Starting phenix.real_space_refine on Wed Aug 5 17:23:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjx_38409/08_2026/8xjx_38409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjx_38409/08_2026/8xjx_38409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xjx_38409/08_2026/8xjx_38409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjx_38409/08_2026/8xjx_38409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xjx_38409/08_2026/8xjx_38409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjx_38409/08_2026/8xjx_38409.map" } resolution = 2.78 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= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5737 atoms to isotropic. 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 32 5.49 5 S 29 5.16 5 C 3914 2.51 5 N 1120 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6311 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5626 Classifications: {'peptide': 693} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 669} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 298 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 18} Link IDs: {None: 18} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.52, per 1000 atoms: 0.24 Number of scatterers: 6311 At special positions: 0 Unit cell: (75.739, 91.908, 107.226, 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 29 16.00 P 32 15.00 O 1215 8.00 N 1120 7.00 C 3914 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: 0.56 Conformation dependent library (CDL) restraints added in 312.1 milliseconds 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 7 sheets defined 36.9% alpha, 18.5% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 108 removed outlier: 3.686A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.856A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.544A pdb=" N LEU A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 removed outlier: 3.606A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.601A pdb=" N GLY A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.643A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.514A pdb=" N LYS A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.974A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.649A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.530A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.644A pdb=" N ALA A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 4.891A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.637A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS A 522 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N HIS A 594 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 382 removed outlier: 9.119A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1650 1.33 - 1.45: 1324 1.45 - 1.57: 3404 1.57 - 1.69: 63 1.69 - 1.81: 51 Bond restraints: 6492 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.599 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" N VAL A 606 " pdb=" CA VAL A 606 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" C3' DT B 14 " pdb=" C2' DT B 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC C 15 " pdb=" C2' DC C 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.72e+00 bond pdb=" C3' DT C 14 " pdb=" C2' DT C 14 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.58e+00 ... (remaining 6487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 8671 1.72 - 3.43: 214 3.43 - 5.15: 25 5.15 - 6.87: 4 6.87 - 8.58: 3 Bond angle restraints: 8917 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.33 110.58 -7.25 9.30e-01 1.16e+00 6.07e+01 angle pdb=" C GLU A 607 " pdb=" CA GLU A 607 " pdb=" CB GLU A 607 " ideal model delta sigma weight residual 110.85 119.43 -8.58 1.70e+00 3.46e-01 2.55e+01 angle pdb=" N VAL A 606 " pdb=" CA VAL A 606 " pdb=" CB VAL A 606 " ideal model delta sigma weight residual 110.55 115.67 -5.12 1.17e+00 7.31e-01 1.92e+01 angle pdb=" O4' DT B 1 " pdb=" C1' DT B 1 " pdb=" N1 DT B 1 " ideal model delta sigma weight residual 108.00 104.94 3.06 7.00e-01 2.04e+00 1.91e+01 angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 8912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 3529 26.50 - 53.00: 240 53.00 - 79.51: 25 79.51 - 106.01: 1 106.01 - 132.51: 1 Dihedral angle restraints: 3796 sinusoidal: 1751 harmonic: 2045 Sorted by residual: dihedral pdb=" CA MET A 610 " pdb=" C MET A 610 " pdb=" N SER A 611 " pdb=" CA SER A 611 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY A 547 " pdb=" C GLY A 547 " pdb=" N HIS A 548 " pdb=" CA HIS A 548 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 87.49 132.51 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 3793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 862 0.066 - 0.131: 123 0.131 - 0.197: 7 0.197 - 0.262: 2 0.262 - 0.328: 1 Chirality restraints: 995 Sorted by residual: chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.66 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB VAL A 606 " pdb=" CA VAL A 606 " pdb=" CG1 VAL A 606 " pdb=" CG2 VAL A 