Starting phenix.real_space_refine on Thu Jul 2 23:36:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjx_38409/07_2026/8xjx_38409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjx_38409/07_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_38409/07_2026/8xjx_38409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjx_38409/07_2026/8xjx_38409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xjx_38409/07_2026/8xjx_38409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjx_38409/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 18 Ad-hoc single atom residues: {' MN': 1} Classifications: {'water': 18} Link IDs: {None: 17} Chain breaks: 1 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: 1.56, per 1000 atoms: 0.25 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 362.7 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: 0.61 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: 1.29 Time building geometry restraints manager: 0.77 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 3.060 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN A 801 " model vdw 1.797 3.060 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: 1.640 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- 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= 0.271 Angle : 0.638 8.585 8917 Z= 0.448 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 0.63805 / 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 : 0.226 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: 0.5825 time to fit residues: 68.2719 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 : 0.243 ------------------------------------------------------------------------------- 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: 0.0470 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: 0.7678 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.206270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.183109 restraints weight = 5800.206| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.49 r_work: 0.3794 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 6492 Z= 0.145 Angle : 0.583 7.348 8917 Z= 0.337 Chirality : 0.045 0.372 995 Planarity : 0.004 0.048 1020 Dihedral : 16.130 131.934 1117 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.49 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: -0.02 (0.31), residues: 687 helix: 0.99 (0.33), residues: 249 sheet: 1.34 (0.44), residues: 115 loop : -1.37 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.010 0.001 TYR A 158 PHE 0.016 0.002 PHE A 351 TRP 0.014 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6492) covalent geometry : angle 0.58300 / 0.34 ( 8917) hydrogen bonds : bond 0.04619 / 2.82 ( 267) hydrogen bonds : angle 5.09183 / 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 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.219 Fit side-chains REVERT: A 53 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7783 (p90) REVERT: A 122 GLN cc_start: 0.6157 (tt0) cc_final: 0.5897 (mt0) REVERT: A 123 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: A 126 GLN cc_start: 0.6888 (tt0) cc_final: 0.6570 (tm-30) REVERT: A 414 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: A 532 ASN cc_start: 0.7412 (m-40) cc_final: 0.7165 (m-40) outliers start: 18 outliers final: 3 residues processed: 85 average time/residue: 0.5092 time to fit residues: 45.6081 Evaluate side-chains 69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 GLN A 548 HIS A 663 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.204234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.183840 restraints weight = 5751.351| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.34 r_work: 0.3788 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6492 Z= 0.141 Angle : 0.568 6.868 8917 Z= 0.328 Chirality : 0.044 0.372 995 Planarity : 0.004 0.041 1020 Dihedral : 16.071 132.493 1114 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.09 % Favored : 94.76 % Rotamer: Outliers : 2.80 % Allowed : 13.32 % Favored : 83.88 % 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: 1.13 (0.33), residues: 249 sheet: 1.34 (0.44), residues: 115 loop : -1.36 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.012 0.001 TYR A 20 PHE 0.018 0.002 PHE A 319 TRP 0.012 0.001 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 6492) covalent geometry : angle 0.56837 / 0.33 ( 8917) hydrogen bonds : bond 0.04338 / 2.65 ( 267) hydrogen bonds : angle 4.90501 / 3.29 ( 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 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.219 Fit side-chains REVERT: A 11 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6846 (mtm180) REVERT: A 122 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5754 (mt0) REVERT: A 155 GLU cc_start: 0.6517 (tp30) cc_final: 0.6128 (tt0) REVERT: A 532 ASN cc_start: 0.7619 (m-40) cc_final: 0.7354 (m-40) outliers start: 17 outliers final: 3 residues processed: 78 average time/residue: 0.5334 time to fit residues: 43.8661 Evaluate side-chains 66 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 575 GLN 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: 6.