Starting phenix.real_space_refine on Wed Sep 17 05:53:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcc_38239/09_2025/8xcc_38239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcc_38239/09_2025/8xcc_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_38239/09_2025/8xcc_38239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcc_38239/09_2025/8xcc_38239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xcc_38239/09_2025/8xcc_38239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcc_38239/09_2025/8xcc_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-2.0-5805/lib/python3.9/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: 1.70, per 1000 atoms: 0.30 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: 0.50 Conformation dependent library (CDL) restraints added in 282.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.73 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: 1.11 Time building geometry restraints manager: 0.66 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=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 1.516 1.508 0.008 8.90e-03 1.26e+04 7.50e-01 bond pdb=" C3' DG C 7 " pdb=" C2' DG C 7 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.36e-01 bond pdb=" O4' DT C 5 " pdb=" C1' DT C 5 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 7.13e-01 bond pdb=" O4' DT C 3 " pdb=" C1' DT C 3 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.95e-01 bond pdb=" CA ASP A 238 " pdb=" C ASP A 238 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.72e-02 3.38e+03 5.85e-01 ... (remaining 5828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 7930 1.70 - 3.41: 159 3.41 - 5.11: 16 5.11 - 6.82: 3 6.82 - 8.52: 2 Bond angle restraints: 8110 Sorted by residual: angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 109.81 115.82 -6.01 2.21e+00 2.05e-01 7.39e+00 angle pdb=" CA LEU A 516 " pdb=" CB LEU A 516 " pdb=" CG LEU A 516 " ideal model delta sigma weight residual 116.30 124.82 -8.52 3.50e+00 8.16e-02 5.93e+00 angle pdb=" N ILE A 481 " pdb=" CA ILE A 481 " pdb=" C ILE A 481 " ideal model delta sigma weight residual 111.90 110.09 1.81 8.10e-01 1.52e+00 4.97e+00 angle pdb=" CA LEU A 362 " pdb=" CB LEU A 362 " pdb=" CG LEU A 362 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" C THR A 514 " pdb=" N GLY A 515 " pdb=" CA GLY A 515 " ideal model delta sigma weight residual 121.03 118.03 3.00 1.51e+00 4.39e-01 3.94e+00 ... (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: 610 0.028 - 0.056: 213 0.056 - 0.084: 63 0.084 - 0.113: 30 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: 3.870 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.140 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 0.024 5833 Z= 0.170 Angle : 0.583 8.523 8110 Z= 0.317 Chirality : 0.036 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 aren 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 covalent geometry : bond 0.00358 ( 5833) covalent geometry : angle 0.58339 ( 8110) hydrogen bonds : bond 0.11207 ( 320) hydrogen bonds : angle 4.61979 ( 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: 0.8639 (ptt) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0837 time to fit residues: 4.2453 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 : 0.246 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 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: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.058566 restraints weight = 15233.206| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.84 r_work: 0.2714 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 5833 Z= 0.220 Angle : 0.572 7.758 8110 Z= 0.302 Chirality : 0.039 0.191 925 Planarity : 0.004 0.033 835 Dihedral : 20.592 173.764 1433 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.54 % Allowed : 12.26 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.38), residues: 530 helix: 2.70 (0.31), residues: 268 sheet: 0.34 (0.48), residues: 102 loop : -0.08 (0.56), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 615 TYR 0.010 0.001 TYR A 44 PHE 0.012 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 covalent geometry : bond 0.00484 ( 5833) covalent geometry : angle 0.57170 ( 8110) hydrogen bonds : bond 0.04708 ( 320) hydrogen bonds : angle 3.70374 ( 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: 12 poor density : 36 time to evaluate : 0.203 Fit side-chains REVERT: A 48 MET cc_start: 0.8701 (mpp) cc_final: 0.8097 (mpp) REVERT: A 70 CYS cc_start: 0.9301 (t) cc_final: 0.8336 (p) REVERT: A 202 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 420 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8489 (tt0) REVERT: A 696 MET cc_start: 0.9027 (ptp) cc_final: 0.8664 (ptt) REVERT: A 797 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6266 (ptm160) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.0787 time to fit residues: 4.9955 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 : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL 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 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: 0.9980 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.060114 