Starting phenix.real_space_refine on Fri Aug 22 16:12:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0j_41781/08_2025/8u0j_41781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0j_41781/08_2025/8u0j_41781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2025/8u0j_41781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2025/8u0j_41781.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2025/8u0j_41781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0j_41781/08_2025/8u0j_41781.map" } resolution = 3.1 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= 0.061 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 P 48 5.49 5 Mg 1 5.21 5 S 10 5.16 5 C 3466 2.51 5 N 963 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.00s 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: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4669 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.61, per 1000 atoms: 0.28 Number of scatterers: 5657 At special positions: 0 Unit cell: (83.32, 81.6536, 102.484, 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) S 10 16.00 P 48 15.00 Mg 1 11.99 O 1169 8.00 N 963 7.00 C 3466 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: 0.54 Conformation dependent library (CDL) restraints added in 137.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 36.7% alpha, 13.2% beta 9 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.618A pdb=" N THR A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.701A pdb=" N TYR A 355 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.834A pdb=" N VAL A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.529A pdb=" N TRP A 384 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 410 removed outlier: 4.174A pdb=" N VAL A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.015A pdb=" N ARG A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.729A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 4.310A pdb=" N ARG A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.772A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.535A pdb=" N GLU A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 571 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.909A pdb=" N LEU A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 656 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.808A pdb=" N LYS A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 144 removed outlier: 5.757A pdb=" N TYR A 137 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 159 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 139 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 157 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.052A pdb=" N LEU A 305 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA A 336 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 307 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN A 345 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 378 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU A 347 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 460 removed outlier: 7.228A pdb=" N LEU A 638 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 506 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER A 636 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 612 through 613 removed outlier: 3.917A pdb=" N PHE A 621 " --> pdb=" O PHE A 612 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.67 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: 940 1.32 - 1.44: 1776 1.44 - 1.57: 3064 1.57 - 1.69: 93 1.69 - 1.81: 16 Bond restraints: 5889 Sorted by residual: bond pdb=" CB VAL A 680 " pdb=" CG1 VAL A 680 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.67e+00 bond pdb=" C GLU A 416 " pdb=" N TYR A 417 " ideal model delta sigma weight residual 1.329 1.293 0.036 1.86e-02 2.89e+03 3.78e+00 bond pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.19e+00 bond pdb=" CG PHE A 656 " pdb=" CD1 PHE A 656 " ideal model delta sigma weight residual 1.384 1.348 0.036 2.10e-02 2.27e+03 2.96e+00 bond pdb=" CB VAL A 251 " pdb=" CG1 VAL A 251 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 5884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 7783 2.00 - 3.99: 329 3.99 - 5.99: 43 5.99 - 7.98: 12 7.98 - 9.98: 2 Bond angle restraints: 8169 Sorted by residual: angle pdb=" C TYR A 363 " pdb=" N GLN A 364 " pdb=" CA GLN A 364 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C PRO A 563 " pdb=" N LEU A 564 " pdb=" CA LEU A 564 " ideal model delta sigma weight residual 121.61 127.34 -5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C CYS A 378 " pdb=" N TYR A 379 " pdb=" CA TYR A 379 " ideal model delta sigma weight residual 121.48 129.48 -8.00 2.04e+00 2.40e-01 1.54e+01 angle pdb=" N SER A 608 " pdb=" CA SER A 608 " pdb=" C