Starting phenix.real_space_refine on Tue Aug 4 18:49:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqs_60390/08_2026/8zqs_60390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqs_60390/08_2026/8zqs_60390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqs_60390/08_2026/8zqs_60390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqs_60390/08_2026/8zqs_60390.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqs_60390/08_2026/8zqs_60390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqs_60390/08_2026/8zqs_60390.cif" } resolution = 3.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 16 5.16 5 C 3692 2.51 5 N 1146 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s 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: 6199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4978 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 850 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna2p': 4, 'rna3p': 35} Chain: "C" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 145 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 1.59, per 1000 atoms: 0.26 Number of scatterers: 6199 At special positions: 0 Unit cell: (71.94, 96.36, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 58 15.00 O 1287 8.00 N 1146 7.00 C 3692 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: 0.59 Conformation dependent library (CDL) restraints added in 287.7 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 7 sheets defined 43.5% alpha, 20.4% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.540A pdb=" N ALA A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 552 removed outlier: 3.853A pdb=" N ALA A 540 " --> pdb=" O CYS A 536 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 578 through 606 removed outlier: 3.793A pdb=" N ARG A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.902A pdb=" N ASP A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 removed outlier: 3.750A pdb=" N LEU A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 689 Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.947A pdb=" N VAL A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Processing helix chain 'A' and resid 820 through 831 Processing helix chain 'A' and resid 881 through 899 Processing helix chain 'A' and resid 900 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 4.351A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 424 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 11 removed outlier: 4.218A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 517 removed outlier: 3.610A pdb=" N PHE A 485 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 697 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 479 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 694 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 501 removed outlier: 4.349A pdb=" N ILE A 499 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 511 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AA7, first strand: chain 'A' and resid 837 through 838 257 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1574 1.33 - 1.45: 1499 1.45 - 1.57: 3224 1.57 - 1.69: 113 1.69 - 1.81: 25 Bond restraints: 6435 Sorted by residual: bond pdb=" N ARG A 652 " pdb=" CA ARG A 652 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.58e+00 bond pdb=" N GLU A 651 " pdb=" CA GLU A 651 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.35e+00 bond pdb=" C3' DA C 4 " pdb=" C2' DA C 4 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.84e+00 bond pdb=" C3' DG C 7 " pdb=" C2' DG C 7 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.39e+00 bond pdb=" C3' DT D 5 " pdb=" O3' DT D 5 " ideal model delta sigma weight residual 1.435 1.409 0.026 1.30e-02 5.92e+03 4.08e+00 ... (remaining 6430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 8499 1.43 - 2.86: 384 2.86 - 4.30: 39 4.30 - 5.73: 11 5.73 - 7.16: 4 Bond angle restraints: 8937 Sorted by residual: angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N ARG A 27 " pdb=" CA ARG A 27 " pdb=" C ARG A 27 " ideal model delta sigma weight residual 111.33 106.16 5.17 1.21e+00 6.83e-01 1.83e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 8932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 3561 35.33 - 70.66: 324 70.66 - 106.00: 25 106.00 - 141.33: 1 141.33 - 176.66: 1 Dihedral angle restraints: 3912 sinusoidal: 2133 harmonic: 1779 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual 232.00 55.34 176.66 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A B -21 " pdb=" C1' A B -21 " pdb=" N9 A B -21 " pdb=" C4 A B -21 " ideal model delta sinusoidal sigma weight residual 70.00 -3.46 73.46 1 2.00e+01 2.50e-03 1.72e+01 dihedral pdb=" CA ASN A 482 " pdb=" C ASN A 482 " pdb=" N PRO A 483 " pdb=" CA PRO A 483 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 