Starting phenix.real_space_refine on Thu Jul 24 12:12:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqs_60390/07_2025/8zqs_60390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqs_60390/07_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_60390/07_2025/8zqs_60390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqs_60390/07_2025/8zqs_60390.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqs_60390/07_2025/8zqs_60390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqs_60390/07_2025/8zqs_60390.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.26, per 1000 atoms: 0.85 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: 1.77 Conformation dependent library (CDL) restraints added in 731.4 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: 2.03 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: 2.24 Time building geometry restraints manager: 1.96 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: 3.600 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- 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 : 11.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 645 HIS 0.003 0.001 HIS A 689 PHE 0.010 0.001 PHE A 485 TYR 0.008 0.001 TYR A 846 ARG 0.007 0.000 ARG A 885 Details of bonding type rmsd hydrogen bonds : bond 0.14443 ( 299) hydrogen bonds : angle 5.43706 ( 817) covalent geometry : bond 0.00310 ( 6435) covalent geometry : angle 0.59311 ( 8937) *********************** 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 : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 ARG cc_start: 0.3356 (ptt90) cc_final: 0.2856 (ptm160) outliers start: 10 outliers final: 0 residues processed: 154 average time/residue: 0.2880 time to fit residues: 53.0595 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 : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 0.0170 chunk 59 optimal weight: 0.5980 overall best weight: 0.6622 ------------------------------------------------------------------------------- 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 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN A 839 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.145661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.131087 restraints weight = 23909.064| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 4.54 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6435 Z= 0.143 Angle : 0.678 12.625 8937 Z= 0.343 Chirality : 0.039 0.181 1010 Planarity : 0.005 0.059 942 Dihedral : 20.903 171.673 1528 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 3.04 % Allowed : 24.48 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.34), residues: 594 helix: 1.76 (0.32), residues: 248 sheet: -0.22 (0.45), residues: 133 loop : -1.57 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 878 HIS 0.007 0.001 HIS A 884 PHE 0.015 0.002 PHE A 604 TYR 0.020 0.002 TYR A 542 ARG 0.008 0.001 ARG A 885 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 299) hydrogen bonds : angle 4.25565 ( 817) covalent geometry : bond 0.00310 ( 6435) covalent geometry : angle 0.67758 ( 8937) *********************** 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 105 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 561 ARG cc_start: 0.9227 (tpt90) cc_final: 0.8968 (ttp80) REVERT: A 580 ASP cc_start: 0.7992 (t0) cc_final: 0.7783 (t0) REVERT: A 643 TYR cc_start: 0.5513 (t80) cc_final: 0.4345 (t80) REVERT: A 644 HIS cc_start: 0.4792 (t-170) cc_final: 0.4583 (t-170) REVERT: A 645 TRP cc_start: 0.6245 (m100) cc_final: 0.5998 (m100) REVERT: A 746 ARG cc_start: 0.6140 (ttt180) cc_final: 0.5838 (ttt180) outliers start: 16 outliers final: 7 residues processed: 101 average time/residue: 0.2981 time to fit residues: 36.2632 Evaluate side-chains 66 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP 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 595 GLN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 748 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 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 414 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 635 ASN A 689 HIS ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.135284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.120546 restraints weight = 24072.957| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 4.48 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 6435 Z= 0.216 Angle : 0.785 11.555 8937 Z= 0.402 Chirality : 0.042 0.180 1010 Planarity : 0.007 0.104 942 Dihedral : 21.073 174.761 1528 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 4.17 % Allowed : 23.53 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.33), residues: 594 helix: 1.57 (0.31), residues: 248 sheet: -0.41 (0.43), residues: 127 loop : -1.36 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 640 HIS 0.007 0.002 HIS A 884 PHE 0.019 0.003 PHE A 390 TYR 0.028 0.003 TYR A 542 ARG 0.020 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.05399 ( 299) hydrogen bonds : angle 4.34582 ( 817) covalent geometry : bond 0.00482 ( 6435) covalent geometry : angle 0.78521 ( 8937) *********************** 