 624 PHE 0.040 0.006 PHE A 154 TRP 0.040 0.008 TRP A 623 HIS 0.015 0.004 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.01401 ( 7123) covalent geometry : angle 1.15460 ( 9783) hydrogen bonds : bond 0.22303 ( 243) hydrogen bonds : angle 9.19079 ( 676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ILE cc_start: 0.7405 (mt) cc_final: 0.7011 (mt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1052 time to fit residues: 26.1254 Evaluate side-chains 129 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 490 GLN A 574 ASN A 612 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053357 restraints weight = 26141.792| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 5.78 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7123 Z= 0.182 Angle : 0.759 11.884 9783 Z= 0.401 Chirality : 0.048 0.295 1072 Planarity : 0.004 0.033 1097 Dihedral : 19.235 134.782 1277 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.29 % Allowed : 11.38 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.40 (0.27), residues: 743 helix: -1.27 (0.30), residues: 225 sheet: -2.39 (0.42), residues: 124 loop : -1.43 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 48 TYR 0.037 0.002 TYR A 511 PHE 0.017 0.002 PHE A 366 TRP 0.021 0.002 TRP A 623 HIS 0.006 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7123) covalent geometry : angle 0.75886 ( 9783) hydrogen bonds : bond 0.05014 ( 243) hydrogen bonds : angle 6.06763 ( 676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9627 (tpp) cc_final: 0.9292 (mmt) REVERT: A 85 ASN cc_start: 0.9535 (m110) cc_final: 0.9270 (m-40) REVERT: A 103 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: A 132 GLU cc_start: 0.8360 (pm20) cc_final: 0.8003 (pm20) REVERT: A 191 MET cc_start: 0.9693 (mmm) cc_final: 0.9458 (mmm) REVERT: A 217 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 289 ASP cc_start: 0.8687 (t0) cc_final: 0.8217 (t0) REVERT: A 363 MET cc_start: 0.9013 (tpp) cc_final: 0.8025 (tpp) REVERT: A 383 LEU cc_start: 0.9507 (mp) cc_final: 0.9301 (mt) REVERT: A 419 HIS cc_start: 0.9446 (m90) cc_final: 0.9239 (m90) REVERT: A 478 PHE cc_start: 0.9061 (m-10) cc_final: 0.8741 (m-10) REVERT: A 482 TRP cc_start: 0.8659 (m100) cc_final: 0.8443 (m100) REVERT: A 491 MET cc_start: 0.8975 (mtp) cc_final: 0.8518 (mtp) REVERT: A 495 LYS cc_start: 0.9711 (tttm) cc_final: 0.9462 (ttmm) REVERT: A 513 HIS cc_start: 0.9179 (m-70) cc_final: 0.8707 (m-70) REVERT: A 514 ASN cc_start: 0.9138 (m-40) cc_final: 0.8915 (t0) REVERT: A 531 LYS cc_start: 0.9660 (tmtt) cc_final: 0.9289 (ptmm) REVERT: A 647 LYS cc_start: 0.9339 (mmtm) cc_final: 0.8763 (mmmt) REVERT: A 673 MET cc_start: 0.8292 (tmm) cc_final: 0.8071 (tmm) REVERT: A 699 MET cc_start: 0.9287 (mmm) cc_final: 0.9030 (mmt) outliers start: 22 outliers final: 9 residues processed: 165 average time/residue: 0.0978 time to fit residues: 21.2898 Evaluate side-chains 126 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053034 restraints weight = 26783.992| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 5.84 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7123 Z= 0.171 Angle : 0.674 9.686 9783 Z= 0.362 Chirality : 0.046 0.246 1072 Planarity : 0.003 0.021 1097 Dihedral : 19.029 131.533 1277 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.04 % Allowed : 14.37 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.28), residues: 