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 992 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 125 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C ARG A 125 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG A 125 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 126 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 43 " 0.012 2.00e-02 2.50e+03 8.90e-03 1.98e+00 pdb=" CG TRP A 43 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 43 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 43 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 43 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 43 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 43 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 43 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 43 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 43 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 511 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " 0.019 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 12 2.37 - 3.00: 3106 3.00 - 3.64: 9087 3.64 - 4.27: 14789 4.27 - 4.90: 24417 Nonbonded interactions: 51411 Sorted by model distance: nonbonded pdb=" OXT VAL A 737 " pdb="MN MN A 801 " model vdw 1.742 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN A 801 " model vdw 1.797 2.320 nonbonded pdb=" O SER A 313 " pdb=" O HOH A 901 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 668 " pdb=" O HOH A 902 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 265 " pdb=" O HOH A 903 " model vdw 2.263 3.040 ... (remaining 51406 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.510 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.004 0.119 6492 Z= 0.272 Angle : 0.639 8.585 8917 Z= 0.450 Chirality : 0.046 0.328 995 Planarity : 0.004 0.035 1020 Dihedral : 16.486 132.512 2474 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.51 % Favored : 95.20 % Rotamer: Outliers : 0.16 % Allowed : 0.49 % Favored : 99.34 % 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 are not related in a simple way. whole: -0.23 (0.31), residues: 687 helix: 0.76 (0.33), residues: 240 sheet: 1.12 (0.43), residues: 130 loop : -1.47 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.009 0.001 TYR A 53 PHE 0.017 0.001 PHE A 351 TRP 0.024 0.002 TRP A 43 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.27 ( 6492) covalent geometry : angle 0.63949 / 0.45 ( 8917) hydrogen bonds : bond 0.12717 / 7.80 ( 267) hydrogen bonds : angle 6.37829 / 4.31 ( 734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.227 Fit side-chains REVERT: A 400 HIS cc_start: 0.7151 (m90) cc_final: 0.6834 (m90) outliers start: 1 outliers final: 2 residues processed: 112 average time/residue: 0.5500 time to fit residues: 64.6571 Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 575 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0010 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 376 GLN A 435 GLN A 552 GLN A 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.206093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189170 restraints weight = 5794.300| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.32 r_work: 0.3819 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6492 Z= 0.146 Angle : 0.581 6.954 8917 Z= 0.336 Chirality : 0.045 0.382 995 Planarity : 0.004 0.047 1020 Dihedral : 16.071 130.959 1117 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.24 % Favored : 94.47 % Rotamer: Outliers : 2.96 % Allowed : 11.18 % Favored : 85.86 % 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 are not related in a simple way. whole: -0.01 (0.31), residues: 687 helix: 1.01 (0.33), residues: 249 sheet: 1.33 (0.44), residues: 115 loop : -1.37 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.010 0.001 TYR A 158 PHE 0.016 0.002 PHE A 351 TRP 0.014 0.001 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 6492) covalent geometry : angle 0.58068 / 0.34 ( 8917) hydrogen bonds : bond 0.04565 / 2.78 ( 267) hydrogen bonds : angle 5.08923 / 3.42 ( 734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.154 Fit side-chains REVERT: A 53 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7862 (p90) REVERT: A 122 GLN cc_start: 0.6144 (tt0) cc_final: 0.5818 (mt0) REVERT: A 123 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6836 (tt0) REVERT: A 126 GLN cc_start: 0.7056 (tt0) cc_final: 0.6446 (tm-30) REVERT: A 155 GLU cc_start: 0.6794 (tt0) cc_final: 0.6374 (tp30) REVERT: A 400 HIS cc_start: 0.7392 (m90) cc_final: 0.7101 (m90) REVERT: A 414 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: A 532 ASN cc_start: 0.7583 (m-40) cc_final: 0.7249 (m-40) outliers start: 18 outliers final: 3 residues processed: 83 average time/residue: 0.4722 time to fit residues: 41.2627 Evaluate side-chains 73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 575 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.0040 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN A 435 GLN A 541 ASN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN