Starting phenix.real_space_refine on Thu Jul 2 02:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqs_60390/07_2026/8zqs_60390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqs_60390/07_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_60390/07_2026/8zqs_60390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqs_60390/07_2026/8zqs_60390.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqs_60390/07_2026/8zqs_60390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqs_60390/07_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-dev-6108/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: 1.56, per 1000 atoms: 0.25 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: 0.57 Conformation dependent library (CDL) restraints added in 344.3 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: 0.61 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: 1.09 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: 8591 1.43 - 2.86: 293 2.86 - 4.30: 38 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: 859 0.052 - 0.104: 124 0.104 - 0.155: 21 0.155 - 0.207: 4 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 0.17 2.00e-01 2.50e+01 7.45e-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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.500 Find NCS groups from input model: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.840 ------------------------------------------------------------------------------- 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= 0.245 Angle : 0.616 7.160 8937 Z= 0.438 Chirality : 0.041 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 0.00342 / 0.25 ( 6435) covalent geometry : angle 0.61606 / 0.44 ( 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 : 0.230 Fit side-chains revert: symmetry clash 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: 0.2858 (ptm160) outliers start: 10 outliers final: 0 residues processed: 154 average time/residue: 0.1239 time to fit residues: 23.0336 Evaluate side-chains 74 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 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: 5.9990 overall best weight: 2.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN A 414 ASN A 575 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 635 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.140199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.125195 restraints weight = 24042.232| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 4.59 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 6435 Z= 0.241 Angle : 0.825 15.546 8937 Z= 0.429 Chirality : 0.045 0.194 1010 Planarity : 0.009 0.145 942 Dihedral : 21.225 169.567 1528 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 5.31 % Allowed : 23.53 % 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: -0.22 (0.33), residues: 594 helix: 1.30 (0.31), residues: 247 sheet: -0.39 (0.43), residues: 129 loop : -1.68 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 885 TYR 0.030 0.004 TYR A 666 PHE 0.020 0.003 PHE A 794 TRP 0.017 0.002 TRP A 640 HIS 0.019 0.003 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 ( 6435) covalent geometry : angle 0.82548 / 0.43 ( 8937) hydrogen bonds : bond 0.05722 / 3.64 ( 299) hydrogen bonds : angle 4.68034 / 3.31 ( 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 117 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.139 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: 0.7064 (OUTLIER) cc_final: 0.6796 (mtt90) REVERT: A 204 VAL cc_start: 0.8243 (p) cc_final: 0.7985 (m) REVERT: A 350 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.5385 (ptt90) REVERT: A 580 ASP cc_start: 0.8058 (t0) cc_final: 0.7852 (t0) REVERT: A 604 PHE cc_start: 0.5874 (t80) cc_final: 0.5203 (t80) REVERT: A 643 TYR cc_start: 0.5806 (t80) cc_final: 0.4585 (t80) outliers start: 28 outliers final: 13 residues processed: 113 average time/residue: 0.1139 time to fit residues: 15.6761 Evaluate side-chains 80 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 199 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 424 ILE Chi-restraints excluded: chain A residue 566 LYS 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 749 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 HIS ** A 803 GLN ** 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 = 0.4562 r_free = 0.4562 target = 0.138787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.124108 restraints weight = 23583.579| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 4.32 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6435 Z= 0.165 Angle : 0.695 11.092 8937 Z= 0.358 Chirality : 0.041 0.221 1010 Planarity : 0.005 0.071 942 Dihedral : 21.226 174.099 1528 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 3.42 % Allowed : 25.43 % 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: 0.18 (0.33), residues: 594 helix: 1.76 (0.31), residues: 248 sheet: -0.43 (0.42), residues: 133 loop : -1.47 