743 helix: -0.46 (0.33), residues: 225 sheet: -2.00 (0.42), residues: 125 loop : -1.05 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 721 TYR 0.024 0.002 TYR A 306 PHE 0.020 0.002 PHE A 738 TRP 0.016 0.002 TRP A 623 HIS 0.007 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7123) covalent geometry : angle 0.67382 ( 9783) hydrogen bonds : bond 0.04120 ( 243) hydrogen bonds : angle 5.74673 ( 676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8579 (m-80) cc_final: 0.8334 (m-80) REVERT: A 30 LYS cc_start: 0.9638 (tmmt) cc_final: 0.9356 (tmmt) REVERT: A 51 MET cc_start: 0.9581 (tpp) cc_final: 0.8960 (tpp) REVERT: A 103 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: A 132 GLU cc_start: 0.8632 (pm20) cc_final: 0.8378 (pm20) REVERT: A 191 MET cc_start: 0.9758 (mmm) cc_final: 0.9493 (mmm) REVERT: A 289 ASP cc_start: 0.8788 (t0) cc_final: 0.8292 (t0) REVERT: A 363 MET cc_start: 0.9077 (tpp) cc_final: 0.7933 (tpp) REVERT: A 383 LEU cc_start: 0.9436 (mp) cc_final: 0.9221 (mt) REVERT: A 478 PHE cc_start: 0.9138 (m-10) cc_final: 0.8702 (m-80) REVERT: A 482 TRP cc_start: 0.8856 (m100) cc_final: 0.8654 (m100) REVERT: A 491 MET cc_start: 0.9028 (mtp) cc_final: 0.8410 (mpp) REVERT: A 495 LYS cc_start: 0.9647 (tttm) cc_final: 0.9437 (ttmm) REVERT: A 513 HIS cc_start: 0.9147 (m-70) cc_final: 0.8676 (m-70) REVERT: A 531 LYS cc_start: 0.9619 (tmtt) cc_final: 0.9259 (ptmm) REVERT: A 536 ASP cc_start: 0.9173 (m-30) cc_final: 0.8836 (p0) REVERT: A 591 PHE cc_start: 0.9521 (m-80) cc_final: 0.9206 (m-80) REVERT: A 673 MET cc_start: 0.8391 (tmm) cc_final: 0.8050 (tmm) REVERT: A 710 THR cc_start: 0.9543 (p) cc_final: 0.9336 (p) REVERT: A 717 THR cc_start: 0.9461 (p) cc_final: 0.9245 (m) outliers start: 27 outliers final: 14 residues processed: 140 average time/residue: 0.0890 time to fit residues: 16.8727 Evaluate side-chains 125 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.068386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053601 restraints weight = 27512.069| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 5.98 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7123 Z= 0.157 Angle : 0.634 9.582 9783 Z= 0.339 Chirality : 0.045 0.276 1072 Planarity : 0.003 0.021 1097 Dihedral : 18.835 131.312 1277 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.89 % Allowed : 15.72 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.30), residues: 743 helix: -0.18 (0.34), residues: 230 sheet: -1.65 (0.39), residues: 164 loop : -0.73 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 158 TYR 0.022 0.002 TYR A 306 PHE 0.016 0.002 PHE A 500 TRP 0.013 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7123) covalent geometry : angle 0.63384 ( 9783) hydrogen bonds : bond 0.03809 ( 243) hydrogen bonds : angle 5.52575 ( 676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8503 (m-80) cc_final: 0.8077 (m-80) REVERT: A 30 LYS cc_start: 0.9625 (tmmt) cc_final: 0.9363 (tmmt) REVERT: A 51 MET cc_start: 0.9635 (tpp) cc_final: 0.8985 (tpp) REVERT: A 103 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8762 (pm20) REVERT: A 132 GLU cc_start: 0.8611 (pm20) cc_final: 0.8328 (pm20) REVERT: A 191 MET cc_start: 0.9781 (mmm) cc_final: 0.9497 (mmm) REVERT: A 289 ASP cc_start: 0.8861 (t0) cc_final: 0.8346 (t0) REVERT: A 302 MET cc_start: 0.8543 (mmm) cc_final: 0.7675 (mmm) REVERT: A 306 TYR cc_start: 0.8770 (t80) cc_final: 0.8497 (t80) REVERT: A 363 MET cc_start: 0.9203 (tpp) cc_final: 0.8080 (tpp) REVERT: A 478 PHE cc_start: 0.9123 (m-10) cc_final: 0.8712 (m-80) REVERT: A 491 MET cc_start: 0.8917 (mtp) cc_final: 0.8294 (mpp) REVERT: A 513 HIS cc_start: 0.9160 (m-70) cc_final: 0.8838 (m-70) REVERT: A 536 ASP cc_start: 0.9220 (m-30) cc_final: 0.8840 (p0) REVERT: A 591 PHE cc_start: 0.9487 (m-80) cc_final: 0.8971 (m-80) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.0879 time to fit residues: 15.5382 Evaluate side-chains 119 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.065924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.051480 restraints weight = 27848.220| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 5.75 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7123 Z= 0.199 Angle : 0.659 10.039 9783 Z= 0.351 Chirality : 0.045 0.223 1072 Planarity : 0.003 0.023 1097 Dihedral : 18.799 132.910 1277 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.04 % Allowed : 16.17 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.31), residues: 743 helix: -0.15 (0.33), residues: 231 sheet: -1.69 (0.38), residues: 170 loop : -0.53 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 158 TYR 0.019 0.002 TYR A 306 PHE 0.015 0.002 PHE A 738 TRP 0.013 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7123) covalent geometry : angle 0.65903 ( 9783) hydrogen bonds : bond 0.03738 ( 243) hydrogen bonds : angle 5.47800 ( 676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8570 (m-80) cc_final: 0.8225 (m-80) REVERT: A 30 LYS cc_start: 0.9559 (tmmt) cc_final: 0.9244 (tmmt) REVERT: A 51 MET cc_start: 0.9586 (tpp) cc_final: 0.8917 (tpp) REVERT: A 98 MET cc_start: 0.9167 (mmt) cc_final: 0.8923 (mmp) REVERT: A 103 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8706 (pm20) REVERT: A 132 GLU cc_start: 0.8671 (pm20) cc_final: 0.8382 (pm20) REVERT: A 169 MET cc_start: 0.9289 (mmm) cc_final: 0.9085 (mmm) REVERT: A 191 MET cc_start: 0.9795 (mmm) cc_final: 0.9514 (mmm) REVERT: A 289 ASP cc_start: 0.8952 (t0) cc_final: 0.8502 (t0) REVERT: A 353 MET cc_start: 0.8716 (ptt) cc_final: 0.8373 (ptt) REVERT: A 363 MET cc_start: 0.9131 (tpp) cc_final: 0.7941 (tpp) REVERT: A 478 PHE cc_start: 0.9139 (m-10) cc_final: 0.8849 (m-10) REVERT: A 491 MET cc_start: 0.8882 (mtp) cc_final: 0.8299 (mpp) REVERT: A 513 HIS cc_start: 0.9099 (m-70) cc_final: 0.8794 (m-70) REVERT: A 536 ASP cc_start: 0.9183 (m-30) cc_final: 0.8872 (p0) REVERT: A 591 PHE cc_start: 0.9495 (m-80) cc_final: 0.8978 (m-80) outliers start: 27 outliers final: 22 residues processed: 125 average time/residue: 0.0829 time to fit residues: 14.2294 Evaluate side-chains 123 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 240 ASN A 741 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.049052 restraints weight = 29446.177| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 5.65 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7123 Z= 0.282 Angle : 0.696 10.012 9783 Z= 0.374 Chirality : 0.045 0.162 1072 Planarity : 0.004 0.052 1097 Dihedral : 19.027 131.299 1277 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.89 % Allowed : 18.86 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.31), residues: 743 helix: -0.05 (0.33), residues: 226 sheet: -1.70 (0.38), residues: 169 loop : -0.36 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 158 TYR 0.019 0.002 TYR A 306 PHE 0.020 0.002 PHE A 738 TRP 0.014 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 7123) covalent geometry : angle 0.69586 ( 9783) hydrogen bonds : bond 0.04036 ( 243) hydrogen bonds : angle 5.59219 ( 676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.8442 (m-80) cc_final: 0.8175 (m-80) REVERT: A 30 LYS cc_start: 0.9519 (tmmt) cc_final: 0.9212 (tmmt) REVERT: A 51 MET cc_start: 0.9582 (tpp) cc_final: 0.8940 (tpp) REVERT: A 132 GLU cc_start: 0.8751 (pm20) cc_final: 0.8459 (pm20) REVERT: A 191 MET cc_start: 0.9797 (mmm) cc_final: 0.9529 (mmm) REVERT: A 289 ASP cc_start: 0.8995 (t0) cc_final: 0.8579 (t0) REVERT: A 363 MET cc_start: 0.9183 (tpp) cc_final: 0.8055 (tpp) REVERT: A 478 PHE cc_start: 0.9205 (m-10) cc_final: 0.8764 (m-10) REVERT: A 491 MET cc_start: 0.8852 (mtp) cc_final: 0.8284 (mpp) REVERT: A 513 HIS cc_start: 0.9222 (m-70) cc_final: 0.8723 (m-70) REVERT: A 531 LYS cc_start: 0.9640 (tmtt) cc_final: 0.9308 (tptp) REVERT: A 533 MET cc_start: 0.8691 (tpt) cc_final: 0.8444 (tpt) REVERT: A 536 ASP cc_start: 0.9202 (m-30) cc_final: 0.8897 (p0) REVERT: A 639 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 734 LYS cc_start: 0.9361 (ttmm) cc_final: 0.9114 (ttmm) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.0817 time to fit residues: 13.1764 Evaluate side-chains 110 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2723 > 50: distance: 4 - 9: 20.826 distance: 9 - 10: 24.939 distance: 10 - 11: 43.127 distance: 10 - 13: 49.047 distance: 11 - 12: 20.450 distance: 11 - 18: 54.435 distance: 13 - 14: 16.671 distance: 14 - 15: 15.037 distance: 15 - 16: 6.370 distance: 15 - 17: 5.194 distance: 18 - 19: 40.080 distance: 18 - 144: 29.645 distance: 19 - 20: 31.701 distance: 20 - 21: 33.587 distance: 20 - 22: 24.406 distance: 22 - 23: 20.544 distance: 22 - 169: 17.782 distance: 23 - 24: 22.478 distance: 23 - 26: 17.097 distance: 24 - 25: 33.796 distance: 24 - 30: 29.519 distance: 25 - 166: 22.939 distance: 26 - 27: 16.465 distance: 26 - 28: 10.506 distance: 27 - 29: 4.869 distance: 30 - 31: 31.302 distance: 31 - 32: 38.130 distance: 32 - 33: 27.143 distance: 32 - 34: 49.806 distance: 34 - 35: 42.385 distance: 35 - 36: 36.648 distance: 35 - 38: 55.473 distance: 36 - 37: 15.827 distance: 36 - 40: 15.592 distance: 38 - 39: 40.638 distance: 40 - 41: 49.282 distance: 41 - 42: 31.126 distance: 41 - 44: 43.466 distance: 42 - 43: 47.272 distance: 42 - 47: 41.632 distance: 44 - 45: 17.368 distance: 44 - 46: 16.418 distance: 47 - 48: 13.325 distance: 48 - 49: 30.984 distance: 48 - 51: 30.526 distance: 49 - 50: 20.497 distance: 49 - 55: 22.956 distance: 51 - 52: 45.235 distance: 52 - 53: 29.250 distance: 52 - 54: 36.666 distance: 55 - 56: 7.635 distance: 55 - 61: 7.898 distance: 56 - 57: 13.747 distance: 56 - 59: 8.591 distance: 57 - 58: 8.960 distance: 57 - 62: 12.649 distance: 59 - 60: 17.445 distance: 60 - 61: 18.306 distance: 62 - 63: 13.486 distance: 63 - 64: 7.936 distance: 63 - 66: 23.189 distance: 64 - 65: 38.628 distance: 64 - 70: 27.409 distance: 66 - 67: 15.672 distance: 67 - 68: 11.073 distance: 68 - 69: 3.618 distance: 70 - 71: 21.125 distance: 71 - 72: 20.075 distance: 71 - 74: 22.631 distance: 72 - 73: 18.782 distance: 72 - 78: 10.895 distance: 74 - 75: 6.466 distance: 75 - 77: 3.272