Starting phenix.real_space_refine on Wed Sep 17 06:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqs_60390/09_2025/8zqs_60390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqs_60390/09_2025/8zqs_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_60390/09_2025/8zqs_60390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqs_60390/09_2025/8zqs_60390.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqs_60390/09_2025/8zqs_60390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqs_60390/09_2025/8zqs_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-2.0-5805/lib/python3.9/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: 1.47, per 1000 atoms: 0.24 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 295.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.77 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: 1.24 Time building geometry restraints manager: 0.81 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=" CA PRO A 203 " pdb=" C PRO A 203 " ideal model delta sigma weight residual 1.522 1.542 -0.021 1.19e-02 7.06e+03 3.01e+00 bond pdb=" N VAL A 204 " pdb=" CA VAL A 204 " ideal model delta sigma weight residual 1.454 1.475 -0.021 1.50e-02 4.44e+03 2.05e+00 bond pdb=" O5' C B 3 " pdb=" C5' C B 3 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.74e+00 ... (remaining 6430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 8637 1.43 - 2.86: 246 2.86 - 4.30: 39 4.30 - 5.73: 11 5.73 - 7.16: 4 Bond angle restraints: 8937 Sorted by residual: 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=" C PHE A 202 " pdb=" N PRO A 203 " pdb=" CA PRO A 203 " ideal model delta sigma weight residual 119.83 115.68 4.15 1.08e+00 8.57e-01 1.48e+01 angle pdb=" N TYR A 4 " pdb=" CA TYR A 4 " pdb=" C TYR A 4 " ideal model delta sigma weight residual 109.72 115.70 -5.98 1.60e+00 3.91e-01 1.40e+01 angle pdb=" N HIS A 26 " pdb=" CA HIS A 26 " pdb=" C HIS A 26 " ideal model delta sigma weight residual 112.45 107.32 5.13 1.39e+00 5.18e-01 1.36e+01 angle pdb=" C4' U B 2 " pdb=" C3' U B 2 " pdb=" O3' U B 2 " ideal model delta sigma weight residual 113.00 107.53 5.47 1.50e+00 4.44e-01 1.33e+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: 880 0.052 - 0.104: 105 0.104 - 0.155: 19 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: 4.230 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4562 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= 0.170 Angle : 0.593 7.160 8937 Z= 0.345 Chirality : 0.040 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 aren 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 covalent geometry : bond 0.00310 ( 6435) covalent geometry : angle 0.59311 ( 8937) hydrogen bonds : bond 0.14443 ( 299) hydrogen bonds : angle 5.43706 ( 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 : 0.207 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: 0.1397 time to fit residues: 25.6060 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 : 0.248 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 414 ASN A 462 ASN A 575 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 635 ASN A 689 HIS ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.138533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.123540 restraints weight = 24053.699| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 4.55 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.3888 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= 0.238 Angle : 0.760 13.174 8937 Z= 0.390 Chirality : 0.042 0.196 1010 Planarity : 0.005 0.053 942 Dihedral : 21.144 171.186 1528 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 3.98 % Allowed : 25.24 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.34), residues: 594 helix: 1.71 (0.32), residues: 248 sheet: -0.21 (0.45), residues: 124 loop : -1.67 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 607 TYR 0.022 0.003 TYR A 666 PHE 0.016 0.003 PHE A 390 TRP 0.020 0.002 TRP A 640 HIS 0.007 0.002 HIS A 644 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 6435) covalent geometry : angle 0.75975 ( 8937) hydrogen bonds : bond 0.05533 ( 299) hydrogen bonds : angle 4.51181 ( 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: 21 poor density : 85 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 TYR cc_start: 0.5830 (t80) cc_final: 0.4646 (t80) outliers start: 21 outliers final: 10 residues processed: 102 average time/residue: 0.1439 time to fit residues: 17.5174 Evaluate side-chains 72 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 586 VAL 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 784 VAL Chi-restraints excluded: chain A residue 892 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.139716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.125033 restraints weight = 23699.316| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 4.48 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6435 Z= 0.135 Angle : 0.653 8.912 8937 Z= 0.333 Chirality : 0.038 0.178 1010 Planarity : 0.004 0.051 942 Dihedral : 20.912 172.804 1528 