SER A 608 " ideal model delta sigma weight residual 114.09 108.35 5.74 1.55e+00 4.16e-01 1.37e+01 angle pdb=" C GLN A 430 " pdb=" N ARG A 431 " pdb=" CA ARG A 431 " ideal model delta sigma weight residual 120.94 127.94 -7.00 1.90e+00 2.77e-01 1.36e+01 ... (remaining 8164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2770 17.94 - 35.88: 404 35.88 - 53.82: 189 53.82 - 71.76: 47 71.76 - 89.70: 9 Dihedral angle restraints: 3419 sinusoidal: 1749 harmonic: 1670 Sorted by residual: dihedral pdb=" CA SER A 437 " pdb=" C SER A 437 " pdb=" N GLU A 438 " pdb=" CA GLU A 438 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLU A 435 " pdb=" C GLU A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta harmonic sigma weight residual -180.00 -140.41 -39.59 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA TYR A 220 " pdb=" C TYR A 220 " pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta harmonic sigma weight residual 180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 3416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 648 0.051 - 0.102: 186 0.102 - 0.153: 35 0.153 - 0.204: 8 0.204 - 0.255: 1 Chirality restraints: 878 Sorted by residual: chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN A 364 " pdb=" N GLN A 364 " pdb=" C GLN A 364 " pdb=" CB GLN A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL A 480 " pdb=" CA VAL A 480 " pdb=" CG1 VAL A 480 " pdb=" CG2 VAL A 480 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 875 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 364 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLN A 364 " 0.058 2.00e-02 2.50e+03 pdb=" O GLN A 364 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 365 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 428 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO A 429 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " 0.015 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR A 363 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " -0.000 2.00e-02 2.50e+03 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 313 2.72 - 3.26: 5253 3.26 - 3.81: 9454 3.81 - 4.35: 11941 4.35 - 4.90: 19173 Nonbonded interactions: 46134 Sorted by model distance: nonbonded pdb=" OP1 DT B 3 " pdb="MG MG B 101 " model vdw 2.170 2.170 nonbonded pdb=" OH TYR A 620 " pdb=" O VAL A 668 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 576 " pdb=" OP1 DA D 23 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG A 202 " pdb=" O GLY A 218 " model vdw 2.256 3.120 nonbonded pdb=" O2 DT D 20 " pdb=" N2 DG F 9 " model vdw 2.300 3.120 ... (remaining 46129 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.008 0.103 5889 Z= 0.329 Angle : 0.915 9.980 8169 Z= 0.526 Chirality : 0.050 0.255 878 Planarity : 0.006 0.057 889 Dihedral : 20.282 89.698 2345 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -1.07 (0.34), residues: 565 helix: 0.11 (0.40), residues: 154 sheet: -0.19 (0.53), residues: 90 loop : -1.30 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 367 TYR 0.034 0.003 TYR A 363 PHE 0.025 0.003 PHE A 685 TRP 0.011 0.001 TRP A 444 HIS 0.006 0.002 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00757 ( 5889) covalent geometry : angle 0.91543 ( 8169) hydrogen bonds : bond 0.16015 ( 174) hydrogen bonds : angle 6.45238 ( 451) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.201 Fit side-chains REVERT: A 302 GLU cc_start: 0.7306 (tp30) cc_final: 0.6769 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0956 time to fit residues: 10.2472 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.229891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182947 restraints weight = 6541.982| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.25 r_work: 0.3953 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5889 Z= 0.179 Angle : 0.644 7.507 8169 Z= 0.355 Chirality : 0.042 0.153 878 Planarity : 0.006 0.044 889 Dihedral : 23.030 74.002 1166 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.98 % Allowed : 8.43 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.71 (0.35), residues: 565 helix: 0.75 (0.41), residues: 157 sheet: -0.07 (0.53), residues: 91 loop : -1.25 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 615 TYR 0.015 0.002 TYR A 293 PHE 0.025 0.002 PHE A 611 TRP 0.005 0.001 TRP A 585 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5889) covalent geometry : angle 0.64419 ( 8169) hydrogen bonds : bond 0.04347 ( 174) hydrogen bonds : angle 4.76001 ( 451) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.184 Fit side-chains REVERT: A 19 GLU cc_start: 0.5940 (tp30) cc_final: 0.5725 (tp30) REVERT: A 302 GLU cc_start: 0.7858 (tp30) cc_final: 0.7179 (tm-30) REVERT: A 371 GLN cc_start: 0.8252 (mt0) cc_final: 0.7997 (mm-40) REVERT: A 440 ARG cc_start: 