3909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 823 0.052 - 0.104: 128 0.104 - 0.155: 54 0.155 - 0.207: 3 0.207 - 0.259: 2 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C3' C B 3 " pdb=" C4' C B 3 " pdb=" O3' C B 3 " pdb=" C2' C B 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3' U B 2 " pdb=" C4' U B 2 " pdb=" O3' U B 2 " pdb=" C2' U B 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1' C B 0 " pdb=" O4' C B 0 " pdb=" C2' C B 0 " pdb=" N1 C B 0 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.89e-01 ... (remaining 1007 not shown) Planarity restraints: 942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B -6 " -0.022 2.00e-02 2.50e+03 1.12e-02 2.82e+00 pdb=" N1 C B -6 " 0.024 2.00e-02 2.50e+03 pdb=" C2 C B -6 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B -6 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C B -6 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C B -6 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C B -6 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C B -6 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C B -6 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B -7 " -0.019 2.00e-02 2.50e+03 9.06e-03 2.26e+00 pdb=" N9 A B -7 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A B -7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B -7 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B -7 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A B -7 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B -7 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B -7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A B -7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B -7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B -7 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 811 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ASP A 811 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP A 811 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY A 812 " 0.008 2.00e-02 2.50e+03 ... (remaining 939 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 958 2.76 - 3.29: 5564 3.29 - 3.83: 10896 3.83 - 4.36: 12602 4.36 - 4.90: 20510 Nonbonded interactions: 50530 Sorted by model distance: nonbonded pdb=" OD2 ASP A 658 " pdb=" O2' A B -14 " model vdw 2.224 3.040 nonbonded pdb=" NH2 ARG A 642 " pdb=" OE1 GLU A 659 " model vdw 2.273 3.120 nonbonded pdb=" OE1 GLU A 528 " pdb=" NH2 ARG A 599 " model vdw 2.277 3.120 nonbonded pdb=" O THR A 908 " pdb=" OG1 THR A 908 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR A 666 " pdb=" OP2 U B -32 " model vdw 2.343 3.040 ... (remaining 50525 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4509 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 : 0.003 0.034 6435 Z= 0.250 Angle : 0.665 7.160 8937 Z= 0.481 Chirality : 0.047 0.259 1010 Planarity : 0.003 0.029 942 Dihedral : 22.306 176.662 2760 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.88 % Favored : 94.78 % Rotamer: Outliers : 1.90 % Allowed : 26.94 % Favored : 71.16 % 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: -0.14 (0.34), residues: 594 helix: 1.48 (0.33), residues: 248 sheet: -0.23 (0.48), residues: 127 loop : -1.87 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 885 TYR 0.008 0.001 TYR A 846 PHE 0.010 0.001 PHE A 485 TRP 0.008 0.001 TRP A 645 HIS 0.003 0.001 HIS A 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.25 ( 6435) covalent geometry : angle 0.66498 / 0.48 ( 8937) hydrogen bonds : bond 0.14443 / 9.73 ( 299) hydrogen bonds : angle 5.43706 / 3.86 ( 817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 ARG cc_start: 0.3356 (ptt90) cc_final: 0.2860 (ptm160) outliers start: 10 outliers final: 0 residues processed: 154 average time/residue: 0.1172 time to fit residues: 21.6827 Evaluate side-chains 75 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 overall best weight: 0.9298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN A 462 ASN A 575 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 644 HIS ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN A 839 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.145422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.130678 restraints weight = 24788.649| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 4.66 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6435 Z= 0.162 Angle : 0.716 14.819 8937 Z= 0.370 Chirality : 0.041 0.192 1010 Planarity : 0.007 0.118 942 Dihedral : 20.964 173.439 1528 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 3.61 % Allowed : 23.72 % Favored : 72.68 % 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: 0.04 (0.34), residues: 594 helix: 1.58 (0.32), residues: 248 sheet: -0.43 (0.44), residues: 135 loop : -1.53 