A 663 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.199644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.183483 restraints weight = 5727.919| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.24 r_work: 0.3738 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6492 Z= 0.217 Angle : 0.680 7.038 8917 Z= 0.382 Chirality : 0.049 0.396 995 Planarity : 0.005 0.051 1020 Dihedral : 16.333 135.210 1114 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.82 % Favored : 93.89 % Rotamer: Outliers : 3.95 % Allowed : 11.84 % Favored : 84.21 % 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 are not related in a simple way. whole: -0.44 (0.30), residues: 687 helix: 0.67 (0.33), residues: 253 sheet: 0.84 (0.43), residues: 122 loop : -1.61 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.013 0.002 TYR A 20 PHE 0.019 0.002 PHE A 253 TRP 0.015 0.002 TRP A 43 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 ( 6492) covalent geometry : angle 0.68046 / 0.38 ( 8917) hydrogen bonds : bond 0.05561 / 3.38 ( 267) hydrogen bonds : angle 5.17487 / 3.48 ( 734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.186 Fit side-chains REVERT: A 11 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6898 (mtm180) REVERT: A 53 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.8107 (p90) REVERT: A 400 HIS cc_start: 0.7394 (m90) cc_final: 0.7140 (m90) REVERT: A 414 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: A 464 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6757 (mp) REVERT: A 532 ASN cc_start: 0.7664 (m-40) cc_final: 0.7426 (m-40) REVERT: A 575 GLN cc_start: 0.7214 (pp30) cc_final: 0.6769 (pp30) outliers start: 24 outliers final: 6 residues processed: 88 average time/residue: 0.5201 time to fit residues: 48.1398 Evaluate side-chains 73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 97 ASN A 435 GLN A 541 ASN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 575 GLN A 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.202959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.177141 restraints weight = 5747.701| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.65 r_work: 0.3728 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6492 Z= 0.135 Angle : 0.582 7.827 8917 Z= 0.336 Chirality : 0.045 0.391 995 Planarity : 0.004 0.045 1020 Dihedral : 16.205 132.907 1111 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.68 % Favored : 94.18 % Rotamer: Outliers : 3.12 % Allowed : 14.47 % Favored : 82.40 % 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 are not related in a simple way. whole: -0.07 (0.31), residues: 687 helix: 1.10 (0.33), residues: 247 sheet: 1.05 (0.43), residues: 122 loop : -1.48 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.017 0.001 TYR A 158 PHE 0.036 0.002 PHE A 351 TRP 0.009 0.001 TRP A 43 HIS 0.005 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 6492) covalent geometry : angle 0.58177 / 0.34 ( 8917) hydrogen bonds : bond 0.04242 / 2.61 ( 267) hydrogen bonds : angle 4.93799 / 3.32 ( 734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.223 Fit side-chains REVERT: A 67 MET cc_start: 0.6291 (tpp) cc_final: 0.5951 (tpt) REVERT: A 126 GLN cc_start: 0.7111 (tt0) cc_final: 0.6590 (tm-30) REVERT: A 414 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: A 464 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7148 (mp) REVERT: A 607 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5959 (mm-30) outliers start: 19 outliers final: 8 residues processed: 76 average time/residue: 0.4181 time to fit residues: 33.7461 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 607 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 0.0060 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 435 GLN A 510 GLN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.200773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.184989 restraints weight = 5839.810| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.24 r_work: 0.3757 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6492 Z= 0.175 Angle : 0.616 7.270 8917 Z= 0.352 Chirality : 0.046 0.394 995 Planarity : 0.004 0.047 1020 Dihedral : 16.237 133.272 1111 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 2.63 % Allowed : 17.11 % Favored : 80.26 % 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 are not related in a simple way. whole: -0.20 (0.31), residues: 687 helix: 0.98 (0.33), residues: 247 sheet: 0.94 (0.44), residues: 122 loop : -1.52 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.009 0.001 TYR A 690 PHE 0.020 0.002 PHE A 351 TRP 0.014 0.002 TRP A 43 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 6492) covalent geometry : angle 0.61575 / 0.35 ( 8917) hydrogen bonds : bond 0.04751 / 2.88 ( 267) hydrogen bonds : angle 5.03223 / 3.38 ( 734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.186 Fit side-chains REVERT: A 126 GLN cc_start: 0.7191 (tt0) cc_final: 0.6450 (tm-30) REVERT: A 155 GLU cc_start: 0.6414 (tp30) cc_final: 0.6072 (tt0) REVERT: A 464 