Starting phenix.real_space_refine on Tue Aug 4 22:10:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xca_38238/08_2026/8xca_38238_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xca_38238/08_2026/8xca_38238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xca_38238/08_2026/8xca_38238_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xca_38238/08_2026/8xca_38238_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xca_38238/08_2026/8xca_38238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xca_38238/08_2026/8xca_38238.map" } resolution = 3.1 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= 0.008 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 79 5.49 5 S 23 5.16 5 C 4179 2.51 5 N 1306 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7106 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5443 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 21, 'TRANS': 646} Chain breaks: 4 Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1066 Classifications: {'RNA': 50} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 6, 'rna3p': 43} Chain: "C" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 1.65, per 1000 atoms: 0.23 Number of scatterers: 7106 At special positions: 0 Unit cell: (81.84, 96.36, 111.54, 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 23 16.00 P 79 15.00 O 1519 8.00 N 1306 7.00 C 4179 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: 0.63 Conformation dependent library (CDL) restraints added in 322.7 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 45.5% alpha, 16.0% beta 32 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.599A pdb=" N ARG A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 240 removed outlier: 3.620A pdb=" N CYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 522 through 553 removed outlier: 3.553A pdb=" N ASP A 551 " --> pdb=" O LYS A 547 " (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 607 removed outlier: 3.730A pdb=" N ARG A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 609 No H-bonds generated for 'chain 'A' and resid 608 through 609' Processing helix chain 'A' and resid 610 through 614 removed outlier: 4.478A pdb=" N ASP A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 removed outlier: 3.772A pdb=" N ARG A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 689 removed outlier: 3.509A pdb=" N HIS A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 719 Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.965A pdb=" N VAL A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 796 removed outlier: 3.590A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 829 removed outlier: 3.500A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 11 removed outlier: 4.400A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 4.111A pdb=" N TYR A 44 " --> pdb=" O VAL A 56 " (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 391 through 397 removed outlier: 5.437A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 removed outlier: 5.743A pdb=" N LEU A 479 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 694 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 501 removed outlier: 4.176A pdb=" N ILE A 499 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 806 through 810 removed outlier: 3.846A pdb=" N LEU A 809 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1743 1.33 - 1.45: 1820 1.45 - 1.57: 3650 1.57 - 1.69: 155 1.69 - 1.81: 35 Bond restraints: 7403 Sorted by residual: bond pdb=" C3' DG C 7 " pdb=" C2' DG C 7 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.03e+00 bond pdb=" C3' DA C -6 " pdb=" C2' DA C -6 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.57e+00 bond pdb=" C1' DC C 6 " pdb=" N1 DC C 6 " ideal model delta sigma weight residual 1.468 1.497 -0.029 1.40e-02 5.10e+03 4.44e+00 bond pdb=" C3' DG C -7 " pdb=" C2' DG C -7 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.41e+00 bond pdb=" C1' DT C 5 " pdb=" N1 DT C 5 " ideal model delta sigma weight residual 1.468 1.497 -0.029 1.40e-02 5.10e+03 4.34e+00 ... (remaining 7398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 9951 1.65 - 3.29: 358 3.29 - 4.94: 24 4.94 - 6.58: 7 6.58 - 8.23: 3 Bond angle restraints: 10343 Sorted by residual: angle pdb=" N3 DT C -8 " pdb=" C4 DT C -8 " pdb=" O4 DT C -8 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4' A B 12 " pdb=" C1' A B 12 " pdb=" N9 A B 12 " ideal model delta sigma weight residual 108.20 111.67 -3.47 8.00e-01 1.56e+00 1.88e+01 angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" O4' DA C 2 " pdb=" C4' DA C 2 " pdb=" C3' DA C 2 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" O5' G B -20 " pdb=" C5' G B -20 " pdb=" C4' G B -20 " ideal model delta sigma weight residual 109.40 112.77 -3.37 8.00e-01 1.56e+00 1.77e+01 ... (remaining 10338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 4111 35.80 - 71.60: 351 71.60 - 107.40: 19 107.40 - 143.21: 1 143.21 - 179.01: 1 Dihedral angle restraints: 4483 sinusoidal: 2529 harmonic: 1954 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 -128.00 51.01 -179.01 1 1.70e+01 3.46e-03 6.64e+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 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+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 -1.31 71.31 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 4480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 827 0.035 - 0.070: 203 0.070 - 0.105: 72 0.105 - 0.139: 66 0.139 - 0.174: 5 Chirality restraints: 1173 Sorted by residual: chirality pdb=" C1' A B -7 " pdb=" O4' A B -7 " pdb=" C2' A B -7 " pdb=" N9 A B -7 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" P G B -20 " pdb=" OP1 G B -20 " pdb=" OP2 G B -20 " pdb=" O5' G B -20 " both_signs ideal model delta sigma weight residual True 2.41 -2.57 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" C2' U B 1 " pdb=" C3' U B 1 " pdb=" O2' U B 1 " pdb=" C1' U B 1 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1170 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 11 " 0.024 2.00e-02 2.50e+03 1.08e-02 3.48e+00 pdb=" N9 G B 11 " -0.027 2.00e-02 2.50e+03 pdb=" C8 G B 11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 11 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 11 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 11 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G B 11 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G B 11 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 11 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G B 11 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 11 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 12 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.91e+00 pdb=" N9 A B 12 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A B 12 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A B 12 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A B 12 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 12 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A B 12 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 658 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C ASP A 658 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A 658 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 659 " 0.009 2.00e-02 2.50e+03 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 826 2.75 - 3.29: 6611 3.29 - 3.82: 12760 3.82 - 4.36: 14435 4.36 - 4.90: 23172 Nonbonded interactions: 57804 Sorted by model distance: nonbonded pdb=" OD2 ASP A 614 " pdb=" NH1 ARG A 615 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR A 666 " pdb=" OP2 U B -32 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A 106 " pdb=" OP2 DA D -3 " model vdw 2.251 3.040 nonbonded pdb=" NH2 ARG A 671 " pdb=" OP2 DG C -7 " model vdw 2.261 3.120 nonbonded pdb=" OG SER A 533 " pdb=" OD1 ASN A 632 " model vdw 2.280 3.040 ... (remaining 57799 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: 4.300 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.040 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 0.050 7403 Z= 0.242 Angle : 0.638 8.227 10343 Z= 0.481 Chirality : 0.046 0.174 1173 Planarity : 0.003 0.031 1048 Dihedral : 21.671 179.008 3219 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.17 % Allowed : 26.07 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.33), residues: 658 helix: 2.48 (0.30), residues: 274 sheet: -0.03 (0.46), residues: 131 loop : -0.81 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 775 TYR 0.010 0.001 TYR A 605 PHE 0.010 0.001 PHE A 202 TRP 0.012 0.001 TRP A 645 HIS 0.002 0.000 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.24 ( 7403) covalent geometry : angle 0.63775 / 0.48 (10343) hydrogen bonds : bond 0.14549 / 8.84 ( 368) hydrogen bonds : angle 5.07243 / 3.62 ( 976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.187 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.0822 time to fit residues: 4.0758 Evaluate side-chains 33 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.060560 restraints weight = 19785.325| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.87 r_work: 0.2835 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7403 Z= 0.175 Angle : 0.536 7.147 10343 Z= 0.302 Chirality : 0.038 0.193 1173 Planarity : 0.004 0.040 1048 Dihedral : 21.374 178.848 1859 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.74 % Allowed : 23.16 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.33), residues: 658 helix: 2.51 (0.30), residues: 279 sheet: 0.05 (0.48), residues: 109 loop : -0.70 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 671 TYR 0.013 0.001 TYR A 538 PHE 0.008 0.001 PHE A 537 TRP 0.007 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 7403) covalent geometry : angle 0.53642 / 0.30 (10343) hydrogen bonds : bond 0.05247 / 3.44 ( 368) hydrogen bonds : angle 4.10305 / 2.90 ( 976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.214 Fit side-chains REVERT: A 202 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 219 MET cc_start: 0.9082 (tpp) cc_final: 0.8764 (tpp) outliers start: 16 outliers final: 11 residues processed: 48 average time/residue: 0.0924 time to fit residues: 5.9275 Evaluate side-chains 42 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.060158 restraints weight = 19668.369| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.84 r_work: 0.2825 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7403 Z= 0.168 Angle : 0.518 6.955 10343 Z= 0.291 Chirality : 0.037 0.185 1173 Planarity : 0.004 0.041 1048 Dihedral : 21.379 178.662 1859 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.12 % Allowed : 23.50 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.33), residues: 658 helix: 2.57 (0.29), residues: 279 sheet: 0.16 (0.48), residues: 109 loop : -0.66 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 775 TYR 0.013 0.001 TYR A 538 PHE 0.007 0.001 PHE A 485 TRP 0.006 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 7403) covalent geometry : angle 0.51801 / 0.29 (10343) hydrogen bonds : bond 0.04660 / 3.11 ( 368) hydrogen bonds : angle 3.86842 / 2.73 ( 976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.242 Fit side-chains REVERT: A 202 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7841 (t80) REVERT: A 547 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8087 (mttt) outliers start: 24 outliers final: 14 residues processed: 53 average time/residue: 0.0854 time to fit residues: 6.1990 Evaluate side-chains 46 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.060920 restraints weight = 19869.640| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.86 r_work: 0.2830 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7403 Z= 0.148 Angle : 0.504 6.831 10343 Z= 0.283 Chirality : 0.036 0.167 1173 Planarity : 0.004 0.037 1048 Dihedral : 21.385 178.579 1859 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.46 % Allowed : 23.50 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.33), residues: 658 helix: 2.63 (0.30), residues: 279 sheet: 0.13 (0.48), residues: 109 loop : -0.65 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 746 TYR 0.012 0.001 TYR A 538 PHE 0.008 0.001 PHE A 202 TRP 0.005 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 7403) covalent geometry : angle 0.50364 / 0.28 (10343) hydrogen bonds : bond 0.04452 / 2.99 ( 368) hydrogen bonds : angle 3.75831 / 2.66 ( 976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.237 Fit side-chains REVERT: A 202 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 544 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8474 (mtm-85) REVERT: A 547 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8086 (mttt) outliers start: 26 outliers final: 15 residues processed: 55 average time/residue: 0.1055 time to fit residues: 7.5715 Evaluate side-chains 48 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 31 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059356 restraints weight = 19967.462| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.87 r_work: 0.2808 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7403 Z= 0.198 Angle : 0.534 7.421 10343 Z= 0.296 Chirality : 0.037 0.155 1173 Planarity : 0.004 0.038 1048 Dihedral : 21.389 178.896 1859 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.95 % Allowed : 23.50 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.33), residues: 658 helix: 2.66 (0.30), residues: 279 sheet: 0.12 (0.47), residues: 109 loop : -0.66 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 527 TYR 0.011 0.001 TYR A 538 PHE 0.007 0.001 PHE A 771 TRP 0.004 0.001 TRP A 720 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 ( 7403) covalent geometry : angle 0.53406 / 0.30 (10343) hydrogen bonds : bond 0.04593 / 3.09 ( 368) hydrogen bonds : angle 3.76387 / 2.67 ( 976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.164 Fit side-chains REVERT: A 202 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7942 (t80) REVERT: A 544 ARG cc_start: 0.8719 (mtm180) cc_final: 0.8426 (mtm-85) REVERT: A 547 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8108 (mttt) outliers start: 23 outliers final: 16 residues processed: 51 average time/residue: 0.0773 time to fit residues: 5.3270 Evaluate side-chains 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.078554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.060359 restraints weight = 19982.426| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.89 r_work: 0.2830 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7403 Z= 0.136 Angle : 0.494 5.840 10343 Z= 0.279 Chirality : 0.036 0.162 1173 Planarity : 0.003 0.037 1048 Dihedral : 21.388 178.430 1859 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.60 % Allowed : 24.01 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.33), residues: 658 helix: 2.61 (0.30), residues: 281 sheet: 0.18 (0.48), residues: 109 loop : -0.72 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 615 TYR 0.009 0.001 TYR A 538 PHE 0.009 0.001 PHE A 202 TRP 0.005 0.001 TRP A 645 HIS 0.002 0.000 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 7403) covalent geometry : angle 0.49434 / 0.28 (10343) hydrogen bonds : bond 0.04291 / 2.89 ( 368) hydrogen bonds : angle 3.69583 / 2.62 ( 976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.204 Fit side-chains REVERT: A 202 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 547 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8083 (mttt) outliers start: 21 outliers final: 14 residues processed: 50 average time/residue: 0.0926 time to fit residues: 6.3719 Evaluate side-chains 48 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.0170 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059853 restraints weight = 19897.859| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.84 r_work: 0.2821 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7403 Z= 0.183 Angle : 0.523 7.268 10343 Z= 0.290 Chirality : 0.037 0.151 1173 Planarity : 0.004 0.037 1048 Dihedral : 21.403 178.962 1859 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.12 % Allowed : 24.19 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.33), residues: 658 helix: 2.63 (0.30), residues: 281 sheet: 0.14 (0.47), residues: 109 loop : -0.72 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 775 TYR 0.010 0.001 TYR A 538 PHE 0.007 0.001 PHE A 202 TRP 0.004 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 ( 7403) covalent geometry : angle 0.52255 / 0.29 (10343) hydrogen bonds : bond 0.04463 / 3.01 ( 368) hydrogen bonds : angle 3.70580 / 2.63 ( 976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.161 Fit side-chains REVERT: A 202 