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN A 435 GLN A 510 GLN A 541 ASN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 575 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.199799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.179337 restraints weight = 5723.408| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.32 r_work: 0.3734 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6492 Z= 0.205 Angle : 0.665 9.218 8917 Z= 0.374 Chirality : 0.048 0.368 995 Planarity : 0.005 0.049 1020 Dihedral : 16.193 121.411 1114 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 3.78 % Allowed : 13.49 % Favored : 82.73 % 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: -0.34 (0.31), residues: 687 helix: 0.80 (0.33), residues: 253 sheet: 0.92 (0.43), residues: 122 loop : -1.60 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 175 TYR 0.010 0.002 TYR A 690 PHE 0.016 0.002 PHE A 253 TRP 0.017 0.002 TRP A 43 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 6492) covalent geometry : angle 0.66465 / 0.37 ( 8917) hydrogen bonds : bond 0.05153 / 3.14 ( 267) hydrogen bonds : angle 5.07915 / 3.41 ( 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 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.211 Fit side-chains REVERT: A 126 GLN cc_start: 0.7257 (tt0) cc_final: 0.6527 (tm-30) REVERT: A 155 GLU cc_start: 0.6491 (tp30) cc_final: 0.6123 (tt0) REVERT: A 464 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6655 (mp) REVERT: A 532 ASN cc_start: 0.7719 (m-40) cc_final: 0.7463 (m-40) REVERT: A 575 GLN cc_start: 0.7227 (pp30) cc_final: 0.6803 (pp30) REVERT: A 607 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6098 (mm-30) outliers start: 23 outliers final: 10 residues processed: 85 average time/residue: 0.4864 time to fit residues: 43.7641 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 : 0.215 ------------------------------------------------------------------------------- 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 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 630 MET Chi-restraints excluded: chain A residue 685 ILE 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: 0.7980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 97 ASN A 435 GLN A 510 GLN A 541 ASN A 548 HIS A 556 ASN A 575 GLN A 675 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.202709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.175782 restraints weight = 5841.376| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.90 r_work: 0.3685 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6492 Z= 0.136 Angle : 0.581 8.193 8917 Z= 0.333 Chirality : 0.044 0.316 995 Planarity : 0.004 0.044 1020 Dihedral : 16.103 119.349 1111 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 2.96 % Allowed : 16.28 % Favored : 80.76 % 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: -0.11 (0.31), residues: 687 helix: 0.99 (0.33), residues: 255 sheet: 1.03 (0.44), residues: 122 loop : -1.48 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.011 0.001 TYR A 158 PHE 0.024 0.001 PHE A 351 TRP 0.012 0.001 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 6492) covalent geometry : angle 0.58057 / 0.33 ( 8917) hydrogen bonds : bond 0.04123 / 2.52 ( 267) hydrogen bonds : angle 4.91965 / 3.31 ( 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 78 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.234 Fit side-chains REVERT: A 126 GLN cc_start: 0.7069 (tt0) cc_final: 0.6509 (tm-30) REVERT: A 464 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6962 (mp) REVERT: A 532 ASN cc_start: 0.7629 (m-40) cc_final: 0.7422 (m-40) REVERT: A 607 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6063 (mm-30) outliers start: 18 outliers final: 8 residues processed: 72 average time/residue: 0.4755 time to fit residues: 36.3433 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 : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 148 PHE 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 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 GLN 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: 4.9990 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 510 GLN A 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.199534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.173024 restraints weight = 5790.200| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.88 r_work: 0.3637 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6492 Z= 0.201 Angle : 0.650 8.115 8917 Z= 0.367 Chirality : 0.047 0.335 995 Planarity : 0.005 0.049 1020 Dihedral : 16.197 121.909 1111 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 3.95 % Allowed : 16.12 % Favored : 79.93 % 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: -0.28 (0.31), residues: 687 helix: 0.93 (0.33), residues: 246 sheet: 0.87 (0.44), residues: 122 loop : -1.56 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.010 0.002 TYR A 440 PHE 0.033 0.002 PHE A 351 TRP 0.019 0.002 TRP A 43 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 6492) covalent geometry : angle 0.65037 / 0.37 ( 8917) hydrogen bonds : bond 0.04987 / 3.01 ( 267) hydrogen bonds : angle 5.03684 / 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 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.187 Fit side-chains REVERT: A 111 ARG cc_start: 0.7757 (ptm160) cc_final: 0.7501 (mtp-110) REVERT: A 126 GLN cc_start: 0.7125 (tt0) cc_final: 0.6502 (tm-30) REVERT: A 464 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7008 (mp) REVERT: A 532 ASN cc_start: 0.7654 (m-40) cc_final: 0.7438 (m-40) REVERT: A 607 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6117 (mm-30) outliers start: 24 outliers final: 10 residues processed: 82 average time/residue: 0.4389 time to fit residues: 38.2433 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 : 0.235 ------------------------------------------------------------------------------- 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 148 PHE 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 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: 0.9980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.200355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.174355 restraints weight = 5749.808| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.64 r_work: 0.3686 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6492 Z= 0.168 Angle : 0.616 8.400 8917 Z= 0.350 Chirality : 0.045 0.330 995 Planarity : 0.004 0.049 1020 Dihedral : 16.204 121.823 1111 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 3.29 % Allowed : 17.76 % Favored : 78.95 % 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: -0.30 (0.31), residues: 687 helix: 0.82 (0.33), residues: 253 sheet: 0.91 (0.44), residues: 122 loop : -1.55 (0.32), residues: 312 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 0.020 0.002 PHE A 351 TRP 0.020 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 6492) covalent geometry : angle 0.61625 / 0.35 ( 8917) hydrogen bonds : bond 0.04560 / 2.77 ( 267) hydrogen bonds : angle 4.98407 / 3.35 ( 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 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.166 Fit side-chains REVERT: A 111 ARG cc_start: 0.7723 (ptm160) cc_final: 0.7495 (mtp-110) REVERT: A 126 GLN cc_start: 0.7056 (tt0) cc_final: 0.6556 (tm-30) REVERT: A 464 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7065 (mp) REVERT: A 575 GLN cc_start: 0.7006 (pp30) cc_final: 0.6690 (pp30) outliers start: 20 outliers final: 10 residues processed: 74 average time/residue: 0.4846 time to fit residues: 37.9163 Evaluate side-chains 69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 148 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.200388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.179281 restraints weight = 5756.565| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.39 r_work: 0.3731 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2487 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= 0.164 Angle : 0.618 9.347 8917 Z= 0.351 Chirality : 0.045 0.323 995 Planarity : 0.004 0.048 1020 Dihedral : 16.196 120.943 1111 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.45 % Rotamer: Outliers : 3.45 % Allowed : 18.59 % 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: -0.29 (0.31), residues: 687 helix: 0.82 (0.33), residues: 255 sheet: 0.89 (0.44), residues: 122 loop : -1.54 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.008 0.001 TYR A 440 PHE 0.016 0.002 PHE A 351 TRP 0.023 0.002 TRP A 43 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 6492) covalent geometry : angle 0.61827 / 0.35 ( 8917) hydrogen bonds : bond 0.04507 / 2.74 ( 267) hydrogen bonds : angle 4.96415 / 3.33 ( 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 78 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.159 Fit side-chains REVERT: A 82 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7101 (mp) REVERT: A 126 GLN cc_start: 0.7058 (tt0) cc_final: 0.6594 (tm-30) REVERT: A 133 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7009 (tt) REVERT: A 464 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7151 (mp) REVERT: A 575 GLN cc_start: 0.6992 (pp30) cc_final: 0.6761 (pp30) REVERT: A 607 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5958 (mm-30) outliers start: 21 outliers final: 11 residues processed: 73 average time/residue: 0.4745 time to fit residues: 36.6238 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 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 607 GLU 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: 4.