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 27 TYR 0.019 0.002 TYR A 542 PHE 0.017 0.002 PHE A 604 TRP 0.011 0.001 TRP A 878 HIS 0.013 0.002 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 6435) covalent geometry : angle 0.71608 / 0.37 ( 8937) hydrogen bonds : bond 0.04644 / 3.06 ( 299) hydrogen bonds : angle 4.43889 / 3.15 ( 817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.6234 (mtt90) REVERT: A 350 ARG cc_start: 0.6665 (mmm-85) cc_final: 0.5403 (ptt90) REVERT: A 643 TYR cc_start: 0.5612 (t80) cc_final: 0.4420 (t80) REVERT: A 746 ARG cc_start: 0.6153 (ttt180) cc_final: 0.5857 (ttt180) outliers start: 19 outliers final: 7 residues processed: 102 average time/residue: 0.1290 time to fit residues: 16.0190 Evaluate side-chains 71 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 869 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 414 ASN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN A 689 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.142678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.128893 restraints weight = 25696.956| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 4.23 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6435 Z= 0.174 Angle : 0.714 11.806 8937 Z= 0.368 Chirality : 0.041 0.193 1010 Planarity : 0.005 0.070 942 Dihedral : 20.986 175.725 1528 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 3.04 % Allowed : 23.72 % Favored : 73.24 % 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: 0.36 (0.33), residues: 594 helix: 1.79 (0.31), residues: 248 sheet: -0.04 (0.45), residues: 124 loop : -1.39 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 885 TYR 0.022 0.002 TYR A 542 PHE 0.019 0.002 PHE A 871 TRP 0.013 0.002 TRP A 640 HIS 0.010 0.002 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 6435) covalent geometry : angle 0.71410 / 0.37 ( 8937) hydrogen bonds : bond 0.04860 / 3.12 ( 299) hydrogen bonds : angle 4.20845 / 2.97 ( 817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8309 (p) cc_final: 0.8027 (m) REVERT: A 529 MET cc_start: 0.8235 (mtt) cc_final: 0.7761 (mtt) REVERT: A 643 TYR cc_start: 0.5485 (t80) cc_final: 0.4539 (t80) REVERT: A 746 ARG cc_start: 0.6707 (ttt180) cc_final: 0.6504 (ttt-90) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.1061 time to fit residues: 11.0826 Evaluate side-chains 72 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 869 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.136091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.121674 restraints weight = 24033.094| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 4.35 r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6435 Z= 0.205 Angle : 0.695 11.518 8937 Z= 0.367 Chirality : 0.042 0.299 1010 Planarity : 0.005 0.065 942 Dihedral : 21.240 174.019 1528 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 4.55 % Allowed : 25.62 % Favored : 69.83 % 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: 0.39 (0.33), residues: 594 helix: 1.82 (0.31), residues: 248 sheet: -0.35 (0.42), residues: 133 loop : -1.19 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 885 TYR 0.022 0.003 TYR A 608 PHE 0.030 0.003 PHE A 485 TRP 0.017 0.002 TRP A 640 HIS 0.008 0.002 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 ( 6435) covalent geometry : angle 0.69546 / 0.37 ( 8937) hydrogen bonds : bond 0.05344 / 3.44 ( 299) hydrogen bonds : angle 4.24523 / 2.97 ( 817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8284 (p) cc_final: 0.8030 (m) REVERT: A 564 GLU cc_start: 0.8797 (pt0) cc_final: 0.8453 (pp20) REVERT: A 597 TYR cc_start: 0.6454 (t80) cc_final: 0.5536 (t80) REVERT: A 643 TYR cc_start: 0.5741 (t80) cc_final: 0.4716 (t80) REVERT: A 644 HIS cc_start: 0.5164 (t-90) cc_final: 0.4781 (t-90) REVERT: A 746 ARG cc_start: 0.7119 (ttt180) cc_final: 0.6843 (ttt-90) outliers start: 24 outliers final: 13 residues processed: 83 average time/residue: 0.1347 time to fit residues: 13.5879 Evaluate side-chains 72 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 801 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS A 803 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.136455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.121967 restraints weight = 24568.138| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 4.44 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6435 Z= 0.150 Angle : 0.630 9.686 8937 Z= 0.333 Chirality : 0.039 0.229 1010 Planarity : 0.004 0.051 942 Dihedral : 21.110 173.100 1528 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.47 % Allowed : 26.38 % Favored : 71.16 % 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: 0.53 (0.34), residues: 594 helix: 2.04 (0.31), residues: 248 sheet: -0.48 (0.42), residues: 141 loop : -1.13 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.031 0.002 TYR A 