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 684 TYR 0.019 0.002 TYR A 608 PHE 0.016 0.002 PHE A 369 TRP 0.012 0.002 TRP A 878 HIS 0.011 0.002 HIS A 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6435) covalent geometry : angle 0.69538 / 0.36 ( 8937) hydrogen bonds : bond 0.04831 / 3.10 ( 299) hydrogen bonds : angle 4.34319 / 3.05 ( 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 91 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 PHE cc_start: 0.5791 (t80) cc_final: 0.5585 (t80) REVERT: A 643 TYR cc_start: 0.5503 (t80) cc_final: 0.4728 (t80) outliers start: 18 outliers final: 12 residues processed: 84 average time/residue: 0.1102 time to fit residues: 11.4576 Evaluate side-chains 76 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 424 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 TRP 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 869 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 747 HIS A 803 GLN A 822 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.138131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.124248 restraints weight = 25250.411| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 4.14 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6435 Z= 0.176 Angle : 0.668 9.269 8937 Z= 0.353 Chirality : 0.040 0.180 1010 Planarity : 0.005 0.076 942 Dihedral : 21.118 174.083 1528 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 3.98 % Allowed : 26.57 % 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: 0.36 (0.34), residues: 594 helix: 1.85 (0.31), residues: 249 sheet: -0.55 (0.42), residues: 131 loop : -1.14 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 397 TYR 0.024 0.003 TYR A 608 PHE 0.027 0.003 PHE A 369 TRP 0.012 0.002 TRP A 640 HIS 0.005 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 6435) covalent geometry : angle 0.66759 / 0.35 ( 8937) hydrogen bonds : bond 0.04952 / 3.21 ( 299) hydrogen bonds : angle 4.27523 / 2.95 ( 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 88 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8355 (p) cc_final: 0.8079 (m) REVERT: A 362 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7226 (mt) REVERT: A 597 TYR cc_start: 0.6451 (t80) cc_final: 0.5959 (t80) REVERT: A 643 TYR cc_start: 0.5809 (t80) cc_final: 0.4799 (t80) outliers start: 21 outliers final: 12 residues processed: 80 average time/residue: 0.1003 time to fit residues: 10.1595 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 362 LEU 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 586 VAL Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 629 LEU 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 Chi-restraints excluded: chain A residue 813 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 52 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** 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 = 0.4529 r_free = 0.4529 target = 0.135900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.121459 restraints weight = 24551.043| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 4.39 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.5587 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= 0.142 Angle : 0.628 8.325 8937 Z= 0.332 Chirality : 0.039 0.190 1010 Planarity : 0.005 0.073 942 Dihedral : 21.090 173.257 1528 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.28 % Allowed : 27.32 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.34), residues: 594 helix: 1.96 (0.31), residues: 249 sheet: -0.80 (0.41), residues: 138 loop : -1.06 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 430 TYR 0.018 0.002 TYR A 608 PHE 0.037 0.002 PHE A 369 TRP 0.009 0.001 TRP A 878 HIS 0.005 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 6435) covalent geometry : angle 0.62774 / 0.33 ( 8937) hydrogen bonds : bond 0.04476 / 2.95 ( 299) hydrogen bonds : angle 4.13640 / 2.90 ( 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 69 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8271 (p) cc_final: 0.8003 (m) REVERT: A 562 LEU cc_start: 0.9059 (tp) cc_final: 0.8816 (tt) REVERT: A 564 GLU cc_start: 0.8912 (pt0) cc_final: 0.8489 (pp20) REVERT: A 565 GLU cc_start: 0.8665 (pt0) cc_final: 0.8174 (pt0) REVERT: A 643 TYR cc_start: 0.5860 (t80) cc_final: 0.4706 (t80) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1061 time to fit residues: 8.8572 Evaluate side-chains 63 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 490 CYS 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 760 TYR Chi-restraints excluded: chain A residue 784 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.132318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.118059 restraints weight = 24667.471| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 4.32 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6435 Z= 0.200 Angle : 0.710 12.327 8937 Z= 0.370 Chirality : 0.049 0.861 1010 Planarity : 0.005 0.063 942 Dihedral : 21.184 173.433 