0.6724 (mmm160) cc_final: 0.5864 (mmm160) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.0881 time to fit residues: 9.4927 Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.228217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.181246 restraints weight = 6534.403| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 3.25 r_work: 0.3933 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5889 Z= 0.196 Angle : 0.634 6.837 8169 Z= 0.347 Chirality : 0.042 0.156 878 Planarity : 0.005 0.044 889 Dihedral : 23.068 77.644 1166 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.18 % Allowed : 12.55 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.55 (0.35), residues: 565 helix: 1.04 (0.41), residues: 156 sheet: 0.02 (0.52), residues: 94 loop : -1.25 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.015 0.002 TYR A 671 PHE 0.017 0.002 PHE A 685 TRP 0.004 0.001 TRP A 456 HIS 0.005 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 5889) covalent geometry : angle 0.63424 ( 8169) hydrogen bonds : bond 0.04162 ( 174) hydrogen bonds : angle 4.71642 ( 451) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.188 Fit side-chains REVERT: A 302 GLU cc_start: 0.7885 (tp30) cc_final: 0.7274 (tm-30) REVERT: A 440 ARG cc_start: 0.6739 (mmm160) cc_final: 0.5611 (mmm160) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.0717 time to fit residues: 8.0126 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.228634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181544 restraints weight = 6483.063| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.26 r_work: 0.3938 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5889 Z= 0.186 Angle : 0.615 6.378 8169 Z= 0.336 Chirality : 0.041 0.156 878 Planarity : 0.005 0.044 889 Dihedral : 22.997 72.232 1166 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.16 % Allowed : 13.33 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.44 (0.36), residues: 565 helix: 1.16 (0.41), residues: 156 sheet: -0.00 (0.53), residues: 92 loop : -1.16 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.014 0.002 TYR A 671 PHE 0.027 0.002 PHE A 611 TRP 0.006 0.001 TRP A 444 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 5889) covalent geometry : angle 0.61529 ( 8169) hydrogen bonds : bond 0.03945 ( 174) hydrogen bonds : angle 4.64078 ( 451) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.179 Fit side-chains REVERT: A 302 GLU cc_start: 0.7867 (tp30) cc_final: 0.7277 (tm-30) REVERT: A 341 ARG cc_start: 0.7295 (mtm110) cc_final: 0.6614 (mtp180) REVERT: A 440 ARG cc_start: 0.6695 (mmm160) cc_final: 0.5911 (mmm160) REVERT: A 486 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7774 (mtt180) REVERT: A 611 PHE cc_start: 0.7359 (t80) cc_final: 0.6968 (t80) REVERT: A 633 GLU cc_start: 0.8204 (pm20) cc_final: 0.7760 (pm20) outliers start: 11 outliers final: 8 residues processed: 89 average time/residue: 0.0916 time to fit residues: 10.3714 Evaluate side-chains 83 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 0.0170 chunk 8 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.230955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184539 restraints weight = 6550.565| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.23 r_work: 0.3966 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5889 Z= 0.154 Angle : 0.583 6.217 8169 Z= 0.320 Chirality : 0.040 0.153 878 Planarity : 0.005 0.045 889 Dihedral : 22.847 70.155 1166 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.57 % Allowed : 14.90 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.28 (0.36), residues: 565 helix: 1.36 (0.41), residues: 157 sheet: 0.02 (0.53), residues: 92 loop : -1.09 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 520 TYR 0.011 0.001 TYR A 671 PHE 0.023 0.002 PHE A 611 TRP 0.006 0.001 TRP A 444 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5889) covalent geometry : angle 0.58330 ( 8169) hydrogen bonds : bond 0.03651 ( 174) hydrogen bonds : angle 4.42534 ( 451) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.122 Fit side-chains REVERT: A 302 GLU cc_start: 0.7810 (tp30) cc_final: 0.7269 (tm-30) REVERT: A 341 ARG cc_start: 0.7302 (mtm110) cc_final: 0.6632 (mtp180) REVERT: A 440 ARG cc_start: 0.6568 (mmm160) cc_final: 0.5676 (mmm160) REVERT: A 486 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7574 (mtt180) REVERT: A 509 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7989 (mt) REVERT: A 578 ASP cc_start: 0.8327 (t0) cc_final: 0.8084 (t0) REVERT: A 611 PHE cc_start: 0.7314 (t80) cc_final: 0.7059 (t80) REVERT: A 619 MET cc_start: 0.5728 (mtm) cc_final: 0.5429 (mtm) REVERT: A 633 GLU cc_start: 0.8296 (pm20) cc_final: 0.7320 (pt0) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.0799 time to fit residues: 