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 1.71 % Allowed : 26.38 % Favored : 71.92 % 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 aren not related in a simple way. whole: 0.55 (0.34), residues: 594 helix: 2.09 (0.31), residues: 248 sheet: -0.15 (0.43), residues: 128 loop : -1.37 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 684 TYR 0.018 0.002 TYR A 608 PHE 0.015 0.002 PHE A 436 TRP 0.010 0.001 TRP A 640 HIS 0.006 0.001 HIS A 884 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6435) covalent geometry : angle 0.65280 ( 8937) hydrogen bonds : bond 0.04182 ( 299) hydrogen bonds : angle 4.03930 ( 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 80 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8261 (p) cc_final: 0.7976 (m) REVERT: A 219 MET cc_start: 0.3233 (OUTLIER) cc_final: 0.2795 (ttt) REVERT: A 564 GLU cc_start: 0.8927 (pt0) cc_final: 0.8512 (pp20) REVERT: A 565 GLU cc_start: 0.8663 (pt0) cc_final: 0.8352 (pt0) REVERT: A 643 TYR cc_start: 0.5700 (t80) cc_final: 0.4534 (t80) outliers start: 9 outliers final: 4 residues processed: 77 average time/residue: 0.1344 time to fit residues: 12.4928 Evaluate side-chains 62 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 645 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.135906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.121368 restraints weight = 24115.938| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 4.35 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6435 Z= 0.152 Angle : 0.639 8.326 8937 Z= 0.333 Chirality : 0.039 0.200 1010 Planarity : 0.005 0.063 942 Dihedral : 20.929 172.435 1528 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 3.23 % Allowed : 24.86 % Favored : 71.92 % 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 aren not related in a simple way. whole: 0.70 (0.34), residues: 594 helix: 2.28 (0.31), residues: 252 sheet: -0.44 (0.41), residues: 142 loop : -1.23 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 607 TYR 0.023 0.002 TYR A 608 PHE 0.029 0.003 PHE A 604 TRP 0.012 0.002 TRP A 640 HIS 0.005 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6435) covalent geometry : angle 0.63892 ( 8937) hydrogen bonds : bond 0.04354 ( 299) hydrogen bonds : angle 4.00471 ( 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 76 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8287 (p) cc_final: 0.8049 (m) REVERT: A 362 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7314 (mt) REVERT: A 564 GLU cc_start: 0.8875 (pt0) cc_final: 0.8482 (pp20) REVERT: A 565 GLU cc_start: 0.8563 (pt0) cc_final: 0.8283 (pt0) REVERT: A 643 TYR cc_start: 0.5812 (t80) cc_final: 0.4561 (t80) outliers start: 17 outliers final: 8 residues processed: 73 average time/residue: 0.1331 time to fit residues: 11.7224 Evaluate side-chains 66 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 362 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 725 VAL 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: 10.0000 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.136821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.122369 restraints weight = 24560.060| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 4.45 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6435 Z= 0.125 Angle : 0.609 7.521 8937 Z= 0.313 Chirality : 0.037 0.201 1010 Planarity : 0.004 0.046 942 Dihedral : 20.866 171.772 1528 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % Rotamer: Outliers : 2.47 % Allowed : 26.57 % Favored : 70.97 % 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 aren not related in a simple way. whole: 0.72 (0.34), residues: 594 helix: 2.40 (0.31), residues: 252 sheet: -0.60 (0.40), residues: 141 loop : -1.20 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 397 TYR 0.019 0.001 TYR A 608 PHE 0.034 0.002 PHE A 369 TRP 0.008 0.001 TRP A 878 HIS 0.003 0.001 HIS A 884 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6435) covalent geometry : angle 0.60910 ( 8937) hydrogen bonds : bond 0.03804 ( 299) hydrogen bonds : angle 4.00399 ( 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 74 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8249 (p) cc_final: 0.8029 (m) REVERT: A 516 LEU cc_start: 0.7120 (pt) cc_final: 0.6730 (pp) REVERT: A 564 GLU cc_start: 0.8889 (pt0) cc_final: 0.8493 (pp20) REVERT: A 565 GLU cc_start: 0.8658 (pt0) cc_final: 0.8318 (pt0) REVERT: A 597 TYR cc_start: 0.6402 (t80) cc_final: 0.5570 (t80) REVERT: A 643 TYR cc_start: 0.5795 (t80) cc_final: 0.4503 (t80) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.1097 time to fit residues: 9.9798 Evaluate side-chains 61 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET 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 645 TRP Chi-restraints excluded: chain A residue 801 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.133743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.119302 restraints weight = 24945.969| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 4.41 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6435 