1528 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 0.23 (0.34), residues: 594 helix: 1.68 (0.31), residues: 254 sheet: -0.60 (0.42), residues: 129 loop : -1.20 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 430 TYR 0.026 0.003 TYR A 608 PHE 0.038 0.003 PHE A 369 TRP 0.011 0.002 TRP A 878 HIS 0.006 0.002 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 ( 6435) covalent geometry : angle 0.71046 / 0.37 ( 8937) hydrogen bonds : bond 0.05281 / 3.51 ( 299) hydrogen bonds : angle 4.32294 / 3.01 ( 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 79 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.154 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: 0.8351 (p) cc_final: 0.8080 (m) REVERT: A 597 TYR cc_start: 0.6641 (t80) cc_final: 0.5889 (t80) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 0.1096 time to fit residues: 10.0484 Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 490 CYS Chi-restraints excluded: chain A residue 629 LEU 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 Chi-restraints excluded: chain A residue 900 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.134494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.120173 restraints weight = 24731.984| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 4.29 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6435 Z= 0.132 Angle : 0.665 14.749 8937 Z= 0.342 Chirality : 0.040 0.203 1010 Planarity : 0.005 0.071 942 Dihedral : 21.075 172.349 1528 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.28 % Allowed : 28.27 % 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: 0.38 (0.34), residues: 594 helix: 1.89 (0.31), residues: 252 sheet: -0.73 (0.42), residues: 133 loop : -1.07 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 561 TYR 0.016 0.002 TYR A 663 PHE 0.025 0.002 PHE A 485 TRP 0.010 0.001 TRP A 878 HIS 0.005 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 6435) covalent geometry : angle 0.66484 / 0.34 ( 8937) hydrogen bonds : bond 0.04424 / 2.99 ( 299) hydrogen bonds : angle 4.21138 / 2.99 ( 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 71 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8296 (p) cc_final: 0.8034 (m) REVERT: A 374 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7714 (mtmm) REVERT: A 516 LEU cc_start: 0.7256 (pt) cc_final: 0.6903 (pp) REVERT: A 529 MET cc_start: 0.8235 (mtt) cc_final: 0.7793 (mtt) REVERT: A 564 GLU cc_start: 0.9028 (pt0) cc_final: 0.8606 (pp20) REVERT: A 565 GLU cc_start: 0.8623 (pt0) cc_final: 0.8249 (pt0) REVERT: A 597 TYR cc_start: 0.6528 (t80) cc_final: 0.5762 (t80) REVERT: A 643 TYR cc_start: 0.5998 (t80) cc_final: 0.4745 (t80) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.1031 time to fit residues: 8.5831 Evaluate side-chains 67 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 405 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 869 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.134660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.120111 restraints weight = 24371.864| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 4.41 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.6505 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= 0.131 Angle : 0.651 13.833 8937 Z= 0.335 Chirality : 0.039 0.201 1010 Planarity : 0.004 0.046 942 Dihedral : 21.011 172.956 1528 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.42 % Allowed : 27.51 % 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: 0.36 (0.34), residues: 594 helix: 1.94 (0.31), residues: 253 sheet: -0.87 (0.40), residues: 140 loop : -1.09 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 561 TYR 0.018 0.002 TYR A 798 PHE 0.033 0.002 PHE A 485 TRP 0.009 0.001 TRP A 741 HIS 0.004 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 6435) covalent geometry : angle 0.65069 / 0.34 ( 8937) hydrogen bonds : bond 0.04218 / 2.86 ( 299) hydrogen bonds : angle 4.08452 / 2.90 ( 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 76 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7523 (mtmt) REVERT: A 564 GLU cc_start: 0.9000 (pt0) cc_final: 0.8603 (pp20) REVERT: A 565 GLU cc_start: 0.8576 (pt0) cc_final: 0.8278 (pt0) REVERT: A 597 TYR cc_start: 0.6539 (t80) cc_final: 0.5710 (t80) REVERT: A 606 LEU cc_start: 0.8064 (tt) cc_final: 0.7731 (mt) REVERT: A 643 TYR cc_start: 0.5955 (t80) cc_final: 0.4719 (t80) outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.0796 time to fit residues: 7.2893 Evaluate side-chains 70 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 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 604 PHE Chi-restraints excluded: chain A residue 629 LEU 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 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: 6.9990 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.134469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.119941 restraints weight = 24560.979| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 