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6680 (mp) REVERT: A 607 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6108 (mm-30) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 0.4242 time to fit residues: 33.3360 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 435 GLN A 510 GLN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.200387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178410 restraints weight = 5803.001| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.39 r_work: 0.3725 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6492 Z= 0.171 Angle : 0.615 7.328 8917 Z= 0.351 Chirality : 0.046 0.396 995 Planarity : 0.004 0.048 1020 Dihedral : 16.294 133.910 1111 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 3.45 % Allowed : 17.27 % Favored : 79.28 % 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 are not related in a simple way. whole: -0.32 (0.31), residues: 687 helix: 0.78 (0.33), residues: 254 sheet: 0.91 (0.44), residues: 122 loop : -1.56 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.009 0.001 TYR A 690 PHE 0.019 0.002 PHE A 148 TRP 0.018 0.002 TRP A 43 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 6492) covalent geometry : angle 0.61480 / 0.35 ( 8917) hydrogen bonds : bond 0.04661 / 2.85 ( 267) hydrogen bonds : angle 5.02346 / 3.38 ( 734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.132 Fit side-chains REVERT: A 111 ARG cc_start: 0.7936 (ptm160) cc_final: 0.7592 (mtp-110) REVERT: A 126 GLN cc_start: 0.7261 (tt0) cc_final: 0.6493 (tm-30) REVERT: A 155 GLU cc_start: 0.6505 (tp30) cc_final: 0.6125 (tt0) REVERT: A 464 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6778 (mp) REVERT: A 575 GLN cc_start: 0.7105 (pp30) cc_final: 0.6740 (pp30) REVERT: A 607 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6251 (mm-30) outliers start: 21 outliers final: 10 residues processed: 79 average time/residue: 0.4412 time to fit residues: 36.8649 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 435 GLN A 510 GLN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.202870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.177160 restraints weight = 5777.464| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.65 r_work: 0.3714 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6492 Z= 0.133 Angle : 0.566 7.521 8917 Z= 0.327 Chirality : 0.044 0.382 995 Planarity : 0.004 0.045 1020 Dihedral : 16.212 131.394 1111 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 2.63 % Allowed : 18.59 % Favored : 78.78 % 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 are not related in a simple way. whole: -0.13 (0.32), residues: 687 helix: 0.83 (0.33), residues: 260 sheet: 1.02 (0.44), residues: 122 loop : -1.40 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.009 0.001 TYR A 158 PHE 0.015 0.001 PHE A 351 TRP 0.017 0.001 TRP A 43 HIS 0.004 0.000 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 6492) covalent geometry : angle 0.56603 / 0.33 ( 8917) hydrogen bonds : bond 0.04048 / 2.48 ( 267) hydrogen bonds : angle 4.89240 / 3.29 ( 734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.224 Fit side-chains REVERT: A 111 ARG cc_start: 0.7686 (ptm160) cc_final: 0.7468 (mtp-110) REVERT: A 126 GLN cc_start: 0.7002 (tt0) cc_final: 0.6526 (tm-30) REVERT: A 464 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7104 (mp) outliers start: 16 outliers final: 9 residues processed: 72 average time/residue: 0.4637 time to fit residues: 35.3122 Evaluate side-chains 69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 69 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 510 GLN A 541 ASN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.203856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.187339 restraints weight = 5778.539| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.29 r_work: 0.3795 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6492 Z= 0.126 Angle : 0.558 7.534 8917 Z= 0.323 Chirality : 0.044 0.370 995 Planarity : 0.004 0.042 1020 Dihedral : 16.145 128.985 1111 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.68 % Favored : 94.18 % Rotamer: Outliers : 2.47 % Allowed : 18.75 % Favored : 78.78 % 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 are not related in a simple way. whole: -0.01 (0.32), residues: 687 helix: 0.92 (0.34), residues: 258 sheet: 1.23 (0.46), residues: 117 loop : -1.33 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.008 0.001 TYR A 617 PHE 0.013 0.001 PHE A 351 TRP 0.017 0.001 TRP A 43 HIS 0.004 0.000 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 ( 6492) covalent geometry : angle 0.55782 / 0.32 ( 8917) hydrogen bonds : bond 0.03907 / 2.40 ( 267) hydrogen bonds : angle 4.89641 / 3.29 ( 734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.152 Fit side-chains REVERT: A 111 ARG cc_start: 0.7829 (ptm160) cc_final: 0.7491 (mtp-110) REVERT: A 126 GLN cc_start: 0.7159 (tt0) cc_final: 0.6479 (tm-30) REVERT: A 155 GLU cc_start: 0.6703 (tt0) cc_final: 0.6341 (tp30) REVERT: A 464 