Z= 0.189 Angle : 0.661 9.109 8937 Z= 0.345 Chirality : 0.038 0.190 1010 Planarity : 0.005 0.045 942 Dihedral : 21.050 172.380 1528 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.85 % Allowed : 27.13 % Favored : 70.02 % 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 aren not related in a simple way. whole: 0.59 (0.34), residues: 594 helix: 2.14 (0.31), residues: 252 sheet: -0.43 (0.43), residues: 129 loop : -1.22 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 561 TYR 0.021 0.002 TYR A 608 PHE 0.040 0.003 PHE A 485 TRP 0.009 0.002 TRP A 878 HIS 0.004 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6435) covalent geometry : angle 0.66130 ( 8937) hydrogen bonds : bond 0.04528 ( 299) hydrogen bonds : angle 4.20704 ( 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 75 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.221 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: 0.8318 (p) cc_final: 0.8114 (m) REVERT: A 219 MET cc_start: 0.3500 (OUTLIER) cc_final: 0.2992 (ttt) REVERT: A 564 GLU cc_start: 0.8912 (pt0) cc_final: 0.8510 (pp20) REVERT: A 565 GLU cc_start: 0.8653 (pt0) cc_final: 0.8384 (pt0) REVERT: A 597 TYR cc_start: 0.6652 (t80) cc_final: 0.6171 (t80) REVERT: A 746 ARG cc_start: 0.7196 (ttt180) cc_final: 0.6926 (ttt180) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.1277 time to fit residues: 11.1515 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 : 0.234 ------------------------------------------------------------------------------- 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 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 490 CYS 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 801 LEU 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: 4.9990 chunk 22 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN A 609 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.135480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.121127 restraints weight = 24532.885| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 4.39 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.6772 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= 0.129 Angle : 0.622 8.069 8937 Z= 0.317 Chirality : 0.037 0.191 1010 Planarity : 0.004 0.046 942 Dihedral : 20.942 171.199 1528 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.47 % Allowed : 27.89 % 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 aren not related in a simple way. whole: 0.75 (0.34), residues: 594 helix: 2.32 (0.30), residues: 252 sheet: -0.56 (0.40), residues: 142 loop : -1.06 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 561 TYR 0.013 0.001 TYR A 608 PHE 0.019 0.002 PHE A 369 TRP 0.010 0.001 TRP A 878 HIS 0.004 0.001 HIS A 884 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6435) covalent geometry : angle 0.62241 ( 8937) hydrogen bonds : bond 0.03810 ( 299) hydrogen bonds : angle 3.96746 ( 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: 13 poor density : 60 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 LEU cc_start: 0.7068 (pt) cc_final: 0.6760 (pp) REVERT: A 564 GLU cc_start: 0.8907 (pt0) cc_final: 0.8499 (pp20) REVERT: A 565 GLU cc_start: 0.8725 (pt0) cc_final: 0.8446 (pt0) REVERT: A 571 PHE cc_start: 0.3878 (OUTLIER) cc_final: 0.1568 (t80) REVERT: A 597 TYR cc_start: 0.6498 (t80) cc_final: 0.5921 (t80) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.1138 time to fit residues: 9.7927 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 : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU 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 571 PHE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 784 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS A 889 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.131882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.117162 restraints weight = 24735.151| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 4.42 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6435 Z= 0.207 Angle : 0.706 12.364 8937 Z= 0.364 Chirality : 0.039 0.190 1010 Planarity : 0.005 0.056 942 Dihedral : 21.153 172.321 1528 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.61 % Allowed : 28.27 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.34), residues: 594 helix: 2.03 (0.31), residues: 253 sheet: -0.66 (0.43), residues: 133 loop : -1.15 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 572 TYR 0.023 0.002 TYR A 608 PHE 0.018 0.002 PHE A 351 TRP 0.019 0.002 TRP A 741 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 6435) covalent geometry : angle 0.70584 ( 8937) hydrogen bonds : bond 0.04813 ( 299) hydrogen bonds : angle 4.33262 ( 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 75 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 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: A 516 LEU cc_start: 0.6927 (pt) cc_final: 0.6613 (pp) REVERT: A 564 GLU cc_start: 0.8928 (pt0) cc_final: 0.8510 (pp20) REVERT: A 565 GLU cc_start: 0.8764 (pt0) cc_final: 0.8510 (pt0) REVERT: A 583 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.4914 (ttt90) REVERT: A 716 LEU cc_start: 0.8094 (mt) cc_final: 0.7063 (mp) outliers start: 19 outliers final: 12 residues processed: 68 average time/residue: 0.1212 time to fit residues: 10.0814 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 : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU 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 583 ARG Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 697 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 0.0040 chunk 18 optimal weight: 0.0060 chunk 23 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 overall best weight: 0.