Starting phenix.real_space_refine on Sat May 10 00:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrv_37791/05_2025/8wrv_37791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrv_37791/05_2025/8wrv_37791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrv_37791/05_2025/8wrv_37791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrv_37791/05_2025/8wrv_37791.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrv_37791/05_2025/8wrv_37791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrv_37791/05_2025/8wrv_37791.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 92 5.49 5 S 11 5.16 5 C 2479 2.51 5 N 813 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4471 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2537 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 3 Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1188 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 6, 'rna3p': 49} Time building chain proxies: 4.48, per 1000 atoms: 1.00 Number of scatterers: 4471 At special positions: 0 Unit cell: (60.72, 77.22, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 92 15.00 O 1076 8.00 N 813 7.00 C 2479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 325.3 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 37.3% alpha, 20.9% beta 24 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.756A pdb=" N HIS A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.506A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 4.118A pdb=" N SER A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.534A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.597A pdb=" N LEU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.552A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 237 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.998A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.852A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 428 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 434 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 426 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 436 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 424 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP A 438 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 422 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 417 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 407 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 394 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.817A pdb=" N PHE A 369 " --> pdb=" O ALA A 384 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1019 1.33 - 1.45: 1438 1.45 - 1.57: 2091 1.57 - 1.69: 181 1.69 - 1.81: 16 Bond restraints: 4745 Sorted by residual: bond pdb=" O3' A B -10 " pdb=" P G B -9 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.31e+01 bond pdb=" C SER A 345 " pdb=" N PRO A 346 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.31e-02 5.83e+03 8.06e+00 bond pdb=" O3' C B 14 " pdb=" P C B 15 " ideal model delta sigma weight residual 1.607 1.649 -0.042 1.50e-02 4.44e+03 7.67e+00 bond pdb=" O3' G B -36 " pdb=" P U B -35 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.50e-02 4.44e+03 7.11e+00 bond pdb=" O3' U B -35 " pdb=" P G B -34 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.35e+00 ... (remaining 4740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 6625 2.05 - 4.11: 178 4.11 - 6.16: 20 6.16 - 8.21: 2 8.21 - 10.27: 1 Bond angle restraints: 6826 Sorted by residual: angle pdb=" O3' C B -6 " pdb=" C3' C B -6 " pdb=" C2' C B -6 " ideal model delta sigma weight residual 113.70 107.79 5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" O2' U B -5 " pdb=" C2' U B -5 " pdb=" C1' U B -5 " ideal model delta sigma weight residual 111.80 106.16 5.64 1.50e+00 4.44e-01 1.41e+01 angle pdb=" C4' A B -7 " pdb=" C3' A B -7 " pdb=" O3' A B -7 " ideal model delta sigma weight residual 113.00 107.73 5.27 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N VAL A 395 " pdb=" CA VAL A 395 " pdb=" C VAL A 395 " ideal model delta sigma weight residual 108.46 113.41 -4.95 1.49e+00 4.50e-01 1.10e+01 angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 109.81 117.06 -7.25 2.21e+00 2.05e-01 1.08e+01 ... (remaining 6821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 2533 35.81 - 71.62: 278 71.62 - 107.43: 26 107.43 - 143.24: 2 143.24 - 179.05: 3 Dihedral angle restraints: 2842 sinusoidal: 1921 harmonic: 921 Sorted by residual: dihedral pdb=" O4' C B -6 " pdb=" C1' C B -6 " pdb=" N1 C B -6 " pdb=" C2 C B -6 " ideal model delta sinusoidal sigma weight residual 200.00 50.44 149.56 1 1.50e+01 4.44e-03 7.95e+01 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 200.00 53.31 146.69 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' U B -5 " pdb=" C1' U B -5 " pdb=" N1 U B -5 " pdb=" C2 U B -5 " ideal model delta sinusoidal sigma weight residual -128.00 51.05 -179.