restraints weight = 14933.336| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.82 r_work: 0.2749 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0858 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= 0.144 Angle : 0.518 8.059 8110 Z= 0.274 Chirality : 0.036 0.162 925 Planarity : 0.003 0.031 835 Dihedral : 20.461 174.114 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.75 % Allowed : 12.47 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.38), residues: 530 helix: 3.02 (0.31), residues: 265 sheet: 0.39 (0.49), residues: 95 loop : 0.20 (0.55), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 615 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 covalent geometry : bond 0.00309 ( 5833) covalent geometry : angle 0.51807 ( 8110) hydrogen bonds : bond 0.04175 ( 320) hydrogen bonds : angle 3.47222 ( 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 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8686 (mpp) cc_final: 0.8012 (mpp) REVERT: A 202 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 420 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8496 (tt0) REVERT: A 696 MET cc_start: 0.9003 (ptp) cc_final: 0.8682 (ptt) REVERT: A 797 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6212 (ptm160) outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 0.0744 time to fit residues: 4.9761 Evaluate side-chains 48 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL 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 512 ASP Chi-restraints excluded: chain A residue 545 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.061714 restraints weight = 15090.695| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.87 r_work: 0.2792 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.002 0.024 5833 Z= 0.116 Angle : 0.493 8.181 8110 Z= 0.259 Chirality : 0.036 0.168 925 Planarity : 0.003 0.037 835 Dihedral : 20.364 174.721 1433 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.75 % Allowed : 12.90 % 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 aren not related in a simple way. whole: 2.67 (0.38), residues: 530 helix: 3.28 (0.31), residues: 264 sheet: 0.40 (0.49), residues: 95 loop : 0.15 (0.54), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.009 0.001 TYR A 44 PHE 0.010 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 covalent geometry : bond 0.00242 ( 5833) covalent geometry : angle 0.49339 ( 8110) hydrogen bonds : bond 0.03769 ( 320) hydrogen bonds : angle 3.26587 ( 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 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8647 (mpp) cc_final: 0.7996 (mpp) REVERT: A 99 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9095 (tt) REVERT: A 202 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 420 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8488 (tt0) REVERT: A 696 MET cc_start: 0.9020 (ptp) cc_final: 0.8677 (ptt) REVERT: A 714 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6109 (p0) REVERT: A 797 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6087 (ptp-170) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.0710 time to fit residues: 4.8985 Evaluate side-chains 48 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.059428 restraints weight = 15264.122| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.90 r_work: 0.2736 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1166 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= 0.176 Angle : 0.531 8.848 8110 Z= 0.276 Chirality : 0.037 0.175 925 Planarity : 0.003 0.035 835 Dihedral : 20.408 174.666 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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 aren not related in a simple way. whole: 2.61 (0.38), residues: 530 helix: 3.21 (0.31), residues: 265 sheet: 0.46 (0.48), residues: 100 loop : 0.07 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.010 0.001 TYR A 22 PHE 0.009 0.001 PHE A 369 TRP 0.007 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5833) covalent geometry : angle 0.53108 ( 8110) hydrogen bonds : bond 0.04141 ( 320) hydrogen bonds : angle 3.37136 ( 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: 16 poor density : 38 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8632 (mpp) cc_final: 0.7895 (mpp) REVERT: A 70 CYS cc_start: 0.9278 (t) cc_final: 0.8328 (p) REVERT: A 99 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9128 (tt) REVERT: A 202 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 420 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8490 (tt0) REVERT: A 696 MET cc_start: 0.9027 (ptp) cc_final: 0.8588 (ptt) REVERT: A 797 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6128 (ptp-170) outliers start: 16 outliers final: 11 residues processed: 52 average time/residue: 0.0741 time to fit residues: 5.3139 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 : 0.199 ------------------------------------------------------------------------------- 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 382 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.059780 restraints weight = 15005.187| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.84 