Starting phenix.real_space_refine on Tue Aug 4 17:46:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcc_38239/08_2026/8xcc_38239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcc_38239/08_2026/8xcc_38239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcc_38239/08_2026/8xcc_38239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcc_38239/08_2026/8xcc_38239.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcc_38239/08_2026/8xcc_38239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcc_38239/08_2026/8xcc_38239.cif" } resolution = 3.2 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 56 5.49 5 S 21 5.16 5 C 3332 2.51 5 N 1034 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5617 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4435 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 17, 'TRANS': 528} Chain breaks: 7 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: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 1.59, per 1000 atoms: 0.28 Number of scatterers: 5617 At special positions: 0 Unit cell: (91.08, 72.6, 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 21 16.00 P 56 15.00 O 1174 8.00 N 1034 7.00 C 3332 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: 0.55 Conformation dependent library (CDL) restraints added in 298.4 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 53.3% alpha, 19.2% beta 23 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.569A pdb=" N ARG A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.648A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.657A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 238 Processing helix chain 'A' and resid 387 through 391 removed outlier: 4.059A pdb=" N TRP A 391 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 552 removed outlier: 3.912A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.542A pdb=" N LYS A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 578 through 606 removed outlier: 3.640A pdb=" N ARG A 582 " --> pdb=" O ASP A 578 " (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 621 through 642 removed outlier: 3.538A 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 715 through 720 removed outlier: 3.696A pdb=" N LEU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 737 Processing helix chain 'A' and resid 784 through 797 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 11 removed outlier: 4.162A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 11 removed outlier: 4.162A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 517 removed outlier: 3.704A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.70 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: 1327 1.33 - 1.45: 1427 1.45 - 1.57: 2937 1.57 - 1.69: 109 1.69 - 1.81: 33 Bond restraints: 5833 Sorted by residual: bond pdb=" C3' DG C 7 " pdb=" C2' DG C 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT C 5 " pdb=" C2' DT C 5 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.17e+00 bond pdb=" C3' DT C 3 " pdb=" C2' DT C 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.36e+00 bond pdb=" O4' DT C 5 " pdb=" C1' DT C 5 " ideal model delta sigma weight residual 1.420 1.397 0.023 1.10e-02 8.26e+03 4.33e+00 bond pdb=" O4' DT C 3 " pdb=" C1' DT C 3 " ideal model delta sigma weight residual 1.420 1.399 0.021 1.10e-02 8.26e+03 3.80e+00 ... (remaining 5828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 7799 1.70 - 3.41: 290 3.41 - 5.11: 16 5.11 - 6.82: 3 6.82 - 8.52: 2 Bond angle restraints: 8110 Sorted by residual: angle pdb=" N3 DT D -4 " pdb=" C4 DT D -4 " pdb=" O4 DT D -4 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" O5' G B -4 " pdb=" C5' G B -4 " pdb=" C4' G B -4 " ideal model delta sigma weight residual 109.40 112.62 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" O4 DT D -4 " pdb=" C4 DT D -4 " pdb=" C5 DT D -4 " ideal model delta sigma weight residual 124.90 122.16 2.74 7.00e-01 2.04e+00 1.53e+01 angle pdb=" C1' C B -11 " pdb=" N1 C B -11 " pdb=" C2 C B -11 " ideal model delta sigma weight residual 118.80 123.06 -4.26 1.10e+00 8.26e-01 1.50e+01 ... (remaining 8105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 3356 34.93 - 69.87: 189 69.87 - 104.80: 21 104.80 - 139.74: 1 139.74 - 174.67: 1 Dihedral angle restraints: 3568 sinusoidal: 1976 harmonic: 1592 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 46.67 -174.67 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N ARG A 572 " pdb=" CA ARG A 572 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+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 -90.00 -14.24 -75.76 1 2.00e+01 2.50e-03 1.81e+01 ... (remaining 3565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 555 0.028 - 0.056: 215 0.056 - 0.084: 70 0.084 - 0.113: 37 0.113 - 0.141: 48 Chirality restraints: 925 Sorted by residual: chirality pdb=" CA PHE A 202 " pdb=" N PHE A 202 " pdb=" C PHE A 202 " pdb=" CB PHE A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" C2' C B -22 " pdb=" C3' C B -22 " pdb=" O2' C B -22 " pdb=" C1' C B -22 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" C2' C B -1 " pdb=" C3' C B -1 " pdb=" O2' C B -1 " pdb=" C1' C B -1 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 922 not shown) Planarity restraints: 835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B -35 " -0.021 2.00e-02 2.50e+03 1.10e-02 2.74e+00 pdb=" N1 U B -35 " 0.024 2.00e-02 2.50e+03 pdb=" C2 U B -35 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U B -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B -35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B -35 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B -35 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -36 " -0.020 2.00e-02 2.50e+03 8.65e-03 2.24e+00 pdb=" N9 G B -36 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G B -36 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B -36 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B -36 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B -36 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B -36 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B -36 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B -36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B -36 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 482 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 483 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.019 5.00e-02 4.00e+02 ... (remaining 832 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 513 2.74 - 3.28: 5397 3.28 - 3.82: 9880 3.82 - 4.36: 11174 4.36 - 4.90: 18481 Nonbonded interactions: 45445 Sorted by model distance: nonbonded pdb=" OH TYR A 389 " pdb=" OP2 C B 0 " model vdw 2.197 3.040 nonbonded pdb=" O2' C B 0 " pdb=" O5' U B 1 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 666 " pdb=" OP2 U B -32 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU A 111 " pdb=" NZ LYS A 112 " model vdw 2.297 3.120 nonbonded pdb=" O LEU A 110 " pdb=" NH2 ARG A 197 " model vdw 2.311 3.120 ... (remaining 45440 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: 3.170 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.210 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 : 0.004 0.026 5833 Z= 0.277 Angle : 0.669 8.523 8110 Z= 0.479 Chirality : 0.046 0.141 925 Planarity : 0.003 0.034 835 Dihedral : 19.549 174.670 2536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.21 % Allowed : 11.42 % Favored : 88.37 % 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: 1.81 (0.38), residues: 530 helix: 2.54 (0.32), residues: 257 sheet: 0.71 (0.52), residues: 92 loop : -0.54 (0.51), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.009 0.001 TYR A 22 PHE 0.013 0.001 PHE A 202 TRP 0.013 0.002 TRP A 229 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.28 ( 5833) covalent geometry : angle 0.66908 / 0.48 ( 8110) hydrogen bonds : bond 0.11207 / 7.53 ( 320) hydrogen bonds : angle 4.61979 / 3.27 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.225 Fit side-chains REVERT: A 420 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8382 (tt0) REVERT: A 696 MET cc_start: 0.8900 (ptp) cc_final: 0.8638 (ptt) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0887 time to fit residues: 4.5390 Evaluate side-chains 34 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.074348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.058919 restraints weight = 15263.740| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.91 r_work: 0.2724 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5833 Z= 0.206 Angle : 0.567 7.749 8110 Z= 0.312 Chirality : 0.040 0.213 925 Planarity : 0.004 0.035 835 Dihedral : 20.690 174.496 1433 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.54 % Allowed : 11.84 % Favored : 85.62 % 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: 2.11 (0.38), residues: 530 helix: 2.69 (0.31), residues: 268 sheet: 0.37 (0.48), residues: 102 loop : -0.12 (0.56), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 615 TYR 0.010 0.001 TYR A 44 PHE 0.013 0.002 PHE A 390 TRP 0.011 0.002 TRP A 229 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 ( 5833) covalent geometry : angle 0.56698 / 0.31 ( 8110) hydrogen bonds : bond 0.05151 / 3.54 ( 320) hydrogen bonds : angle 3.76099 / 2.70 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.203 Fit side-chains REVERT: A 48 MET cc_start: 0.8687 (mpp) cc_final: 0.8080 (mpp) REVERT: A 102 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: A 202 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7175 (t80) REVERT: A 420 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8515 (tt0) REVERT: A 696 MET cc_start: 0.8985 (ptp) cc_final: 0.8757 (ptt) REVERT: A 797 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6259 (ptp-170) outliers start: 12 outliers final: 7 residues processed: 45 average time/residue: 0.0759 time to fit residues: 4.7576 Evaluate side-chains 44 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.075215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.059792 restraints weight = 15019.712| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.84 r_work: 0.2740 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5833 Z= 0.153 Angle : 0.516 8.142 8110 Z= 0.288 Chirality : 0.038 0.207 925 Planarity : 0.003 0.029 835 Dihedral : 20.675 175.015 1433 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.17 % Allowed : 11.21 % Favored : 85.62 % 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: 2.23 (0.38), residues: 530 helix: 2.84 (0.31), residues: 268 sheet: 0.21 (0.48), residues: 97 loop : 0.02 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.012 0.001 TYR A 44 PHE 0.009 0.001 PHE A 537 TRP 0.011 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 5833) covalent geometry : angle 0.51553 / 0.29 ( 8110) hydrogen bonds : bond 0.04747 / 3.27 ( 320) hydrogen bonds : angle 3.57091 / 2.57 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.202 Fit side-chains REVERT: A 48 MET cc_start: 0.8699 (mpp) cc_final: 0.8007 (mpp) REVERT: A 99 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9157 (tt) REVERT: A 102 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: A 202 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7241 (t80) REVERT: A 420 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8494 (tt0) REVERT: A 696 MET cc_start: 0.8997 (ptp) cc_final: 0.8645 (ptt) REVERT: A 797 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6235 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 46 average time/residue: 0.0659 time to fit residues: 4.3595 Evaluate side-chains 48 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.075514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.060106 restraints weight = 15156.101| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.86 r_work: 0.2752 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5833 Z= 0.131 Angle : 0.494 8.507 8110 Z= 0.277 Chirality : 0.037 0.199 925 Planarity : 0.003 0.038 835 Dihedral : 20.610 175.593 1433 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.59 % Allowed : 11.84 % Favored : 84.57 % 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: 2.34 (0.38), residues: 530 helix: 2.98 (0.31), residues: 267 sheet: 0.29 (0.48), residues: 95 loop : -0.04 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.010 0.001 TYR A 44 PHE 0.010 0.001 PHE A 390 TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5833) covalent geometry : angle 0.49426 / 0.28 ( 8110) hydrogen bonds : bond 0.04453 / 3.06 ( 320) hydrogen bonds : angle 3.43124 / 2.47 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.251 Fit side-chains REVERT: A 48 MET cc_start: 0.8710 (mpp) cc_final: 0.7964 (mpp) REVERT: A 99 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9129 (tt) REVERT: A 102 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8782 (mp0) REVERT: A 202 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7329 (t80) REVERT: A 420 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8497 (tt0) REVERT: A 696 MET cc_start: 0.8999 (ptp) cc_final: 0.8664 (ptt) REVERT: A 714 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6153 (p0) REVERT: A 797 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6230 (ptm160) outliers start: 17 outliers final: 9 residues processed: 52 average time/residue: 0.0709 time to fit residues: 5.3450 Evaluate side-chains 50 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.074148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.058684 restraints weight = 15340.662| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.86 r_work: 0.2717 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5833 Z= 0.201 Angle : 0.543 7.853 8110 Z= 0.297 Chirality : 0.039 0.193 925 Planarity : 0.004 0.032 835 Dihedral : 20.590 175.299 1433 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.59 % Allowed : 13.11 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.29 (0.38), residues: 530 helix: 2.94 (0.31), residues: 267 sheet: 0.38 (0.48), residues: 100 loop : -0.17 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.010 0.001 TYR A 22 PHE 0.012 0.001 PHE A 390 TRP 0.008 0.001 TRP A 229 HIS 0.005 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 5833) covalent geometry : angle 0.54258 / 0.30 ( 8110) hydrogen bonds : bond 0.04695 / 3.23 ( 320) hydrogen bonds : angle 3.52984 / 2.53 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8696 (mpp) cc_final: 0.8001 (mpp) REVERT: A 99 