Starting phenix.real_space_refine on Thu Jul 2 02:00:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcc_38239/07_2026/8xcc_38239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcc_38239/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xcc_38239/07_2026/8xcc_38239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcc_38239/07_2026/8xcc_38239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xcc_38239/07_2026/8xcc_38239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcc_38239/07_2026/8xcc_38239.map" } 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-dev-6108/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: 1.26, per 1000 atoms: 0.22 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: 0.52 Conformation dependent library (CDL) restraints added in 135.9 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: 0.66 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: 0.89 Time building geometry restraints manager: 0.61 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: 7906 1.70 - 3.41: 183 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=" 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 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.22 -2.32 6.00e-01 2.78e+00 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: 595 0.028 - 0.056: 215 0.056 - 0.084: 69 0.084 - 0.113: 37 0.113 - 0.141: 9 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=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 573 " pdb=" N ILE A 573 " pdb=" C ILE A 573 " pdb=" CB ILE A 573 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-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: 3.300 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: 6.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.400 ------------------------------------------------------------------------------- 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= 0.269 Angle : 0.605 8.523 8110 Z= 0.428 Chirality : 0.038 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 0.00385 / 0.27 ( 5833) covalent geometry : angle 0.60541 / 0.43 ( 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 : 0.204 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: 0.0716 time to fit residues: 3.6642 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 : 0.208 ------------------------------------------------------------------------------- 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: 8.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 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: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.074056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.058589 restraints weight = 15271.698| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.91 r_work: 0.2716 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5833 Z= 0.225 Angle : 0.567 7.888 8110 Z= 0.315 Chirality : 0.039 0.187 925 Planarity : 0.004 0.034 835 Dihedral : 20.732 174.520 1433 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.75 % Allowed : 11.42 % Favored : 85.84 % 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: 2.06 (0.38), residues: 530 helix: 2.67 (0.31), residues: 268 sheet: 0.45 (0.49), residues: 97 loop : -0.25 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 615 TYR 0.012 0.001 TYR A 44 PHE 0.015 0.002 PHE A 390 TRP 0.010 0.002 TRP A 229 HIS 0.005 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 ( 5833) covalent geometry : angle 0.56736 / 0.31 ( 8110) hydrogen bonds : bond 0.05171 / 3.56 ( 320) hydrogen bonds : angle 3.77632 / 2.71 ( 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 48 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.197 Fit side-chains REVERT: A 48 MET cc_start: 0.8692 (mpp) cc_final: 0.8084 (mpp) REVERT: A 102 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: A 202 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7201 (t80) REVERT: A 420 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8514 (tt0) REVERT: A 696 MET cc_start: 0.8994 (ptp) cc_final: 0.8757 (ptt) REVERT: A 797 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6264 (ptp-170) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.0687 time to fit residues: 4.4128 Evaluate side-chains 45 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 574 VAL 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: 3.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.075226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.059927 restraints weight = 14961.063| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.83 r_work: 0.2747 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5833 Z= 0.140 Angle : 0.498 8.312 8110 Z= 0.282 Chirality : 0.037 0.169 925 Planarity : 0.003 0.030 835 Dihedral : 20.725 174.529 1433 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.54 % Allowed : 12.05 % Favored : 85.41 % 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: 2.26 (0.38), residues: 530 helix: 2.83 (0.31), residues: 268 sheet: 0.34 (0.49), residues: 95 loop : -0.01 (0.55), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 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 0.00286 / 0.14 ( 5833) covalent geometry : angle 0.49787 / 0.28 ( 8110) hydrogen bonds : bond 0.04644 / 3.20 ( 320) hydrogen bonds : angle 3.54698 / 2.55 ( 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 49 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.212 Fit side-chains REVERT: A 48 MET cc_start: 0.8714 (mpp) cc_final: 0.8046 (mpp) REVERT: A 202 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7205 (t80) REVERT: A 420 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8499 (tt0) REVERT: A 696 MET cc_start: 0.9011 (ptp) cc_final: 0.8676 (ptt) REVERT: A 714 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6103 (p0) REVERT: A 797 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6236 (ptp-170) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.0609 time to fit residues: 4.0012 Evaluate side-chains 46 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 637 LEU Chi-restraints excluded: chain A residue 714 ASN 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: 0.6980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.060229 restraints weight = 15121.443| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.84 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: 0.8679 moved from start: 0.0853 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= 0.134 Angle : 0.486 8.466 8110 Z= 0.275 Chirality : 0.037 0.157 925 Planarity : 0.003 0.039 835 Dihedral : 20.631 175.365 1433 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.17 % Allowed : 12.47 % Favored : 84.36 % 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: 2.32 (0.38), residues: 530 helix: 2.98 (0.31), residues: 267 sheet: 0.27 (0.48), residues: 95 loop : -0.06 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.009 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 0.00273 / 0.13 ( 5833) covalent geometry : angle 0.48630 / 0.27 ( 8110) hydrogen bonds : bond 0.04357 / 3.00 ( 320) hydrogen bonds : angle 3.42684 / 2.46 ( 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 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8703 (mpp) cc_final: 0.8017 (mpp) REVERT: A 99 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9126 (tt) REVERT: A 202 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7302 (t80) REVERT: A 420 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8494 (tt0) REVERT: A 696 MET cc_start: 0.8995 (ptp) cc_final: 0.8666 (ptt) REVERT: A 797 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6221 (ptm160) outliers start: 15 outliers final: 10 residues processed: 50 average time/residue: 0.0574 time to fit residues: 4.0794 Evaluate side-chains 49 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 797 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 0.0050 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.073757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.058198 restraints weight = 15381.619| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.88 r_work: 0.2706 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5833 Z= 0.240 Angle : 0.558 7.634 8110 Z= 0.307 Chirality : 0.040 0.194 925 Planarity : 0.004 0.031 835 Dihedral : 20.630 175.138 1433 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.59 % Allowed : 13.53 % 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: 2.20 (0.38), residues: 530 helix: 2.90 (0.31), residues: 267 sheet: 0.24 (0.48), residues: 102 loop : -0.20 (0.55), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.011 0.001 TYR A 22 PHE 0.014 0.002 PHE A 390 TRP 0.007 0.002 TRP A 229 HIS 0.006 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 ( 5833) covalent geometry : angle 0.55787 / 0.31 ( 8110) hydrogen bonds : bond 0.04775 / 3.31 ( 320) hydrogen bonds : angle 3.60568 / 2.58 ( 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 : 0.161 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8655 (mpp) cc_final: 0.7859 (mpp) REVERT: A 99 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9165 (tt) REVERT: A 202 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7232 (t80) REVERT: A 420 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8482 (tt0) REVERT: A 797 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6090 (ptp-170) outliers start: 17 outliers final: 11 residues processed: 50 average time/residue: 0.0596 time to fit residues: 4.1823 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 : 0.175 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 = 0.3240 r_free = 0.3240 target = 0.074997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.059606 restraints weight = 15043.887| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.82 r_work: 0.2735 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0993 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= 0.137 Angle : 0.497 8.493 8110 Z= 0.279 Chirality : 0.037 0.177 925 Planarity : 0.003 0.037 835 Dihedral : 20.669 174.809 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.38 % Allowed : 13.32 % 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: 2.30 (0.38), residues: 530 helix: 2.99 (0.31), residues: 267 sheet: 0.32 (0.48), residues: 100 loop : -0.17 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.010 0.001 TYR A 44 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 0.00281 / 0.14 ( 5833) covalent geometry : angle 0.49714 / 0.28 ( 8110) hydrogen bonds : bond 0.04449 / 3.08 ( 320) hydrogen bonds : angle 3.47155 / 2.50 ( 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 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8662 (mpp) cc_final: 0.7951 (mpp) REVERT: A 70 CYS cc_start: 0.9306 (t) cc_final: 0.8336 (p) REVERT: A 99 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9132 (tt) REVERT: A 202 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7279 (t80) REVERT: A 420 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8406 (tt0) REVERT: A 696 MET cc_start: 0.9012 (ptp) cc_final: 0.8751 (ptt) REVERT: A 714 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6183 (p0) REVERT: A 797 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6181 (ptm160) outliers start: 16 outliers final: 9 residues processed: 51 average time/residue: 0.0738 time to fit residues: 5.0022 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 : 0.190 ------------------------------------------------------------------------------- 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 714 ASN 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: 0.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.074916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059372 restraints weight = 15278.759| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.87 r_work: 0.2732 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1068 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= 0.156 Angle : 0.506 8.554 8110 Z= 0.281 Chirality : 0.037 0.174 925 Planarity : 0.003 0.035 835 Dihedral : 20.614 175.033 1433 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.96 % Allowed : 14.16 % 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: 2.30 (0.38), residues: 530 helix: 3.02 (0.31), residues: 267 sheet: 0.28 (0.47), residues: 100 loop : -0.22 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.009 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 0.00328 / 0.16 ( 5833) covalent geometry : angle 0.50590 / 0.28 ( 8110) hydrogen bonds : bond 0.04416 / 3.05 ( 320) hydrogen bonds : angle 3.46375 / 2.49 ( 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 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8655 (mpp) cc_final: 0.7949 (mpp) REVERT: A 70 CYS cc_start: 0.9305 (t) cc_final: 0.8353 (p) REVERT: A 99 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9134 (tt) REVERT: A 202 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7297 (t80) REVERT: A 420 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8418 (tt0) REVERT: A 696 MET cc_start: 0.9027 (ptp) cc_final: 0.8774 (ptt) REVERT: A 714 