Starting phenix.real_space_refine on Mon Feb 10 23:57:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq0_33387/02_2025/7xq0_33387_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq0_33387/02_2025/7xq0_33387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xq0_33387/02_2025/7xq0_33387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq0_33387/02_2025/7xq0_33387.map" model { file = "/net/cci-nas-00/data/ceres_data/7xq0_33387/02_2025/7xq0_33387_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq0_33387/02_2025/7xq0_33387_neut.cif" } resolution = 3.0 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= 0.000 sd= 0.004 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 4 5.49 5 S 10 5.16 5 C 2189 2.51 5 N 553 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3320 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3232 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Classifications: {'RNA': 2} Link IDs: {'rna3p': 1} Chain breaks: 1 Time building chain proxies: 2.87, per 1000 atoms: 0.86 Number of scatterers: 3320 At special positions: 0 Unit cell: (78, 75, 67, 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 10 16.00 P 4 15.00 O 564 8.00 N 553 7.00 C 2189 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: 0.91 Conformation dependent library (CDL) restraints added in 414.4 milliseconds 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.621A pdb=" N TRP A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.923A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.879A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.531A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.582A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.414A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.686A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.712A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.540A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 4.142A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.797A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 removed outlier: 4.070A pdb=" N ALA A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.586A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.682A pdb=" N CYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 392 through 418 removed outlier: 3.765A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.962A pdb=" N ILE A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 973 1.34 - 1.45: 637 1.45 - 1.57: 1781 1.57 - 1.69: 12 1.69 - 1.80: 18 Bond restraints: 3421 Sorted by residual: bond pdb="C1'1 2BA A 601 " pdb="C2'1 2BA A 601 " ideal model delta sigma weight residual 1.532 1.294 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb="C1'1 2BA A 602 " pdb="C2'1 2BA A 602 " ideal model delta sigma weight residual 1.532 1.297 0.235 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' 2BA A 601 " pdb=" C2' 2BA A 601 " ideal model delta sigma weight residual 1.541 1.317 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1' 2BA A 602 " pdb=" C2' 2BA A 602 " ideal model delta sigma weight residual 1.541 1.318 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb="C1'1 2BA A 601 " pdb="O4'1 2BA A 601 " ideal model delta sigma weight residual 1.408 1.617 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 3416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 4576 3.31 - 6.62: 67 6.62 - 9.93: 22 9.93 - 13.24: 10 13.24 - 16.55: 6 Bond angle restraints: 4681 Sorted by residual: angle pdb=" CA VAL A 380 " pdb=" C VAL A 380 " pdb=" N PRO A 381 " ideal model delta sigma weight residual 120.83 116.29 4.54 6.10e-01 2.69e+00 5.53e+01 angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 112.23 105.18 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" O1P 2BA A 601 " pdb=" P 2BA A 601 " pdb=" O2P 2BA A 601 " ideal model delta sigma weight residual 121.18 104.63 16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1P 2BA A 602 " pdb=" P 2BA A 602 " pdb=" O2P 2BA A 602 " ideal model delta sigma weight residual 121.18 104.64 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb="O1P1 2BA A 602 " pdb=" P1 2BA A 602 " pdb="O2P1 2BA A 602 " ideal model delta sigma weight residual 122.22 106.86 15.36 3.00e+00 1.11e-01 2.62e+01 ... (remaining 4676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1870 17.70 - 35.39: 137 35.39 - 53.09: 24 53.09 - 70.79: 3 70.79 - 88.48: 3 Dihedral angle restraints: 2037 sinusoidal: 854 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP A 363 " pdb=" C TRP A 363 " pdb=" N LEU A 364 " pdb=" CA LEU A 364 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.099: 514 0.099 - 0.198: 23 0.198 - 0.297: 3 0.297 - 0.396: 0 0.396 - 0.494: 2 Chirality restraints: 542 Sorted by residual: chirality pdb=" C2' 2BA A 602 " pdb=" C1' 2BA A 602 " pdb=" C3' 2BA A 602 " pdb=" O2' 2BA A 602 " both_signs ideal model delta sigma weight residual False -2.80 -2.31 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C2' 