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.200927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.184403 restraints weight = 5836.648| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.25 r_work: 0.3754 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6492 Z= 0.154 Angle : 0.615 9.977 8917 Z= 0.349 Chirality : 0.045 0.313 995 Planarity : 0.004 0.060 1020 Dihedral : 16.188 119.332 1111 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 2.80 % Allowed : 18.91 % Favored : 78.29 % 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: -0.24 (0.31), residues: 687 helix: 0.84 (0.33), residues: 255 sheet: 0.91 (0.45), residues: 122 loop : -1.49 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 111 TYR 0.009 0.001 TYR A 617 PHE 0.014 0.002 PHE A 351 TRP 0.024 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6492) covalent geometry : angle 0.61464 / 0.35 ( 8917) hydrogen bonds : bond 0.04380 / 2.66 ( 267) hydrogen bonds : angle 4.93935 / 3.31 ( 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 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.207 Fit side-chains REVERT: A 82 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7009 (mp) REVERT: A 124 ILE cc_start: 0.6322 (OUTLIER) cc_final: 0.6069 (pp) REVERT: A 126 GLN cc_start: 0.7275 (tt0) cc_final: 0.6533 (tm-30) REVERT: A 133 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7028 (tt) REVERT: A 155 GLU cc_start: 0.6783 (tt0) cc_final: 0.6362 (tp30) REVERT: A 464 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6615 (mp) REVERT: A 575 GLN cc_start: 0.7078 (pp30) cc_final: 0.6750 (pp30) outliers start: 17 outliers final: 9 residues processed: 73 average time/residue: 0.4453 time to fit residues: 34.5940 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 68 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.200855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.184267 restraints weight = 5769.824| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 1.24 r_work: 0.3759 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2602 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= 0.152 Angle : 0.608 9.939 8917 Z= 0.345 Chirality : 0.045 0.306 995 Planarity : 0.004 0.062 1020 Dihedral : 16.173 117.775 1111 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 2.47 % Allowed : 19.08 % Favored : 78.45 % 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: 0.89 (0.34), residues: 252 sheet: 1.10 (0.46), residues: 108 loop : -1.48 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 111 TYR 0.008 0.001 TYR A 440 PHE 0.013 0.002 PHE A 351 TRP 0.029 0.002 TRP A 43 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 6492) covalent geometry : angle 0.60827 / 0.34 ( 8917) hydrogen bonds : bond 0.04356 / 2.65 ( 267) hydrogen bonds : angle 4.91691 / 3.30 ( 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 73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.219 Fit side-chains REVERT: A 82 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7103 (mp) REVERT: A 124 ILE cc_start: 0.6419 (OUTLIER) cc_final: 0.6094 (pp) REVERT: A 126 GLN cc_start: 0.7050 (tt0) cc_final: 0.6653 (tm-30) REVERT: A 133 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.6999 (tt) REVERT: A 464 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7193 (mp) REVERT: A 575 GLN cc_start: 0.6935 (pp30) cc_final: 0.6714 (pp30) outliers start: 15 outliers final: 9 residues processed: 69 average time/residue: 0.4620 time to fit residues: 33.9470 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.200529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.176203 restraints weight = 5766.832| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.59 r_work: 0.3707 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6492 Z= 0.161 Angle : 0.623 10.061 8917 Z= 0.351 Chirality : 0.045 0.308 995 Planarity : 0.004 0.056 1020 Dihedral : 16.208 117.281 1111 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.45 % Rotamer: Outliers : 2.96 % Allowed : 18.75 % Favored : 78.29 % 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: -0.28 (0.31), residues: 687 helix: 0.85 (0.33), residues: 252 sheet: 1.08 (0.46), residues: 108 loop : -1.51 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 111 TYR 0.010 0.001 TYR A 617 PHE 0.012 0.002 PHE A 351 TRP 0.034 0.002 TRP A 43 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 6492) covalent geometry : angle 0.62293 / 0.35 ( 8917) hydrogen bonds : bond 0.04493 / 2.73 ( 267) hydrogen bonds : angle 4.93786 / 3.31 ( 734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.45 seconds wall clock time: 34 minutes 35.12 seconds (2075.12 seconds total)