8.8322 Evaluate side-chains 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.231798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.185220 restraints weight = 6482.838| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.22 r_work: 0.3975 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5889 Z= 0.151 Angle : 0.577 6.072 8169 Z= 0.316 Chirality : 0.040 0.151 878 Planarity : 0.005 0.046 889 Dihedral : 22.837 71.345 1166 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.96 % Allowed : 15.88 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.19 (0.36), residues: 565 helix: 1.54 (0.42), residues: 156 sheet: 0.01 (0.53), residues: 92 loop : -1.06 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 686 TYR 0.011 0.001 TYR A 671 PHE 0.020 0.002 PHE A 611 TRP 0.005 0.001 TRP A 444 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5889) covalent geometry : angle 0.57730 ( 8169) hydrogen bonds : bond 0.03522 ( 174) hydrogen bonds : angle 4.34992 ( 451) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.187 Fit side-chains REVERT: A 302 GLU cc_start: 0.7829 (tp30) cc_final: 0.7267 (tm-30) REVERT: A 341 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6642 (mtp180) REVERT: A 440 ARG cc_start: 0.6580 (mmm160) cc_final: 0.5635 (mmm160) REVERT: A 486 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7517 (mtt180) REVERT: A 509 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7975 (mt) REVERT: A 619 MET cc_start: 0.5719 (mtm) cc_final: 0.5414 (mtm) REVERT: A 633 GLU cc_start: 0.8309 (pm20) cc_final: 0.7635 (pm20) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.0877 time to fit residues: 9.2019 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.230988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184502 restraints weight = 6494.707| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.20 r_work: 0.3966 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5889 Z= 0.163 Angle : 0.589 6.090 8169 Z= 0.323 Chirality : 0.040 0.150 878 Planarity : 0.005 0.045 889 Dihedral : 22.885 72.061 1166 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.37 % Allowed : 17.45 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.15 (0.37), residues: 565 helix: 1.57 (0.42), residues: 156 sheet: -0.03 (0.53), residues: 92 loop : -1.01 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 367 TYR 0.013 0.001 TYR A 620 PHE 0.013 0.002 PHE A 685 TRP 0.005 0.001 TRP A 444 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5889) covalent geometry : angle 0.58883 ( 8169) hydrogen bonds : bond 0.03550 ( 174) hydrogen bonds : angle 4.39500 ( 451) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.206 Fit side-chains REVERT: A 302 GLU cc_start: 0.7893 (tp30) cc_final: 0.7276 (tm-30) REVERT: A 341 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6621 (mtp180) REVERT: A 440 ARG cc_start: 0.6562 (mmm160) cc_final: 0.5541 (mmm160) REVERT: A 486 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7483 (mtt180) REVERT: A 509 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 619 MET cc_start: 0.5744 (mtm) cc_final: 0.5436 (mtm) REVERT: A 633 GLU cc_start: 0.8278 (pm20) cc_final: 0.7601 (pm20) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.0901 time to fit residues: 9.0137 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.232023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.185382 restraints weight = 6491.262| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.22 r_work: 0.3977 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5889 Z= 0.156 Angle : 0.587 6.123 8169 Z= 0.320 Chirality : 0.040 0.150 878 Planarity : 0.005 0.045 889 Dihedral : 22.897 71.287 1166 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.96 % Allowed : 17.25 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.11 (0.36), residues: 565 helix: 1.62 (0.42), residues: 156 sheet: 0.03 (0.52), residues: 92 loop : -1.00 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 440 TYR 0.012 0.001 TYR A 671 PHE 0.029 0.002 PHE A 621 TRP 0.005 0.001 TRP A 444 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5889) covalent geometry : angle 0.58730 ( 8169) hydrogen bonds : bond 0.03422 ( 174) hydrogen bonds : angle 4.35076 ( 451) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.191 Fit side-chains REVERT: A 302 GLU cc_start: 0.7904 (tp30) cc_final: 0.7234 (tm-30) REVERT: A 341 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6600 (mtp180) REVERT: A 417 TYR cc_start: 0.7703 (m-80) cc_final: 0.7300 (m-80) REVERT: A 435 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6748 (pm20) REVERT: A 440 ARG cc_start: 0.6476 (mmm160) cc_final: 0.5379 (mmm160) REVERT: A 486 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7496 (mtt180) REVERT: A 509 