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 86 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8316 (p) cc_final: 0.8029 (m) REVERT: A 580 ASP cc_start: 0.8073 (t0) cc_final: 0.7839 (t0) REVERT: A 597 TYR cc_start: 0.6333 (t80) cc_final: 0.5918 (t80) REVERT: A 604 PHE cc_start: 0.6157 (t80) cc_final: 0.5832 (t80) REVERT: A 746 ARG cc_start: 0.7206 (ttt180) cc_final: 0.6458 (ttt-90) outliers start: 22 outliers final: 14 residues processed: 80 average time/residue: 0.2624 time to fit residues: 26.1920 Evaluate side-chains 70 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 LEU 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 595 GLN Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 661 LYS 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 801 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.138821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.125103 restraints weight = 26268.400| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 4.31 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.5384 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= 0.137 Angle : 0.638 8.518 8937 Z= 0.327 Chirality : 0.038 0.190 1010 Planarity : 0.005 0.055 942 Dihedral : 20.932 171.680 1528 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.04 % Allowed : 24.67 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.34), residues: 594 helix: 2.12 (0.31), residues: 248 sheet: -0.43 (0.41), residues: 139 loop : -1.24 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 878 HIS 0.005 0.001 HIS A 884 PHE 0.025 0.002 PHE A 485 TYR 0.015 0.002 TYR A 542 ARG 0.012 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 299) hydrogen bonds : angle 4.03880 ( 817) covalent geometry : bond 0.00295 ( 6435) covalent geometry : angle 0.63828 ( 8937) *********************** 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 74 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8362 (p) cc_final: 0.8117 (m) REVERT: A 580 ASP cc_start: 0.8008 (t0) cc_final: 0.7776 (t0) REVERT: A 643 TYR cc_start: 0.5711 (t80) cc_final: 0.4471 (t80) REVERT: A 746 ARG cc_start: 0.7120 (ttt180) cc_final: 0.6733 (ttt180) REVERT: A 882 GLU cc_start: 0.8161 (mp0) cc_final: 0.7933 (pm20) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.3188 time to fit residues: 28.6685 Evaluate side-chains 63 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 383 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 608 TYR Chi-restraints excluded: chain A residue 645 TRP Chi-restraints excluded: chain A residue 760 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 A 747 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.129738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.115229 restraints weight = 24913.784| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 4.47 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6435 Z= 0.261 Angle : 0.789 7.839 8937 Z= 0.412 Chirality : 0.044 0.172 1010 Planarity : 0.007 0.066 942 Dihedral : 21.300 170.191 1528 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.07 % Allowed : 23.72 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.33), residues: 594 helix: 1.42 (0.30), residues: 252 sheet: -0.55 (0.43), residues: 130 loop : -1.38 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 640 HIS 0.008 0.002 HIS A 602 PHE 0.027 0.004 PHE A 369 TYR 0.018 0.003 TYR A 389 ARG 0.012 0.001 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.05931 ( 299) hydrogen bonds : angle 4.76634 ( 817) covalent geometry : bond 0.00560 ( 6435) covalent geometry : angle 0.78924 ( 8937) *********************** 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 90 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8400 (p) cc_final: 0.8181 (m) REVERT: A 580 ASP cc_start: 0.8042 (t0) cc_final: 0.7821 (t0) REVERT: A 661 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7762 (pttt) REVERT: A 716 LEU cc_start: 0.8186 (mt) cc_final: 0.7189 (mp) REVERT: A 813 ARG cc_start: 0.4767 (ppt170) cc_final: 0.4491 (ppt170) outliers start: 32 outliers final: 16 residues processed: 82 average time/residue: 0.3869 time to fit residues: 40.1956 Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 595 GLN Chi-restraints excluded: chain A residue 600 ILE 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 661 LYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 784 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.131792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.117133 restraints weight = 24753.379| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 4.46 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6435 Z= 0.158 Angle : 0.670 7.489 8937 Z= 0.345 Chirality : 0.039 0.238 1010 Planarity : 0.004 0.050 942 Dihedral : 21.142 168.764 1528 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.42 % Allowed : 26.76 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.34), residues: 594 helix: 1.92 (0.30), residues: 252 sheet: -0.90 (0.42), residues: 141 loop : -1.36 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 878 HIS 0.004 0.001 HIS A 602 PHE 0.036 0.002 PHE