798 PHE 0.032 0.002 PHE A 369 TRP 0.011 0.002 TRP A 878 HIS 0.006 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 6435) covalent geometry : angle 0.62973 / 0.33 ( 8937) hydrogen bonds : bond 0.04589 / 2.97 ( 299) hydrogen bonds : angle 4.05927 / 2.84 ( 817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8276 (p) cc_final: 0.8016 (m) REVERT: A 529 MET cc_start: 0.8217 (mtt) cc_final: 0.7772 (mtt) REVERT: A 564 GLU cc_start: 0.8792 (pt0) cc_final: 0.8450 (pp20) REVERT: A 597 TYR cc_start: 0.6405 (t80) cc_final: 0.5536 (t80) REVERT: A 643 TYR cc_start: 0.5683 (t80) cc_final: 0.4630 (t80) REVERT: A 644 HIS cc_start: 0.5078 (t-90) cc_final: 0.4686 (t-90) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 0.1113 time to fit residues: 10.1066 Evaluate side-chains 64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 869 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.132491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.117978 restraints weight = 25236.441| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 4.47 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6435 Z= 0.227 Angle : 0.720 9.697 8937 Z= 0.382 Chirality : 0.043 0.252 1010 Planarity : 0.005 0.049 942 Dihedral : 21.246 173.073 1528 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.04 % Allowed : 26.76 % Favored : 70.21 % 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: 0.16 (0.34), residues: 594 helix: 1.61 (0.31), residues: 252 sheet: -0.62 (0.43), residues: 132 loop : -1.22 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 430 TYR 0.018 0.003 TYR A 826 PHE 0.041 0.003 PHE A 485 TRP 0.013 0.002 TRP A 878 HIS 0.008 0.002 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 ( 6435) covalent geometry : angle 0.71974 / 0.38 ( 8937) hydrogen bonds : bond 0.05782 / 3.79 ( 299) hydrogen bonds : angle 4.44968 / 3.10 ( 817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8267 (p) cc_final: 0.8025 (m) REVERT: A 564 GLU cc_start: 0.8775 (pt0) cc_final: 0.8444 (pp20) REVERT: A 597 TYR cc_start: 0.6673 (t80) cc_final: 0.6119 (t80) REVERT: A 606 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7758 (mt) outliers start: 16 outliers final: 11 residues processed: 68 average time/residue: 0.1248 time to fit residues: 10.4796 Evaluate side-chains 67 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.133427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.119265 restraints weight = 25097.630| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 4.34 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6435 Z= 0.153 Angle : 0.636 9.151 8937 Z= 0.335 Chirality : 0.039 0.265 1010 Planarity : 0.004 0.051 942 Dihedral : 21.183 171.987 1528 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.23 % Allowed : 27.13 % Favored : 69.64 % 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: 0.48 (0.34), residues: 594 helix: 2.02 (0.31), residues: 252 sheet: -0.59 (0.43), residues: 130 loop : -1.15 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 430 TYR 0.013 0.002 TYR A 608 PHE 0.016 0.002 PHE A 485 TRP 0.012 0.002 TRP A 878 HIS 0.005 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6435) covalent geometry : angle 0.63593 / 0.34 ( 8937) hydrogen bonds : bond 0.04688 / 3.13 ( 299) hydrogen bonds : angle 4.21671 / 2.95 ( 817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8263 (p) cc_final: 0.8052 (m) REVERT: A 516 LEU cc_start: 0.7199 (pt) cc_final: 0.6875 (pp) REVERT: A 564 GLU cc_start: 0.8758 (pt0) cc_final: 0.8424 (pp20) REVERT: A 597 TYR cc_start: 0.6643 (t80) cc_final: 0.6081 (t80) REVERT: A 606 LEU cc_start: 0.8110 (tt) cc_final: 0.7725 (mt) REVERT: A 643 TYR cc_start: 0.5909 (t80) cc_final: 0.4687 (t80) REVERT: A 696 MET cc_start: 0.7583 (mmm) cc_final: 0.7283 (mmm) REVERT: A 746 ARG cc_start: 0.7152 (ttt-90) cc_final: 0.6890 (ttt-90) outliers start: 17 outliers final: 14 residues processed: 69 average time/residue: 0.0920 time to fit residues: 8.0453 Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 900 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.131836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.117263 restraints weight = 24626.979| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 4.47 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6435 Z= 0.191 Angle : 0.668 8.787 8937 Z= 0.357 Chirality : 0.040 0.262 1010 Planarity : 0.004 0.041 942 Dihedral : 21.248 172.690 1528 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.23 % Allowed : 27.32 % Favored : 69.45 % 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: 0.17 (0.34), residues: 594 helix: 1.71 (0.31), residues: 253 sheet: -0.78 (0.43), residues: 130 loop : -1.23 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 797 TYR 0.026 0.003 TYR A 542 PHE 0.018 0.002 PHE A 351 TRP 0.012 0.002 TRP A 878 