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7942 (mt) REVERT: A 619 MET cc_start: 0.5698 (mtm) cc_final: 0.5393 (mtm) REVERT: A 633 GLU cc_start: 0.8267 (pm20) cc_final: 0.7405 (pm20) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.0866 time to fit residues: 8.7027 Evaluate side-chains 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 9 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.233622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186982 restraints weight = 6412.262| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.20 r_work: 0.3992 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5889 Z= 0.137 Angle : 0.572 5.922 8169 Z= 0.313 Chirality : 0.039 0.149 878 Planarity : 0.005 0.046 889 Dihedral : 22.866 70.478 1166 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.57 % Allowed : 17.25 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.01 (0.36), residues: 565 helix: 1.77 (0.42), residues: 156 sheet: 0.10 (0.52), residues: 92 loop : -0.96 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 526 TYR 0.012 0.001 TYR A 671 PHE 0.024 0.002 PHE A 621 TRP 0.005 0.001 TRP A 444 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5889) covalent geometry : angle 0.57247 ( 8169) hydrogen bonds : bond 0.03348 ( 174) hydrogen bonds : angle 4.29933 ( 451) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.188 Fit side-chains REVERT: A 302 GLU cc_start: 0.7850 (tp30) cc_final: 0.7177 (tm-30) REVERT: A 341 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6589 (mtp180) REVERT: A 435 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6760 (pm20) REVERT: A 440 ARG cc_start: 0.6441 (mmm160) cc_final: 0.5324 (mmm160) REVERT: A 486 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7444 (mtt180) REVERT: A 509 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 619 MET cc_start: 0.5588 (mtm) cc_final: 0.5313 (mtm) REVERT: A 633 GLU cc_start: 0.8250 (pm20) cc_final: 0.7388 (pm20) outliers start: 8 outliers final: 6 residues processed: 78 average time/residue: 0.0958 time to fit residues: 9.5419 Evaluate side-chains 75 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.229220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.181850 restraints weight = 6558.973| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.24 r_work: 0.3942 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5889 Z= 0.191 Angle : 0.613 6.278 8169 Z= 0.333 Chirality : 0.041 0.151 878 Planarity : 0.005 0.045 889 Dihedral : 22.951 76.429 1166 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.96 % Allowed : 16.86 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.17 (0.36), residues: 565 helix: 1.50 (0.41), residues: 156 sheet: 0.03 (0.52), residues: 92 loop : -1.02 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.012 0.002 TYR A 363 PHE 0.024 0.002 PHE A 621 TRP 0.006 0.001 TRP A 444 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 5889) covalent geometry : angle 0.61326 ( 8169) hydrogen bonds : bond 0.03690 ( 174) hydrogen bonds : angle 4.56561 ( 451) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.186 Fit side-chains REVERT: A 341 ARG cc_start: 0.7314 (mtm110) cc_final: 0.6557 (mtp180) REVERT: A 364 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5980 (pt0) REVERT: A 435 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7311 (pm20) REVERT: A 440 ARG cc_start: 0.6458 (mmm160) cc_final: 0.5157 (mmm160) REVERT: A 482 HIS cc_start: 0.7678 (t-90) cc_final: 0.7455 (t-90) REVERT: A 619 MET cc_start: 0.5764 (mtm) cc_final: 0.5456 (mtm) REVERT: A 633 GLU cc_start: 0.8330 (pm20) cc_final: 0.7375 (pm20) outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.0838 time to fit residues: 8.3373 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.230638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.183519 restraints weight = 6415.223| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.21 r_work: 0.3959 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5889 Z= 0.169 Angle : 0.596 5.868 8169 Z= 0.324 Chirality : 0.040 0.151 878 Planarity : 0.005 0.048 889 Dihedral : 22.900 72.636 1166 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.16 % Allowed : 16.47 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.12 (0.36), residues: 565 helix: 1.60 (0.41), residues: 156 sheet: 0.02 (0.52), residues: 92 loop : -0.99 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 552 TYR 0.012 0.002 TYR A 639 PHE 0.023 0.002 PHE A 621 TRP 0.006 0.001 TRP A 444 HIS 0.002 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5889) covalent geometry : angle 0.59583 ( 8169) hydrogen bonds : bond 0.03543 ( 174) hydrogen bonds : angle 4.47946 ( 451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.22 seconds wall clock time: 25 minutes 46.76 seconds (1546.76 seconds total)