4.41 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6435 Z= 0.140 Angle : 0.666 11.803 8937 Z= 0.344 Chirality : 0.040 0.249 1010 Planarity : 0.004 0.060 942 Dihedral : 21.019 173.046 1528 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 28.27 % 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: 0.30 (0.34), residues: 594 helix: 1.89 (0.31), residues: 253 sheet: -0.84 (0.41), residues: 137 loop : -1.17 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 430 TYR 0.018 0.002 TYR A 798 PHE 0.033 0.002 PHE A 369 TRP 0.010 0.001 TRP A 741 HIS 0.003 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 6435) covalent geometry : angle 0.66633 / 0.34 ( 8937) hydrogen bonds : bond 0.04183 / 2.84 ( 299) hydrogen bonds : angle 4.08992 / 2.91 ( 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 70 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.226 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 201 VAL cc_start: 0.8050 (m) cc_final: 0.7841 (p) REVERT: A 359 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8331 (ptmm) REVERT: A 564 GLU cc_start: 0.8982 (pt0) cc_final: 0.8585 (pp20) REVERT: A 565 GLU cc_start: 0.8538 (pt0) cc_final: 0.8224 (pt0) REVERT: A 597 TYR cc_start: 0.6567 (t80) cc_final: 0.5770 (t80) REVERT: A 606 LEU cc_start: 0.8073 (tt) cc_final: 0.7742 (mt) REVERT: A 643 TYR cc_start: 0.5985 (t80) cc_final: 0.4666 (t80) outliers start: 11 outliers final: 11 residues processed: 68 average time/residue: 0.0927 time to fit residues: 8.1090 Evaluate side-chains 69 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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 604 PHE 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 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 60 optimal weight: 0.0070 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.9602 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.132072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.117351 restraints weight = 24605.589| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 4.45 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.7171 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= 0.193 Angle : 0.710 11.389 8937 Z= 0.373 Chirality : 0.041 0.195 1010 Planarity : 0.004 0.042 942 Dihedral : 21.187 173.081 1528 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.04 % Allowed : 28.08 % 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: 0.17 (0.34), residues: 594 helix: 1.72 (0.31), residues: 253 sheet: -0.75 (0.44), residues: 123 loop : -1.25 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 561 TYR 0.022 0.003 TYR A 608 PHE 0.033 0.003 PHE A 351 TRP 0.012 0.002 TRP A 741 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 6435) covalent geometry : angle 0.71033 / 0.37 ( 8937) hydrogen bonds : bond 0.04935 / 3.30 ( 299) hydrogen bonds : angle 4.32749 / 3.06 ( 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 73 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.137 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 564 GLU cc_start: 0.9009 (pt0) cc_final: 0.8592 (pp20) REVERT: A 565 GLU cc_start: 0.8588 (pt0) cc_final: 0.8225 (pt0) REVERT: A 571 PHE cc_start: 0.4294 (OUTLIER) cc_final: 0.2464 (t80) REVERT: A 597 TYR cc_start: 0.6797 (t80) cc_final: 0.6189 (t80) REVERT: A 606 LEU cc_start: 0.8055 (tt) cc_final: 0.7750 (mt) REVERT: A 716 LEU cc_start: 0.8054 (mt) cc_final: 0.6990 (mp) outliers start: 16 outliers final: 14 residues processed: 67 average time/residue: 0.0870 time to fit residues: 7.5936 Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 405 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 629 LEU 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 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: 0.6980 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.133847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.119364 restraints weight = 24118.023| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 4.37 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.7228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6435 Z= 0.129 Angle : 0.660 10.291 8937 Z= 0.342 Chirality : 0.039 0.196 1010 Planarity : 0.004 0.044 942 Dihedral : 21.102 172.292 1528 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.90 % Allowed : 29.79 % Favored : 68.31 % 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: 1.85 (0.31), residues: 253 sheet: -0.92 (0.42), residues: 132 loop : -1.12 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 561 TYR 0.019 0.002 TYR A 798 PHE 0.031 0.002 PHE A 351 TRP 0.012 0.001 TRP A 878 HIS 0.004 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 6435) covalent geometry : angle 0.65982 / 0.34 ( 8937) hydrogen bonds : bond 0.04156 / 2.83 ( 299) hydrogen bonds : angle 4.14343 / 2.95 ( 817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.05 seconds wall clock time: 22 minutes 14.55 seconds (1334.55 seconds total)