A 369 TYR 0.016 0.002 TYR A 608 ARG 0.011 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 299) hydrogen bonds : angle 4.44253 ( 817) covalent geometry : bond 0.00347 ( 6435) covalent geometry : angle 0.66990 ( 8937) *********************** 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 81 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4640 (mpp-170) REVERT: A 516 LEU cc_start: 0.7137 (pt) cc_final: 0.6865 (pp) REVERT: A 580 ASP cc_start: 0.8080 (t0) cc_final: 0.7849 (t0) REVERT: A 597 TYR cc_start: 0.6654 (t80) cc_final: 0.6253 (t80) REVERT: A 716 LEU cc_start: 0.8128 (mt) cc_final: 0.7110 (mp) REVERT: A 813 ARG cc_start: 0.4820 (ppt170) cc_final: 0.4594 (ppt170) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.2411 time to fit residues: 23.7777 Evaluate side-chains 72 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 382 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 558 ILE Chi-restraints excluded: chain A residue 565 GLU 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 826 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 48 optimal weight: 0.2980 chunk 12 optimal weight: 0.0020 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.0010 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN A 889 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.133236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.118645 restraints weight = 24593.611| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 4.50 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6435 Z= 0.132 Angle : 0.657 13.400 8937 Z= 0.332 Chirality : 0.038 0.214 1010 Planarity : 0.004 0.049 942 Dihedral : 20.995 170.364 1528 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.23 % Allowed : 27.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.34), residues: 594 helix: 1.99 (0.31), residues: 253 sheet: -0.82 (0.41), residues: 141 loop : -1.21 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 878 HIS 0.004 0.001 HIS A 884 PHE 0.028 0.002 PHE A 369 TYR 0.013 0.001 TYR A 608 ARG 0.013 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 299) hydrogen bonds : angle 4.27453 ( 817) covalent geometry : bond 0.00296 ( 6435) covalent geometry : angle 0.65713 ( 8937) *********************** 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 80 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 LEU cc_start: 0.7094 (pt) cc_final: 0.6873 (pp) REVERT: A 580 ASP cc_start: 0.8126 (t0) cc_final: 0.7895 (t0) REVERT: A 597 TYR cc_start: 0.6612 (t80) cc_final: 0.6101 (t80) REVERT: A 606 LEU cc_start: 0.7907 (tt) cc_final: 0.7528 (mt) REVERT: A 716 LEU cc_start: 0.8055 (mt) cc_final: 0.7009 (mp) REVERT: A 746 ARG cc_start: 0.7312 (ttt-90) cc_final: 0.7034 (ttt-90) outliers start: 17 outliers final: 12 residues processed: 73 average time/residue: 0.4552 time to fit residues: 44.1419 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 : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 382 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 558 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 760 TYR Chi-restraints excluded: chain A residue 826 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.130102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.115540 restraints weight = 24982.031| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 4.39 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.7810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6435 Z= 0.204 Angle : 0.726 12.152 8937 Z= 0.373 Chirality : 0.041 0.192 1010 Planarity : 0.005 0.048 942 Dihedral : 21.124 170.994 1528 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.80 % Allowed : 28.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.34), residues: 594 helix: 1.79 (0.31), residues: 253 sheet: -0.67 (0.44), residues: 134 loop : -1.32 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 741 HIS 0.005 0.001 HIS A 602 PHE 0.023 0.002 PHE A 369 TYR 0.019 0.003 TYR A 608 ARG 0.015 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 299) hydrogen bonds : angle 4.49309 ( 817) covalent geometry : bond 0.00447 ( 6435) covalent geometry : angle 0.72645 ( 8937) *********************** 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: 20 poor density : 56 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.4647 (mpp-170) REVERT: A 516 LEU cc_start: 0.7032 (pt) cc_final: 0.6816 (pp) REVERT: A 580 ASP cc_start: 0.8083 (t0) cc_final: 0.7791 (t0) REVERT: A 583 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5057 (ttt-90) REVERT: A 597 TYR cc_start: 0.6837 (t80) cc_final: 0.6507 (t80) REVERT: A 606 LEU cc_start: 0.8009 (tt) cc_final: 0.7617 (mt) REVERT: A 716 LEU cc_start: 0.8176 (mt) cc_final: 0.7149 (mp) REVERT: A 746 ARG cc_start: 0.7428 (ttt180) cc_final: 0.7103 (ttt-90) outliers start: 20 outliers final: 15 residues processed: 71 average time/residue: 0.5085 time to fit residues: 47.7802 Evaluate side-chains 72 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 382 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 477 ILE Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 583 ARG 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 826 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 64 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 61 optimal weight: 7.9990 chunk 12 optimal weight: 0.0050 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.133163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.118729 restraints weight = 25068.297| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 4.41 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6435 Z= 0.130 Angle : 0.672 11.012 8937 Z= 0.339 Chirality : 0.039 0.192 1010 Planarity : 0.004 0.049 942 Dihedral : 20.914 170.176 1528 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.47 % Allowed : 29.