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 547 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8096 (mttt) REVERT: A 828 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.4096 (mm-30) outliers start: 24 outliers final: 19 residues processed: 52 average time/residue: 0.0904 time to fit residues: 6.4025 Evaluate side-chains 54 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 828 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.060645 restraints weight = 19795.833| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.87 r_work: 0.2835 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7403 Z= 0.130 Angle : 0.506 7.925 10343 Z= 0.282 Chirality : 0.036 0.147 1173 Planarity : 0.003 0.036 1048 Dihedral : 21.416 178.503 1859 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.77 % Allowed : 24.87 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.33), residues: 658 helix: 2.58 (0.30), residues: 281 sheet: 0.18 (0.47), residues: 109 loop : -0.70 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 775 TYR 0.009 0.001 TYR A 605 PHE 0.009 0.001 PHE A 202 TRP 0.006 0.001 TRP A 645 HIS 0.002 0.000 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 7403) covalent geometry : angle 0.50636 / 0.28 (10343) hydrogen bonds : bond 0.04227 / 2.86 ( 368) hydrogen bonds : angle 3.65875 / 2.60 ( 976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.179 Fit side-chains REVERT: A 202 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7870 (t80) outliers start: 22 outliers final: 18 residues processed: 51 average time/residue: 0.0875 time to fit residues: 5.8786 Evaluate side-chains 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.079730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.061672 restraints weight = 19769.300| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.87 r_work: 0.2863 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7403 Z= 0.115 Angle : 0.498 8.348 10343 Z= 0.278 Chirality : 0.035 0.154 1173 Planarity : 0.003 0.036 1048 Dihedral : 21.368 178.551 1859 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.43 % Allowed : 24.70 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.33), residues: 658 helix: 2.62 (0.30), residues: 281 sheet: 0.21 (0.48), residues: 109 loop : -0.70 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 775 TYR 0.009 0.001 TYR A 605 PHE 0.009 0.001 PHE A 485 TRP 0.008 0.001 TRP A 640 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 7403) covalent geometry : angle 0.49759 / 0.28 (10343) hydrogen bonds : bond 0.04064 / 2.75 ( 368) hydrogen bonds : angle 3.60346 / 2.56 ( 976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.234 Fit side-chains REVERT: A 202 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7806 (t80) REVERT: A 828 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.3840 (mm-30) outliers start: 20 outliers final: 14 residues processed: 53 average time/residue: 0.0787 time to fit residues: 5.7731 Evaluate side-chains 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 828 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.076545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058532 restraints weight = 20166.274| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.88 r_work: 0.2780 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 7403 Z= 0.326 Angle : 0.656 9.710 10343 Z= 0.351 Chirality : 0.042 0.176 1173 Planarity : 0.005 0.045 1048 Dihedral : 21.474 179.481 1859 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.43 % Allowed : 24.53 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.33), residues: 658 helix: 2.51 (0.30), residues: 279 sheet: 0.08 (0.48), residues: 109 loop : -0.64 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 544 TYR 0.016 0.002 TYR A 798 PHE 0.010 0.002 PHE A 628 TRP 0.010 0.002 TRP A 640 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.33 ( 7403) covalent geometry : angle 0.65566 / 0.35 (10343) hydrogen bonds : bond 0.05298 / 3.58 ( 368) hydrogen bonds : angle 3.88668 / 2.76 ( 976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.239 Fit side-chains REVERT: A 202 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8122 (t80) REVERT: A 458 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8191 (ptm160) REVERT: A 828 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.4329 (mm-30) outliers start: 20 outliers final: 17 residues processed: 45 average time/residue: 0.0699 time to fit residues: 4.5344 Evaluate side-chains 48 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 828 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.060864 restraints weight = 19779.363| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.88 r_work: 0.2840 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7403 Z= 0.125 Angle : 0.521 8.880 10343 Z= 0.290 Chirality : 0.036 0.140 1173 Planarity : 0.004 0.036 1048 Dihedral : 21.478 177.877 1859 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 24.87 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.33), residues: 658 helix: 2.60 (0.30), residues: 279 sheet: 0.11 (0.49), residues: 109 loop : -0.58 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 544 TYR 0.011 0.001 TYR A 22 PHE 0.011 0.001 PHE A 202 TRP 0.010 0.001 TRP A 640 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 7403) covalent geometry : angle 0.52064 / 0.29 (10343) hydrogen bonds : bond 0.04210 / 2.84 ( 368) hydrogen bonds : angle 3.71201 / 2.64 ( 976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1326.57 seconds wall clock time: 23 minutes 27.10 seconds (1407.10 seconds total)