2BA A 601 " pdb=" C1' 2BA A 601 " pdb=" C3' 2BA A 601 " pdb=" O2' 2BA A 601 " both_signs ideal model delta sigma weight residual False -2.80 -2.34 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb="C2'1 2BA A 602 " pdb="C1'1 2BA A 602 " pdb="C3'1 2BA A 602 " pdb="O2'1 2BA A 602 " both_signs ideal model delta sigma weight residual False -2.67 -2.39 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 539 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 71 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C VAL A 71 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 71 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO A 82 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 70 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.031 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 742 2.77 - 3.30: 3009 3.30 - 3.83: 5785 3.83 - 4.37: 7298 4.37 - 4.90: 11921 Nonbonded interactions: 28755 Sorted by model distance: nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.232 3.040 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.258 3.040 nonbonded pdb=" O1P 2BA A 601 " pdb=" N6 2BA A 602 " model vdw 2.328 3.120 nonbonded pdb=" O ARG A 61 " pdb=" OG1 THR A 65 " model vdw 2.336 3.040 nonbonded pdb=" OG SER A 392 " pdb=" OE1 GLU A 394 " model vdw 2.339 3.040 ... (remaining 28750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.014 0.238 3421 Z= 0.723 Angle : 1.263 16.547 4681 Z= 0.569 Chirality : 0.057 0.494 542 Planarity : 0.006 0.057 552 Dihedral : 13.005 88.484 1277 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.86 % Allowed : 8.36 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.72 (0.21), residues: 398 helix: -4.46 (0.12), residues: 313 sheet: None (None), residues: 0 loop : -3.02 (0.49), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.011 0.001 PHE A 37 TYR 0.009 0.002 TYR A 76 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.376 Fit side-chains REVERT: A 26 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7168 (mmp-170) REVERT: A 62 GLU cc_start: 0.7399 (pp20) cc_final: 0.6862 (tm-30) REVERT: A 122 MET cc_start: 0.8531 (tmm) cc_final: 0.8278 (ttp) REVERT: A 333 ARG cc_start: 0.7603 (tmt170) cc_final: 0.7023 (tpt-90) REVERT: A 416 PHE cc_start: 0.8211 (t80) cc_final: 0.7976 (t80) REVERT: A 451 MET cc_start: 0.6313 (mmt) cc_final: 0.6057 (mmt) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.9439 time to fit residues: 55.0062 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 266 GLN A 293 ASN A 431 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092482 restraints weight = 3919.660| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.83 r_work: 0.2888 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3421 Z= 0.203 Angle : 0.582 6.014 4681 Z= 0.303 Chirality : 0.038 0.120 542 Planarity : 0.005 0.034 552 Dihedral : 5.992 23.606 574 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.88 % Allowed : 11.53 % Favored : 85.59 % 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: -3.03 (0.33), residues: 398 helix: -1.76 (0.23), residues: 314 sheet: None (None), residues: 0 loop : -2.12 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.008 0.001 PHE A 400 TYR 0.009 0.001 TYR A 35 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.327 Fit side-chains REVERT: A 26 ARG cc_start: 0.7470 (mtp85) cc_final: 0.6613 (mmp-170) REVERT: A 62 GLU cc_start: 0.7798 (pp20) cc_final: 0.6831 (pm20) REVERT: A 333 ARG cc_start: 0.7599 (tmt170) cc_final: 0.7021 (tpt-90) REVERT: A 416 PHE cc_start: 0.8561 (t80) cc_final: 0.8295 (t80) REVERT: A 451 MET cc_start: 0.6834 (mmt) cc_final: 0.6478 (mpp) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.6414 time to fit residues: 38.6488 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.109592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.091734 restraints weight = 3812.579| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.82 r_work: 0.2871 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3421 Z= 0.197 Angle : 0.542 7.891 4681 Z= 0.270 Chirality : 0.038 0.114 542 Planarity : 0.004 0.028 552 Dihedral : 5.632 23.198 574 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.88 % Allowed : 13.54 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.39), residues: 398 helix: -0.18 (0.27), residues: 319 sheet: None (None), residues: 0 loop : -2.01 (0.61), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.009 0.001 PHE A 125 TYR 0.009 0.001 TYR A 438 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.390 Fit side-chains REVERT: A 26 ARG cc_start: 0.7369 (mtp85) cc_final: 0.6480 (mmp-170) REVERT: A 62 GLU cc_start: 0.7882 (pp20) cc_final: 0.7404 (pm20) REVERT: A 333 ARG cc_start: 0.7471 (tmt170) cc_final: 0.6904 (tpt-90) REVERT: A 416 PHE cc_start: 0.8518 (t80) cc_final: 0.8137 (t80) REVERT: A 451 MET cc_start: 0.6783 (mmt) cc_final: 0.6513 (mpp) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.7259 time to fit residues: 