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.34), residues: 594 helix: 1.88 (0.31), residues: 253 sheet: -0.79 (0.42), residues: 143 loop : -1.18 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 741 HIS 0.005 0.001 HIS A 884 PHE 0.021 0.002 PHE A 369 TYR 0.015 0.001 TYR A 542 ARG 0.013 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 299) hydrogen bonds : angle 4.25226 ( 817) covalent geometry : bond 0.00288 ( 6435) covalent geometry : angle 0.67219 ( 8937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.4873 (mpp-170) REVERT: A 201 VAL cc_start: 0.8154 (m) cc_final: 0.7788 (p) REVERT: A 204 VAL cc_start: 0.8257 (p) cc_final: 0.8020 (m) REVERT: A 359 LYS cc_start: 0.8461 (mtpp) cc_final: 0.7803 (mmtt) REVERT: A 580 ASP cc_start: 0.8161 (t0) cc_final: 0.7848 (t0) REVERT: A 583 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.4887 (ttt-90) REVERT: A 597 TYR cc_start: 0.6482 (t80) cc_final: 0.5737 (t80) REVERT: A 606 LEU cc_start: 0.7869 (tt) cc_final: 0.7454 (mt) REVERT: A 716 LEU cc_start: 0.8078 (mt) cc_final: 0.7033 (mp) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.2257 time to fit residues: 21.0220 Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 382 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 565 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 826 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.132893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.118575 restraints weight = 25109.409| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 4.40 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6435 Z= 0.133 Angle : 0.665 10.354 8937 Z= 0.336 Chirality : 0.039 0.224 1010 Planarity : 0.004 0.049 942 Dihedral : 20.867 172.011 1528 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.47 % Allowed : 29.79 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.35), residues: 594 helix: 1.93 (0.31), residues: 253 sheet: -0.44 (0.44), residues: 129 loop : -1.13 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 741 HIS 0.004 0.001 HIS A 884 PHE 0.020 0.002 PHE A 369 TYR 0.013 0.002 TYR A 542 ARG 0.014 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 299) hydrogen bonds : angle 4.19334 ( 817) covalent geometry : bond 0.00293 ( 6435) covalent geometry : angle 0.66461 ( 8937) ********************** 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 71 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.4917 (mpp-170) REVERT: A 204 VAL cc_start: 0.8185 (p) cc_final: 0.7950 (m) REVERT: A 359 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7801 (mmtt) REVERT: A 580 ASP cc_start: 0.8179 (t0) cc_final: 0.7874 (t0) REVERT: A 583 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.4959 (ttt-90) REVERT: A 597 TYR cc_start: 0.6676 (t80) cc_final: 0.6069 (t80) REVERT: A 606 LEU cc_start: 0.7894 (tt) cc_final: 0.7442 (mt) REVERT: A 716 LEU cc_start: 0.8052 (mt) cc_final: 0.6985 (mp) REVERT: A 741 TRP cc_start: 0.6221 (t-100) cc_final: 0.5887 (t-100) REVERT: A 746 ARG cc_start: 0.7199 (ttt-90) cc_final: 0.6908 (ttt-90) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.2173 time to fit residues: 18.8325 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 : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 826 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.131601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.117295 restraints weight = 25305.702| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 4.36 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.8310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6435 Z= 0.153 Angle : 0.694 10.748 8937 Z= 0.348 Chirality : 0.040 0.225 1010 Planarity : 0.004 0.049 942 Dihedral : 20.953 171.539 1528 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.85 % Allowed : 30.17 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.35), residues: 594 helix: 1.98 (0.31), residues: 251 sheet: -0.45 (0.45), residues: 119 loop : -1.23 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 741 HIS 0.003 0.001 HIS A 602 PHE 0.019 0.002 PHE A 369 TYR 0.015 0.002 TYR A 608 ARG 0.015 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 299) hydrogen bonds : angle 4.36038 ( 817) covalent geometry : bond 0.00340 ( 6435) covalent geometry : angle 0.69371 ( 8937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3003.02 seconds wall clock time: 54 minutes 17.43 seconds (3257.43 seconds total)