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 6435) covalent geometry : angle 0.66814 / 0.36 ( 8937) hydrogen bonds : bond 0.05222 / 3.46 ( 299) hydrogen bonds : angle 4.34944 / 3.03 ( 817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 GLU cc_start: 0.8786 (pt0) cc_final: 0.8462 (pp20) REVERT: A 571 PHE cc_start: 0.4352 (OUTLIER) cc_final: 0.1887 (t80) REVERT: A 597 TYR cc_start: 0.6815 (t80) cc_final: 0.6402 (t80) REVERT: A 606 LEU cc_start: 0.8144 (tt) cc_final: 0.7771 (mt) REVERT: A 716 LEU cc_start: 0.8063 (mt) cc_final: 0.7013 (mp) REVERT: A 746 ARG cc_start: 0.7323 (ttt-90) cc_final: 0.7014 (ttt-90) outliers start: 17 outliers final: 14 residues processed: 68 average time/residue: 0.1028 time to fit residues: 8.7096 Evaluate side-chains 67 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.131777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.117321 restraints weight = 24888.008| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 4.42 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6435 Z= 0.174 Angle : 0.661 8.898 8937 Z= 0.348 Chirality : 0.039 0.200 1010 Planarity : 0.004 0.066 942 Dihedral : 21.264 172.333 1528 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.23 % Allowed : 28.27 % Favored : 68.50 % 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: 0.27 (0.34), residues: 594 helix: 1.86 (0.31), residues: 253 sheet: -0.76 (0.43), residues: 130 loop : -1.27 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 572 TYR 0.015 0.002 TYR A 608 PHE 0.016 0.002 PHE A 390 TRP 0.013 0.002 TRP A 878 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 6435) covalent geometry : angle 0.66072 / 0.35 ( 8937) hydrogen bonds : bond 0.04884 / 3.28 ( 299) hydrogen bonds : angle 4.31138 / 3.00 ( 817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7825 (p) REVERT: A 564 GLU cc_start: 0.8789 (pt0) cc_final: 0.8457 (pp20) REVERT: A 606 LEU cc_start: 0.8048 (tt) cc_final: 0.7695 (mt) REVERT: A 716 LEU cc_start: 0.8074 (mt) cc_final: 0.7020 (mp) REVERT: A 746 ARG cc_start: 0.7333 (ttt180) cc_final: 0.7033 (ttt180) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.1005 time to fit residues: 8.6919 Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.130315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.115790 restraints weight = 25067.704| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 4.45 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.7473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6435 Z= 0.214 Angle : 0.727 12.958 8937 Z= 0.385 Chirality : 0.043 0.324 1010 Planarity : 0.005 0.039 942 Dihedral : 21.370 172.670 1528 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.66 % Allowed : 28.27 % Favored : 69.07 % 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: -0.05 (0.34), residues: 594 helix: 1.56 (0.32), residues: 253 sheet: -0.96 (0.43), residues: 134 loop : -1.34 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 561 TYR 0.020 0.003 TYR A 538 PHE 0.035 0.003 PHE A 571 TRP 0.013 0.002 TRP A 878 HIS 0.007 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 ( 6435) covalent geometry : angle 0.72650 / 0.38 ( 8937) hydrogen bonds : bond 0.05469 / 3.64 ( 299) hydrogen bonds : angle 4.50524 / 3.14 ( 817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7830 (p) REVERT: A 564 GLU cc_start: 0.8785 (pt0) cc_final: 0.8428 (pp20) REVERT: A 606 LEU cc_start: 0.8090 (tt) cc_final: 0.7717 (mt) REVERT: A 716 LEU cc_start: 0.8139 (mt) cc_final: 0.7103 (mp) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.1156 time to fit residues: 9.2677 Evaluate side-chains 66 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.127328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.113229 restraints weight = 25003.991| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 4.15 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.8307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6435 Z= 0.260 Angle : 0.811 10.438 8937 Z= 0.431 Chirality : 0.045 0.246 1010 Planarity : 0.005 0.036 942 Dihedral : 21.607 172.090 1528 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.85 % Allowed : 28.27 % Favored : 68.88 % 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: -0.66 (0.33), residues: 594 helix: 1.02 (0.32), residues: 249 sheet: -1.21 (0.45), residues: 124 loop : -1.60 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 634 TYR 0.023 0.003 TYR A 597 PHE 0.029 0.003 PHE A 485 TRP 0.022 0.003 TRP A 878 HIS 0.008 0.002 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.26 ( 6435) covalent geometry : angle 0.81062 / 0.43 ( 8937) hydrogen bonds : bond 0.06348 / 4.26 ( 299) hydrogen bonds : angle 4.98842 / 3.48 ( 817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1308.01 seconds wall clock time: 23 minutes 13.90 seconds (1393.90 seconds total)