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 2839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 714 0.070 - 0.141: 62 0.141 - 0.211: 21 0.211 - 0.282: 1 0.282 - 0.352: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ARG A 41 " pdb=" N ARG A 41 " pdb=" C ARG A 41 " pdb=" CB ARG A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' G B -36 " pdb=" C3' G B -36 " pdb=" O2' G B -36 " pdb=" C1' G B -36 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 797 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 92 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 93 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 205 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C SER A 205 " -0.031 2.00e-02 2.50e+03 pdb=" O SER A 205 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 202 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 203 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.023 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1207 2.82 - 3.34: 3916 3.34 - 3.86: 8362 3.86 - 4.38: 9413 4.38 - 4.90: 13668 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" NH2 ARG A 47 " pdb=" OE2 GLU A 53 " model vdw 2.301 3.120 nonbonded pdb=" O2' C B -30 " pdb=" OP2 U B -29 " model vdw 2.351 3.040 nonbonded pdb=" O2 U B -27 " pdb=" N2 G B -12 " model vdw 2.358 2.496 nonbonded pdb=" OG1 THR A 338 " pdb=" OP1 A B 5 " model vdw 2.368 3.040 nonbonded pdb=" OP1 DA C 2 " pdb=" NZ LYS A 422 " model vdw 2.397 3.120 ... (remaining 36561 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 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 0.054 4745 Z= 0.243 Angle : 0.736 10.266 6826 Z= 0.435 Chirality : 0.050 0.352 800 Planarity : 0.005 0.051 547 Dihedral : 23.712 179.047 2244 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.85 % Allowed : 0.74 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.47), residues: 308 helix: -0.50 (0.48), residues: 109 sheet: -1.31 (0.54), residues: 77 loop : -1.51 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 229 HIS 0.002 0.001 HIS A 26 PHE 0.021 0.001 PHE A 83 TYR 0.010 0.001 TYR A 22 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.16282 ( 165) hydrogen bonds : angle 7.07049 ( 412) covalent geometry : bond 0.00407 ( 4745) covalent geometry : angle 0.73630 ( 6826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.319 Fit side-chains REVERT: A 102 GLU cc_start: 0.7126 (pm20) cc_final: 0.6910 (pm20) REVERT: A 437 ILE cc_start: 0.8140 (mm) cc_final: 0.7937 (mm) outliers start: 5 outliers final: 0 residues processed: 62 average time/residue: 0.2910 time to fit residues: 20.8311 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.2254 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.187090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150055 restraints weight = 6611.972| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.52 r_work: 0.3727 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4745 Z= 0.135 Angle : 0.596 7.218 6826 Z= 0.316 Chirality : 0.036 0.232 800 Planarity : 0.005 0.050 547 Dihedral : 25.301 176.098 1619 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.48), residues: 308 helix: 0.76 (0.48), residues: 112 sheet: -0.99 (0.54), residues: 76 loop : -1.37 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 229 HIS 0.001 0.000 HIS A 26 PHE 0.011 0.001 PHE A 169 TYR 0.007 0.001 TYR A 439 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 165) hydrogen bonds : angle 4.04149 ( 412) covalent geometry : bond 0.00269 ( 4745) covalent geometry : angle 0.59564 ( 6826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.326 Fit side-chains REVERT: A 20 ASP cc_start: 0.7098 (m-30) cc_final: 0.6710 (t0) REVERT: A 96 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7774 (mmm-85) REVERT: A 102 GLU cc_start: 0.7562 (pm20) cc_final: 0.7354 (pm20) REVERT: A 438 ASP cc_start: 0.7141 (m-30) cc_final: 0.6905 (m-30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2329 time to fit residues: 13.3903 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 21 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.182228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146024 restraints weight = 6515.497| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.51 r_work: 0.3650 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4745 Z= 0.172 Angle : 0.609 7.302 6826 Z= 0.322 Chirality : 0.037 0.225 800 Planarity : 0.005 0.051 547 Dihedral : 25.343 178.564 1619 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.48), residues: 308 helix: 1.06 (0.49), residues: 112 sheet: -0.97 (0.57), residues: 75 loop : -1.52 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 229 HIS 0.003 0.001 HIS A 26 PHE 0.013 0.001 PHE A 369 TYR 0.009 0.001 TYR A 22 ARG 0.004 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 165) hydrogen bonds : angle 3.85462 ( 412) covalent geometry : bond 0.00362 ( 4745) covalent geometry : angle 0.60872 ( 6826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.326 Fit side-chains REVERT: A 96 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7806 (mmm-85) REVERT: A 102 GLU cc_start: 0.7588 (pm20) cc_final: 0.7339 (pm20) REVERT: A 416 ARG cc_start: 0.7970 (tpt170) cc_final: 0.7589 (tpt90) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.2527 time to fit residues: 14.3377 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.181181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145157 restraints weight = 6572.395| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.54 r_work: 0.3640 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4745 Z= 0.194 Angle : 0.632 6.934 6826 Z= 0.334 Chirality : 0.039 0.234 800 Planarity : 0.005 0.051 547 Dihedral : 25.437 178.403 1619 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.74 % Allowed : 12.59 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.49), residues: 308 helix: 1.13 (0.49), residues: 113 sheet: -1.08 (0.57), residues: 75 loop : -1.55 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 229 HIS 0.004 0.001 HIS A 26 PHE 0.014 0.002 PHE A 169 TYR 0.011 0.002 TYR A 22 ARG 0.003 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 165) hydrogen bonds : angle 3.82486 ( 412) covalent geometry : bond 0.00417 ( 4745) covalent geometry : angle 0.63235 ( 6826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.362 Fit side-chains REVERT: A 102 GLU cc_start: 0.7666 (pm20) cc_final: 0.7363 (pm20) REVERT: A 185 ASP cc_start: 0.7202 (t0) cc_final: 0.6843 (t0) REVERT: A 416 ARG cc_start: 0.8010 (tpt170) cc_final: 0.7769 (tpt90) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.2535 time to fit residues: 15.1555 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 17 optimal weight: 0.5980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.182628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146370 restraints weight = 6651.560| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.54 r_work: 0.3653 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4745 Z= 0.160 Angle : 0.606 7.905 6826 Z= 0.317 Chirality : 0.037 0.209 800 Planarity : 0.005 0.048 547 Dihedral : 25.222 178.797 1619 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.22 % Allowed : 12.22 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.49), residues: 308 helix: 1.30 (0.50), residues: 113 sheet: -1.26 (0.55), residues: 80 loop : -1.21 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 PHE 0.014 0.001 PHE A 169 TYR 0.009 0.001 TYR A 22 ARG 0.006 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 165) hydrogen bonds : angle 3.71417 ( 412) covalent geometry : bond 0.00338 ( 4745) covalent geometry : angle 0.60598 ( 6826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.506 Fit side-chains REVERT: A 102 GLU cc_start: 0.7596 (pm20) cc_final: 0.7325 (pm20) REVERT: A 129 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7578 (ttmm) REVERT: A 179 ARG cc_start: 0.7248 (mpp80) cc_final: 0.6841 (mtm-85) REVERT: A 416 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7683 (tpt170) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.2761 time to fit residues: 16.5607 Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0370 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.183104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.146889 restraints weight = 6572.142| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.52 r_work: 0.3657 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4745 Z= 0.142 Angle : 0.594 7.377 6826 Z= 0.313 Chirality : 0.037 0.209 800 Planarity : 0.005 0.057 547 Dihedral : 25.206 179.136 1619 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.22 % Allowed : 13.33 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.49), residues: 308 helix: 1.42 (0.50), residues: 113 sheet: -1.27 (0.55), residues: 80 loop : -1.12 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.002 0.001 HIS A 26 PHE 0.009 0.001 PHE A 369 TYR 0.007 0.001 TYR A 44 ARG 0.004 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 165) hydrogen bonds : angle 3.63819 ( 412) covalent geometry : bond 0.00295 ( 4745) covalent geometry : angle 0.59449 ( 6826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.353 Fit side-chains REVERT: A 102 GLU cc_start: 0.7606 (pm20) cc_final: 0.7338 (pm20) REVERT: A 129 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7568 (ttmm) REVERT: A 179 ARG cc_start: 0.7243 (mpp80) cc_final: 0.6811 (mtm-85) REVERT: A 190 MET cc_start: 0.7848 (tpp) cc_final: 0.7587 (tpt) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.2132 time to fit residues: 13.0678 Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.180111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143516 restraints weight = 6590.381| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.52 r_work: 0.3613 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4745 Z= 0.231 Angle : 0.668 9.355 6826 Z= 0.349 Chirality : 0.041 0.198 800 Planarity : 0.006 0.060 547 Dihedral : 25.259 177.384 1619 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.96 % Allowed : 13.33 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.49), residues: 308 helix: 1.10 (0.50), residues: 114 sheet: -0.99 (0.57), residues: 76 loop : -1.56 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 229 HIS 0.005 0.002 HIS A 26 PHE 0.012 0.002 PHE A 369 TYR 0.012 0.002 TYR A 22 ARG 0.006 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 165) hydrogen bonds : angle 3.87758 ( 412) covalent geometry : bond 0.00496 ( 4745) covalent geometry : angle 0.66823 ( 6826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.324 Fit side-chains REVERT: A 102 GLU cc_start: 0.7643 (pm20) cc_final: 0.7367 (pm20) REVERT: A 129 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7568 (ttmm) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.2417 time to fit residues: 15.7484 Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 0.0060 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.181537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145186 restraints weight = 6505.272| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.51 r_work: 0.3637 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4745 Z= 0.165 Angle : 0.638 8.634 6826 Z= 0.334 Chirality : 0.039 0.197 800 Planarity : 0.005 0.064 547 Dihedral : 25.220 178.015 1619 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.85 % Allowed : 14.