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: 0.8568 moved from start: 0.1252 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= 0.150 Angle : 0.515 8.290 8110 Z= 0.268 Chirality : 0.036 0.162 925 Planarity : 0.003 0.036 835 Dihedral : 20.408 174.350 1433 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.17 % Allowed : 13.95 % 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 aren not related in a simple way. whole: 2.63 (0.38), residues: 530 helix: 3.25 (0.31), residues: 265 sheet: 0.40 (0.47), residues: 100 loop : 0.08 (0.56), residues: 165 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 0.009 0.001 PHE A 390 TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5833) covalent geometry : angle 0.51510 ( 8110) hydrogen bonds : bond 0.04022 ( 320) hydrogen bonds : angle 3.33099 ( 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 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8642 (mpp) cc_final: 0.7792 (mpp) REVERT: A 70 CYS cc_start: 0.9260 (t) cc_final: 0.8322 (p) REVERT: A 99 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9116 (tt) REVERT: A 202 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7277 (t80) REVERT: A 420 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8490 (tt0) REVERT: A 714 ASN cc_start: 0.7233 (OUTLIER) cc_final: 0.6118 (p0) REVERT: A 797 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6142 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 48 average time/residue: 0.0784 time to fit residues: 5.2046 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 : 0.207 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.058129 restraints weight = 15417.948| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.92 r_work: 0.2706 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5833 Z= 0.213 Angle : 0.551 8.561 8110 Z= 0.287 Chirality : 0.038 0.189 925 Planarity : 0.004 0.035 835 Dihedral : 20.455 173.823 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.44 % Allowed : 13.53 % 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 aren not related in a simple way. whole: 2.32 (0.38), residues: 530 helix: 3.06 (0.31), residues: 267 sheet: 0.23 (0.47), residues: 102 loop : -0.21 (0.55), residues: 161 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 0.010 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 covalent geometry : bond 0.00471 ( 5833) covalent geometry : angle 0.55096 ( 8110) hydrogen bonds : bond 0.04345 ( 320) hydrogen bonds : angle 3.43100 ( 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 57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8607 (mpp) cc_final: 0.7787 (mpp) REVERT: A 70 CYS cc_start: 0.9299 (t) cc_final: 0.8366 (p) REVERT: A 99 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9161 (tt) REVERT: A 202 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7402 (t80) REVERT: A 420 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8452 (tt0) REVERT: A 696 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8776 (ptt) REVERT: A 714 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6184 (p0) REVERT: A 797 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6223 (ptm160) outliers start: 21 outliers final: 12 residues processed: 54 average time/residue: 0.0894 time to fit residues: 6.3019 Evaluate side-chains 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 377 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.060266 restraints weight = 15018.398| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.84 r_work: 0.2759 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1427 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= 0.125 Angle : 0.504 8.363 8110 Z= 0.263 Chirality : 0.035 0.151 925 Planarity : 0.003 0.036 835 Dihedral : 20.388 173.848 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.38 % Allowed : 14.16 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.39), residues: 530 helix: 3.31 (0.31), residues: 265 sheet: 0.39 (0.48), residues: 100 loop : 0.08 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.008 0.001 TYR A 22 PHE 0.010 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 covalent geometry : bond 0.00265 ( 5833) covalent geometry : angle 0.50424 ( 8110) hydrogen bonds : bond 0.03889 ( 320) hydrogen bonds : angle 3.27246 ( 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 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8629 (mpp) cc_final: 0.7939 (mpp) REVERT: A 99 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9094 (tt) REVERT: A 182 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.5135 (pp) REVERT: A 202 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7314 (t80) REVERT: A 420 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8458 (tt0) REVERT: A 696 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8805 (ptt) REVERT: A 714 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6079 (p0) REVERT: A 797 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6186 (ptp-170) outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 0.0780 time to fit residues: 5.5153 Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 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 382 LEU 