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6767 (mp) REVERT: A 575 GLN cc_start: 0.7206 (pp30) cc_final: 0.6902 (pp30) outliers start: 15 outliers final: 8 residues processed: 76 average time/residue: 0.4262 time to fit residues: 34.3958 Evaluate side-chains 71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 376 GLN A 510 GLN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.202365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.175902 restraints weight = 5851.487| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.71 r_work: 0.3706 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6492 Z= 0.142 Angle : 0.580 7.619 8917 Z= 0.334 Chirality : 0.045 0.372 995 Planarity : 0.004 0.043 1020 Dihedral : 16.165 128.624 1111 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 2.96 % Allowed : 18.91 % Favored : 78.12 % 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 are not related in a simple way. whole: -0.09 (0.32), residues: 687 helix: 0.96 (0.34), residues: 255 sheet: 1.05 (0.45), residues: 122 loop : -1.43 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.010 0.001 TYR A 617 PHE 0.010 0.001 PHE A 351 TRP 0.021 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 6492) covalent geometry : angle 0.57957 / 0.33 ( 8917) hydrogen bonds : bond 0.04114 / 2.50 ( 267) hydrogen bonds : angle 4.91821 / 3.30 ( 734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.145 Fit side-chains REVERT: A 82 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7054 (mp) REVERT: A 111 ARG cc_start: 0.7660 (ptm160) cc_final: 0.7436 (mtp-110) REVERT: A 124 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.6079 (pp) REVERT: A 126 GLN cc_start: 0.7068 (tt0) cc_final: 0.6664 (tm-30) REVERT: A 133 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7042 (tt) REVERT: A 464 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7203 (mp) REVERT: A 575 GLN cc_start: 0.7114 (pp30) cc_final: 0.6770 (pp30) outliers start: 18 outliers final: 10 residues processed: 77 average time/residue: 0.4057 time to fit residues: 33.1131 Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 510 GLN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.202713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.177592 restraints weight = 5787.130| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.64 r_work: 0.3725 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6492 Z= 0.137 Angle : 0.578 8.347 8917 Z= 0.333 Chirality : 0.045 0.353 995 Planarity : 0.004 0.043 1020 Dihedral : 16.130 123.175 1111 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.32 % Rotamer: Outliers : 2.63 % Allowed : 19.41 % Favored : 77.96 % 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 are not related in a simple way. whole: -0.10 (0.32), residues: 687 helix: 0.99 (0.34), residues: 252 sheet: 0.99 (0.45), residues: 122 loop : -1.42 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.010 0.001 TYR A 493 PHE 0.011 0.001 PHE A 351 TRP 0.023 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 6492) covalent geometry : angle 0.57837 / 0.33 ( 8917) hydrogen bonds : bond 0.04026 / 2.47 ( 267) hydrogen bonds : angle 4.91016 / 3.29 ( 734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.236 Fit side-chains REVERT: A 82 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6996 (mp) REVERT: A 124 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5919 (pp) REVERT: A 126 GLN cc_start: 0.7195 (tt0) cc_final: 0.6559 (tm-30) REVERT: A 133 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7062 (tt) REVERT: A 155 GLU cc_start: 0.6312 (tp30) cc_final: 0.5978 (tt0) REVERT: A 464 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6874 (mp) REVERT: A 575 GLN cc_start: 0.7246 (pp30) cc_final: 0.6850 (pp30) outliers start: 16 outliers final: 9 residues processed: 72 average time/residue: 0.3815 time to fit residues: 29.2837 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.201833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.179066 restraints weight = 5793.260| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.52 r_work: 0.3739 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6492 Z= 0.146 Angle : 0.592 8.302 8917 Z= 0.338 Chirality : 0.045 0.346 995 Planarity : 0.004 0.043 1020 Dihedral : 16.149 122.022 1111 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 2.47 % Allowed : 20.07 % Favored : 77.47 % 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 are not related in a simple way. whole: -0.12 (0.32), residues: 687 helix: 0.99 (0.34), residues: 250 sheet: 0.94 (0.45), residues: 122 loop : -1.41 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.009 0.001 TYR A 20 PHE 0.010 0.001 PHE A 351 TRP 0.026 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 6492) covalent geometry : angle 0.59179 / 0.34 ( 8917) hydrogen bonds : bond 0.04164 / 2.54 ( 267) hydrogen bonds : angle 4.97975 / 3.34 ( 734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1855.95 seconds wall clock time: 32 minutes 13.44 seconds (1933.44 seconds total)