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.49), residues: 308 helix: 1.18 (0.49), residues: 114 sheet: -1.15 (0.57), residues: 78 loop : -1.40 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 229 HIS 0.002 0.001 HIS A 26 PHE 0.009 0.001 PHE A 369 TYR 0.009 0.001 TYR A 22 ARG 0.007 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 165) hydrogen bonds : angle 3.77588 ( 412) covalent geometry : bond 0.00348 ( 4745) covalent geometry : angle 0.63780 ( 6826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.352 Fit side-chains REVERT: A 102 GLU cc_start: 0.7642 (pm20) cc_final: 0.7373 (pm20) REVERT: A 129 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7432 (ttmm) REVERT: A 179 ARG cc_start: 0.7243 (mpp80) cc_final: 0.6818 (mtm-85) REVERT: A 190 MET cc_start: 0.7844 (tpp) cc_final: 0.7599 (tpt) REVERT: A 362 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7431 (tt) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.2246 time to fit residues: 14.2965 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.0020 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5026 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.181435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145078 restraints weight = 6587.648| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.52 r_work: 0.3632 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4745 Z= 0.177 Angle : 0.636 8.440 6826 Z= 0.332 Chirality : 0.039 0.198 800 Planarity : 0.005 0.062 547 Dihedral : 25.214 177.920 1619 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.85 % Allowed : 14.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.49), residues: 308 helix: 1.20 (0.49), residues: 113 sheet: -0.98 (0.58), residues: 76 loop : -1.41 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 229 HIS 0.003 0.001 HIS A 89 PHE 0.010 0.001 PHE A 369 TYR 0.010 0.001 TYR A 22 ARG 0.007 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 165) hydrogen bonds : angle 3.78883 ( 412) covalent geometry : bond 0.00376 ( 4745) covalent geometry : angle 0.63561 ( 6826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.333 Fit side-chains REVERT: A 102 GLU cc_start: 0.7644 (pm20) cc_final: 0.7422 (pm20) REVERT: A 129 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7506 (ttmm) REVERT: A 179 ARG cc_start: 0.7252 (mpp80) cc_final: 0.6826 (mtm-85) REVERT: A 190 MET cc_start: 0.7844 (tpp) cc_final: 0.7594 (tpt) REVERT: A 362 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7467 (tt) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.2398 time to fit residues: 15.4887 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.181120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.144792 restraints weight = 6524.812| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.51 r_work: 0.3626 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4745 Z= 0.205 Angle : 0.646 8.145 6826 Z= 0.337 Chirality : 0.040 0.199 800 Planarity : 0.006 0.063 547 Dihedral : 25.215 177.440 1619 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.48 % Allowed : 15.56 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.49), residues: 308 helix: 1.20 (0.50), residues: 113 sheet: -0.97 (0.59), residues: 76 loop : -1.42 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 PHE 0.011 0.002 PHE A 436 TYR 0.011 0.002 TYR A 22 ARG 0.007 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 165) hydrogen bonds : angle 3.82352 ( 412) covalent geometry : bond 0.00438 ( 4745) covalent geometry : angle 0.64571 ( 6826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.364 Fit side-chains REVERT: A 102 GLU cc_start: 0.7651 (pm20) cc_final: 0.7422 (pm20) REVERT: A 129 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7512 (ttmm) REVERT: A 179 ARG cc_start: 0.7248 (mpp80) cc_final: 0.6804 (mtm-85) REVERT: A 190 MET cc_start: 0.7841 (tpp) cc_final: 0.7581 (tpt) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.2370 time to fit residues: 14.4969 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.179656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143175 restraints weight = 6437.289| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.49 r_work: 0.3606 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 4745 Z= 0.256 Angle : 0.689 8.066 6826 Z= 0.359 Chirality : 0.042 0.202 800 Planarity : 0.006 0.064 547 Dihedral : 25.271 176.270 1619 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.48 % Allowed : 15.56 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.49), residues: 308 helix: 0.99 (0.49), residues: 112 sheet: -1.05 (0.60), residues: 76 loop : -1.56 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 229 HIS 0.006 0.002 HIS A 26 PHE 0.014 0.002 PHE A 436 TYR 0.013 0.002 TYR A 22 ARG 0.007 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 165) hydrogen bonds : angle 3.99752 ( 412) covalent geometry : bond 0.00559 ( 4745) covalent geometry : angle 0.68864 ( 6826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.88 seconds wall clock time: 52 minutes 55.58 seconds (3175.58 seconds total)