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.136254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.121967 restraints weight = 24900.409| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 4.30 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6435 Z= 0.122 Angle : 0.644 9.612 8937 Z= 0.325 Chirality : 0.037 0.186 1010 Planarity : 0.004 0.043 942 Dihedral : 20.919 171.508 1528 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.14 % Allowed : 30.17 % Favored : 68.69 % 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 aren not related in a simple way. whole: 0.66 (0.34), residues: 594 helix: 2.20 (0.30), residues: 253 sheet: -0.58 (0.42), residues: 135 loop : -1.05 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 561 TYR 0.012 0.001 TYR A 608 PHE 0.028 0.002 PHE A 369 TRP 0.014 0.001 TRP A 741 HIS 0.005 0.001 HIS A 884 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6435) covalent geometry : angle 0.64441 ( 8937) hydrogen bonds : bond 0.03770 ( 299) hydrogen bonds : angle 4.06816 ( 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: 6 poor density : 64 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 VAL cc_start: 0.8038 (m) cc_final: 0.7634 (p) REVERT: A 516 LEU cc_start: 0.7044 (pt) cc_final: 0.6780 (pp) REVERT: A 564 GLU cc_start: 0.8953 (pt0) cc_final: 0.8519 (pp20) REVERT: A 565 GLU cc_start: 0.8739 (pt0) cc_final: 0.8396 (pt0) REVERT: A 597 TYR cc_start: 0.6586 (t80) cc_final: 0.6031 (t80) REVERT: A 746 ARG cc_start: 0.6822 (ttt180) cc_final: 0.6613 (ttt-90) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.1188 time to fit residues: 10.3935 Evaluate side-chains 64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 801 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.131083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.117091 restraints weight = 24989.020| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 4.17 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6435 Z= 0.203 Angle : 0.712 9.820 8937 Z= 0.368 Chirality : 0.040 0.189 1010 Planarity : 0.005 0.049 942 Dihedral : 21.106 173.093 1528 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.71 % Allowed : 30.36 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.35), residues: 594 helix: 2.07 (0.31), residues: 253 sheet: -0.64 (0.46), residues: 126 loop : -1.13 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 799 TYR 0.022 0.002 TYR A 608 PHE 0.031 0.003 PHE A 369 TRP 0.033 0.002 TRP A 741 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 6435) covalent geometry : angle 0.71244 ( 8937) hydrogen bonds : bond 0.04671 ( 299) hydrogen bonds : angle 4.39446 ( 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 65 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 LEU cc_start: 0.7079 (pt) cc_final: 0.6800 (pp) REVERT: A 564 GLU cc_start: 0.8906 (pt0) cc_final: 0.8478 (pp20) REVERT: A 565 GLU cc_start: 0.8745 (pt0) cc_final: 0.8514 (pt0) REVERT: A 716 LEU cc_start: 0.8092 (mt) cc_final: 0.7045 (mp) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.1082 time to fit residues: 8.3220 Evaluate side-chains 62 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 586 VAL Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 813 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.132528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.118305 restraints weight = 24650.871| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 4.26 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6435 Z= 0.149 Angle : 0.659 9.282 8937 Z= 0.337 Chirality : 0.038 0.191 1010 Planarity : 0.004 0.043 942 Dihedral : 21.071 172.115 1528 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.14 % Allowed : 30.55 % 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 aren not related in a simple way. whole: 0.50 (0.35), residues: 594 helix: 2.12 (0.31), residues: 253 sheet: -0.70 (0.44), residues: 131 loop : -1.19 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 561 TYR 0.018 0.002 TYR A 608 PHE 0.028 0.002 PHE A 369 TRP 0.027 0.001 TRP A 741 HIS 0.006 0.001 HIS A 874 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6435) covalent geometry : angle 0.65917 ( 8937) hydrogen bonds : bond 0.04051 ( 299) hydrogen bonds : angle 4.21129 ( 817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.85 seconds wall clock time: 23 minutes 35.43 seconds (1415.43 seconds total)