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6248 (p0) REVERT: A 797 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6089 (ptp-170) outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.0633 time to fit residues: 4.2948 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 : 0.190 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.076206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.060773 restraints weight = 14964.787| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.84 r_work: 0.2766 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5833 Z= 0.117 Angle : 0.482 8.830 8110 Z= 0.269 Chirality : 0.036 0.170 925 Planarity : 0.003 0.038 835 Dihedral : 20.573 175.080 1433 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.96 % Allowed : 14.16 % 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: 2.55 (0.38), residues: 530 helix: 3.18 (0.31), residues: 265 sheet: 0.33 (0.48), residues: 100 loop : 0.09 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.010 0.001 TYR A 44 PHE 0.008 0.001 PHE A 537 TRP 0.011 0.001 TRP A 229 HIS 0.002 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 5833) covalent geometry : angle 0.48172 / 0.27 ( 8110) hydrogen bonds : bond 0.04126 / 2.84 ( 320) hydrogen bonds : angle 3.33386 / 2.41 ( 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 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8677 (mpp) cc_final: 0.7959 (mpp) REVERT: A 99 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9101 (tt) REVERT: A 202 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7311 (t80) REVERT: A 420 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8426 (tt0) REVERT: A 696 MET cc_start: 0.9049 (ptp) cc_final: 0.8751 (ptp) REVERT: A 714 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6210 (p0) REVERT: A 797 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6112 (ptm160) outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 0.0726 time to fit residues: 5.0200 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 : 0.154 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.074140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.058682 restraints weight = 15116.571| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.82 r_work: 0.2719 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5833 Z= 0.215 Angle : 0.548 9.266 8110 Z= 0.300 Chirality : 0.039 0.185 925 Planarity : 0.004 0.038 835 Dihedral : 20.552 175.334 1433 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 15.01 % Favored : 82.03 % 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: 3.04 (0.31), residues: 267 sheet: 0.26 (0.48), residues: 100 loop : -0.26 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.010 0.001 TYR A 22 PHE 0.013 0.001 PHE A 390 TRP 0.007 0.001 TRP A 391 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 5833) covalent geometry : angle 0.54753 / 0.30 ( 8110) hydrogen bonds : bond 0.04531 / 3.13 ( 320) hydrogen bonds : angle 3.49149 / 2.52 ( 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 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8652 (mpp) cc_final: 0.7793 (mpp) REVERT: A 99 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9136 (tt) REVERT: A 202 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7333 (t80) REVERT: A 420 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8427 (tt0) REVERT: A 696 MET cc_start: 0.9037 (ptp) cc_final: 0.8807 (ptt) REVERT: A 797 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6037 (ptp-170) outliers start: 14 outliers final: 10 residues processed: 48 average time/residue: 0.0680 time to fit residues: 4.4786 Evaluate side-chains 49 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 797 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.074797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.059209 restraints weight = 15258.862| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.86 r_work: 0.2731 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1212 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= 0.163 Angle : 0.512 8.681 8110 Z= 0.284 Chirality : 0.037 0.177 925 Planarity : 0.004 0.034 835 Dihedral : 20.597 174.958 1433 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.75 % Allowed : 15.22 % Favored : 82.03 % 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: 2.33 (0.38), residues: 530 helix: 3.06 (0.31), residues: 267 sheet: 0.26 (0.48), residues: 100 loop : -0.21 (0.55), residues: 163 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 0.00347 / 0.16 ( 5833) covalent geometry : angle 0.51216 / 0.28 ( 8110) hydrogen bonds : bond 0.04376 / 3.03 ( 320) hydrogen bonds : angle 3.43305 / 2.48 ( 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 50 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8656 (mpp) cc_final: 0.7934 (mpp) REVERT: A 99 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9137 (tt) REVERT: A 202 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7279 (t80) REVERT: A 420 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8426 (tt0) REVERT: A 696 MET cc_start: 0.9046 (ptp) cc_final: 0.8826 (ptt) REVERT: A 797 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6173 (ptm160) outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.0792 time to fit residues: 5.1294 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 : 0.224 ------------------------------------------------------------------------------- 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 797 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.076057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.060577 restraints weight = 14958.179| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.82 r_work: 0.2765 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5833 Z= 0.119 Angle : 0.488 8.884 8110 Z= 0.272 Chirality : 0.036 0.186 925 Planarity : 0.003 0.039 835 Dihedral : 20.572 174.965 1433 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.75 % Allowed : 15.43 % Favored : 81.82 % 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: 2.58 (0.39), residues: 530 helix: 3.22 (0.31), residues: 265 sheet: 0.32 (0.48), residues: 100 loop : 0.06 (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 44 PHE 0.009 0.001 PHE A 390 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 0.00241 / 0.12 ( 5833) covalent geometry : angle 0.48755 / 0.27 ( 8110) hydrogen bonds : bond 0.04126 / 2.85 ( 320) hydrogen bonds : angle 3.34096 / 2.42 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1311.50 seconds wall clock time: 23 minutes 13.68 seconds (1393.68 seconds total)