38.3082 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.109892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092500 restraints weight = 3901.126| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.80 r_work: 0.2862 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3421 Z= 0.192 Angle : 0.517 8.381 4681 Z= 0.259 Chirality : 0.038 0.128 542 Planarity : 0.003 0.026 552 Dihedral : 5.525 23.980 574 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.17 % Allowed : 13.83 % Favored : 83.00 % 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: 0.10 (0.41), residues: 398 helix: 0.59 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.80 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.014 0.001 PHE A 84 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.368 Fit side-chains REVERT: A 26 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6361 (mmp-170) REVERT: A 62 GLU cc_start: 0.7823 (pp20) cc_final: 0.6827 (pm20) REVERT: A 333 ARG cc_start: 0.7428 (tmt170) cc_final: 0.6869 (tpt-90) REVERT: A 416 PHE cc_start: 0.8505 (t80) cc_final: 0.8169 (t80) REVERT: A 451 MET cc_start: 0.6731 (mmt) cc_final: 0.6531 (mpp) outliers start: 11 outliers final: 5 residues processed: 48 average time/residue: 0.7550 time to fit residues: 38.3134 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.109705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.092016 restraints weight = 3901.306| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.85 r_work: 0.2858 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3421 Z= 0.196 Angle : 0.513 8.773 4681 Z= 0.256 Chirality : 0.039 0.169 542 Planarity : 0.003 0.027 552 Dihedral : 5.525 24.536 574 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.32 % Allowed : 14.99 % Favored : 80.69 % 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 (0.42), residues: 398 helix: 0.96 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.72 (0.61), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.008 0.001 PHE A 372 TYR 0.010 0.001 TYR A 438 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.320 Fit side-chains REVERT: A 26 ARG cc_start: 0.7381 (mtp85) cc_final: 0.6472 (mmp-170) REVERT: A 62 GLU cc_start: 0.7862 (pp20) cc_final: 0.6900 (pm20) REVERT: A 114 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.7111 (m-70) REVERT: A 303 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6635 (ptp90) REVERT: A 333 ARG cc_start: 0.7461 (tmt170) cc_final: 0.6917 (tpt-90) REVERT: A 395 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7609 (tm) REVERT: A 416 PHE cc_start: 0.8535 (t80) cc_final: 0.8264 (t80) outliers start: 15 outliers final: 6 residues processed: 52 average time/residue: 0.7348 time to fit residues: 40.1475 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.109036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.091095 restraints weight = 3960.260| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.89 r_work: 0.2877 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3421 Z= 0.228 Angle : 0.528 8.205 4681 Z= 0.267 Chirality : 0.040 0.153 542 Planarity : 0.003 0.028 552 Dihedral : 5.601 25.401 574 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.46 % Allowed : 16.43 % Favored : 80.12 % 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 (0.42), residues: 398 helix: 1.09 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.65 (0.62), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 114 PHE 0.019 0.001 PHE A 447 TYR 0.011 0.001 TYR A 438 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.376 Fit side-chains REVERT: A 26 ARG cc_start: 0.7481 (mtp85) cc_final: 0.6572 (mmp-170) REVERT: A 62 GLU cc_start: 0.7966 (pp20) cc_final: 0.7072 (pm20) REVERT: A 114 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7143 (m-70) REVERT: A 303 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6803 (ptp90) REVERT: A 333 ARG cc_start: 0.7557 (tmt170) cc_final: 0.7012 (tpt-90) REVERT: A 395 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (tm) REVERT: A 416 PHE cc_start: 0.8594 (t80) cc_final: 0.8327 (t80) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.8371 time to fit residues: 41.2491 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.109198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.091476 restraints weight = 3853.883| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.85 r_work: 0.2854 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3421 Z= 0.223 Angle : 0.527 8.440 4681 Z= 0.266 Chirality : 0.040 0.143 542 Planarity : 0.003 0.028 552 Dihedral : 5.606 26.064 574 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.75 % Allowed : 15.85 % Favored : 80.40 % 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: 0.97 (0.42), residues: 398 helix: 1.22 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.61 (0.63), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.024 0.001 PHE A 447 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.345 