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9186 (tt) REVERT: A 102 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8799 (mp0) REVERT: A 202 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7258 (t80) REVERT: A 420 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8479 (tt0) REVERT: A 797 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6096 (ptp-170) outliers start: 17 outliers final: 11 residues processed: 50 average time/residue: 0.0783 time to fit residues: 5.4197 Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.074098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.058683 restraints weight = 15136.458| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.82 r_work: 0.2718 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5833 Z= 0.191 Angle : 0.533 8.158 8110 Z= 0.294 Chirality : 0.039 0.194 925 Planarity : 0.004 0.037 835 Dihedral : 20.621 175.055 1433 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.02 % Allowed : 13.11 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.38), residues: 530 helix: 2.96 (0.31), residues: 267 sheet: 0.24 (0.48), residues: 102 loop : -0.14 (0.56), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.010 0.001 TYR A 22 PHE 0.011 0.001 PHE A 390 TRP 0.008 0.001 TRP A 229 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 ( 5833) covalent geometry : angle 0.53330 / 0.29 ( 8110) hydrogen bonds : bond 0.04661 / 3.23 ( 320) hydrogen bonds : angle 3.52855 / 2.54 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8674 (mpp) cc_final: 0.7967 (mpp) REVERT: A 99 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9139 (tt) REVERT: A 102 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8684 (mp0) REVERT: A 202 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7372 (t80) REVERT: A 420 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8465 (tt0) REVERT: A 714 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6178 (p0) REVERT: A 797 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6186 (ptm160) outliers start: 19 outliers final: 11 residues processed: 53 average time/residue: 0.0726 time to fit residues: 5.3370 Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.075904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060434 restraints weight = 15246.689| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.85 r_work: 0.2758 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5833 Z= 0.116 Angle : 0.494 8.934 8110 Z= 0.273 Chirality : 0.036 0.190 925 Planarity : 0.003 0.034 835 Dihedral : 20.584 175.266 1433 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.96 % Allowed : 13.95 % Favored : 83.09 % 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: 2.55 (0.38), residues: 530 helix: 3.14 (0.31), residues: 265 sheet: 0.38 (0.48), residues: 100 loop : 0.13 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.011 0.001 TYR A 44 PHE 0.009 0.001 PHE A 537 TRP 0.011 0.001 TRP A 229 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 5833) covalent geometry : angle 0.49419 / 0.27 ( 8110) hydrogen bonds : bond 0.04311 / 2.97 ( 320) hydrogen bonds : angle 3.38605 / 2.44 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8692 (mpp) cc_final: 0.7983 (mpp) REVERT: A 70 CYS cc_start: 0.9299 (t) cc_final: 0.8355 (p) REVERT: A 202 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 420 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8420 (tt0) REVERT: A 714 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6182 (p0) REVERT: A 797 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6186 (ptm160) outliers start: 14 outliers final: 10 residues processed: 51 average time/residue: 0.0823 time to fit residues: 5.6588 Evaluate side-chains 50 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.075387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.059925 restraints weight = 15031.026| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.83 r_work: 0.2747 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5833 Z= 0.142 Angle : 0.506 8.571 8110 Z= 0.278 Chirality : 0.037 0.186 925 Planarity : 0.003 0.041 835 Dihedral : 20.536 175.544 1433 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.96 % Allowed : 14.38 % Favored : 82.66 % 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: 2.56 (0.38), residues: 530 helix: 3.18 (0.31), residues: 265 sheet: 0.36 (0.48), residues: 100 loop : 0.09 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.009 0.001 TYR A 22 PHE 0.010 0.001 PHE A 390 TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 5833) covalent geometry : angle 0.50563 / 0.28 ( 8110) hydrogen bonds : bond 0.04324 / 2.97 ( 320) hydrogen bonds : angle 3.39678 / 2.45 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8661 (mpp) cc_final: 0.7946 (mpp) REVERT: A 70 CYS cc_start: 0.9299 (t) cc_final: 0.8339 (p) REVERT: A 99 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9111 (tt) REVERT: A 202 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 420 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8422 (tt0) REVERT: A 714 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6209 (p0) REVERT: A 797 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6153 (ptm160) outliers start: 14 outliers final: 10 residues processed: 48 average time/residue: 0.0718 time to fit residues: 4.7529 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.075429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.059919 restraints weight = 15148.394| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.84 r_work: 0.2744 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5833 Z= 0.145 Angle : 0.507 8.573 8110 Z= 0.279 Chirality : 0.037 0.183 925 Planarity : 0.003 0.037 835 Dihedral : 20.528 175.564 1433 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.59 % Allowed : 14.16 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.39), residues: 530 helix: 3.19 (0.31), residues: 265 sheet: 0.37 (0.48), residues: 100 loop : 0.13 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.010 0.001 TYR A 22 PHE 0.010 0.001 PHE A 390 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 5833) covalent geometry : angle 0.50720 / 0.28 ( 8110) hydrogen bonds : bond 0.04312 / 2.97 ( 320) hydrogen bonds : angle 3.37381 / 2.44 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8667 (mpp) cc_final: 0.7949 (mpp) REVERT: A 70 CYS cc_start: 0.9301 (t) cc_final: 0.8346 (p) REVERT: A 99 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9108 (tt) REVERT: A 202 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7252 (t80) REVERT: A 420 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8413 (tt0) REVERT: A 714 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6241 (p0) REVERT: A 797 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6148 (ptm160) outliers start: 17 outliers final: 12 residues processed: 50 average time/residue: 0.0753 time to fit residues: 5.2492 Evaluate side-chains 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.075443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059999 restraints weight = 15246.672| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.82 r_work: 0.2752 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5833 Z= 0.139 Angle : 0.503 8.570 8110 Z= 0.277 Chirality : 0.037 0.182 925 Planarity : 0.003 0.041 835 Dihedral : 20.523 175.604 1433 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.38 % Allowed : 14.38 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.39), residues: 530 helix: 3.21 (0.31), residues: 265 sheet: 0.34 (0.48), residues: 100 loop : 0.11 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.009 0.001 TYR A 22 PHE 0.009 0.001 PHE A 390 TRP 0.009 0.001 TRP A 229 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 5833) covalent geometry : angle 0.50275 / 0.28 ( 8110) hydrogen bonds : bond 0.04271 / 2.94 ( 320) hydrogen bonds : angle 3.36342 / 2.43 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8663 (mpp) cc_final: 0.7939 (mpp) REVERT: A 70 CYS cc_start: 0.9300 (t) cc_final: 0.8351 (p) REVERT: A 99 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9112 (tt) REVERT: A 202 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7388 (t80) REVERT: A 420 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8416 (tt0) REVERT: A 714 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6260 (p0) REVERT: A 797 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6094 (ptp-170) outliers start: 16 outliers final: 12 residues processed: 49 average time/residue: 0.0643 time to fit residues: 4.3650 Evaluate side-chains 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.075755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060358 restraints weight = 15013.657| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.83 r_work: 0.2759 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5833 Z= 0.122 Angle : 0.495 8.818 8110 Z= 0.273 Chirality : 0.036 0.180 925 Planarity : 0.003 0.036 835 Dihedral : 20.520 175.637 1433 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.38 % Allowed : 14.38 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.39), residues: 530 helix: 3.21 (0.31), residues: 265 sheet: 0.35 (0.48), residues: 100 loop : 0.11 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.009 0.001 TYR A 22 PHE 0.009 0.001 PHE A 390 TRP 0.010 0.001 TRP A 229 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 5833) covalent geometry : angle 0.49529 / 0.27 ( 8110) hydrogen bonds : bond 0.04234 / 2.91 ( 320) hydrogen bonds : angle 3.33789 / 2.41 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.80 seconds wall clock time: 23 minutes 39.90 seconds (1419.90 seconds total)