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 696 MET 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: 3.9990 chunk 55 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.0020 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.060755 restraints weight = 15071.365| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.86 r_work: 0.2767 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5833 Z= 0.119 Angle : 0.511 8.588 8110 Z= 0.264 Chirality : 0.035 0.173 925 Planarity : 0.003 0.041 835 Dihedral : 20.359 174.180 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.59 % Allowed : 14.59 % 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 aren not related in a simple way. whole: 2.64 (0.39), residues: 530 helix: 3.25 (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 0.012 0.001 TYR A 597 PHE 0.008 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 covalent geometry : bond 0.00252 ( 5833) covalent geometry : angle 0.51131 ( 8110) hydrogen bonds : bond 0.03823 ( 320) hydrogen bonds : angle 3.24131 ( 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 : 0.211 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8619 (mpp) cc_final: 0.7786 (mpp) REVERT: A 99 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9087 (tt) REVERT: A 190 MET cc_start: 0.9033 (tpp) cc_final: 0.8812 (tpp) REVERT: A 202 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7301 (t80) REVERT: A 420 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8469 (tt0) REVERT: A 696 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8773 (ptp) REVERT: A 714 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6106 (p0) REVERT: A 797 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6286 (ptm160) outliers start: 17 outliers final: 10 residues processed: 50 average time/residue: 0.0768 time to fit residues: 5.2819 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 : 0.207 ------------------------------------------------------------------------------- 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 202 PHE Chi-restraints excluded: chain A residue 382 LEU 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 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: 0.8980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.060100 restraints weight = 15254.088| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.85 r_work: 0.2753 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5833 Z= 0.145 Angle : 0.517 8.477 8110 Z= 0.267 Chirality : 0.036 0.154 925 Planarity : 0.004 0.038 835 Dihedral : 20.348 174.445 1433 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.17 % Allowed : 14.80 % 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 aren not related in a simple way. whole: 2.65 (0.39), residues: 530 helix: 3.30 (0.31), residues: 264 sheet: 0.34 (0.48), residues: 100 loop : 0.11 (0.57), residues: 166 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 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5833) covalent geometry : angle 0.51651 ( 8110) hydrogen bonds : bond 0.03921 ( 320) hydrogen bonds : angle 3.26998 ( 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 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8623 (mpp) cc_final: 0.7812 (mpp) REVERT: A 99 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9123 (tt) REVERT: A 190 MET cc_start: 0.9056 (tpp) cc_final: 0.8827 (tpp) REVERT: A 202 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7296 (t80) REVERT: A 420 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8472 (tt0) REVERT: A 696 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8843 (ptt) REVERT: A 714 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6120 (p0) REVERT: A 797 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6282 (ptm160) outliers start: 15 outliers final: 10 residues processed: 48 average time/residue: 0.0774 time to fit residues: 5.1032 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 202 PHE Chi-restraints excluded: chain A residue 382 LEU 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 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: 0.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.060279 restraints weight = 15005.217| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.83 r_work: 0.2757 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5833 Z= 0.134 Angle : 0.516 8.545 8110 Z= 0.267 Chirality : 0.036 0.165 925 Planarity : 0.003 0.040 835 Dihedral : 20.344 174.467 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.17 % Allowed : 14.80 % 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 aren not related in a simple way. whole: 2.64 (0.39), residues: 530 helix: 3.30 (0.31), residues: 264 sheet: 0.31 (0.48), residues: 100 loop : 0.11 (0.57), residues: 166 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 0.008 0.001 PHE A 390 TRP 0.008 0.001 TRP A 229 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5833) covalent geometry : angle 0.51555 ( 8110) hydrogen bonds : bond 0.03896 ( 320) hydrogen bonds : angle 3.25134 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.30 seconds wall clock time: 24 minutes 47.48 seconds (1487.48 seconds total)