Fit side-chains REVERT: A 26 ARG cc_start: 0.7366 (mtp85) cc_final: 0.6431 (mmp-170) REVERT: A 62 GLU cc_start: 0.7835 (pp20) cc_final: 0.6887 (pm20) REVERT: A 114 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7167 (m-70) REVERT: A 303 ARG cc_start: 0.7100 (mtp180) cc_final: 0.6682 (ptp90) REVERT: A 333 ARG cc_start: 0.7451 (tmt170) cc_final: 0.6912 (tpt-90) REVERT: A 395 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7634 (tm) REVERT: A 416 PHE cc_start: 0.8521 (t80) cc_final: 0.8229 (t80) outliers start: 13 outliers final: 6 residues processed: 49 average time/residue: 0.8038 time to fit residues: 41.2521 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091540 restraints weight = 3914.966| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.85 r_work: 0.2866 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3421 Z= 0.222 Angle : 0.527 7.214 4681 Z= 0.266 Chirality : 0.040 0.139 542 Planarity : 0.003 0.028 552 Dihedral : 5.605 26.384 574 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.88 % Allowed : 17.29 % Favored : 79.83 % 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: 1.11 (0.42), residues: 398 helix: 1.33 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.65 (0.63), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.021 0.001 PHE A 447 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.362 Fit side-chains REVERT: A 26 ARG cc_start: 0.7379 (mtp85) cc_final: 0.6458 (mmp-170) REVERT: A 62 GLU cc_start: 0.7866 (pp20) cc_final: 0.6905 (pm20) REVERT: A 114 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7162 (m-70) REVERT: A 303 ARG cc_start: 0.7128 (mtp180) cc_final: 0.6738 (ptp90) REVERT: A 333 ARG cc_start: 0.7470 (tmt170) cc_final: 0.6907 (tpt-90) REVERT: A 395 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7668 (tm) REVERT: A 416 PHE cc_start: 0.8498 (t80) cc_final: 0.8234 (t80) REVERT: A 451 MET cc_start: 0.7217 (mmt) cc_final: 0.6976 (mmt) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.8307 time to fit residues: 40.0082 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.110668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.093417 restraints weight = 3885.504| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.85 r_work: 0.2895 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3421 Z= 0.175 Angle : 0.513 9.086 4681 Z= 0.256 Chirality : 0.038 0.144 542 Planarity : 0.003 0.028 552 Dihedral : 5.484 26.355 574 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.59 % Allowed : 17.00 % Favored : 80.40 % 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: 1.31 (0.42), residues: 398 helix: 1.48 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.63 (0.62), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.022 0.001 PHE A 84 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.371 Fit side-chains REVERT: A 26 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6475 (mmp-170) REVERT: A 62 GLU cc_start: 0.7821 (pp20) cc_final: 0.6847 (pm20) REVERT: A 114 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7145 (m-70) REVERT: A 303 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6756 (ptp90) REVERT: A 333 ARG cc_start: 0.7471 (tmt170) cc_final: 0.6930 (tpt-90) REVERT: A 363 TRP cc_start: 0.8070 (m100) cc_final: 0.6572 (p-90) REVERT: A 416 PHE cc_start: 0.8469 (t80) cc_final: 0.8246 (t80) REVERT: A 451 MET cc_start: 0.7158 (mmt) cc_final: 0.6882 (mmt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.8207 time to fit residues: 41.3443 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 8 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 = 0.3216 r_free = 0.3216 target = 0.109833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.092318 restraints weight = 3848.484| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.85 r_work: 0.2872 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3421 Z= 0.214 Angle : 0.547 8.228 4681 Z= 0.268 Chirality : 0.040 0.152 542 Planarity : 0.003 0.028 552 Dihedral : 5.557 26.807 574 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.02 % Allowed : 18.16 % Favored : 79.83 % 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: 1.30 (0.42), residues: 398 helix: 1.46 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.60 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.024 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 796 Ramachandran restraints generated. 398 Oldfield, 0 Emsley, 398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.326 Fit side-chains REVERT: A 26 ARG cc_start: 0.7359 (mtp85) cc_final: 0.6441 (mmp-170) REVERT: A 62 GLU cc_start: 0.7808 (pp20) cc_final: 0.6815 (pm20) REVERT: A 114 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7124 (m-70) REVERT: A 130 MET cc_start: 0.7932 (mtp) cc_final: 0.7634 (mtm) REVERT: A 303 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6713 (ptp90) REVERT: A 333 ARG cc_start: 0.7433 (tmt170) cc_final: 0.6898 (tpt-90) REVERT: A 363 TRP cc_start: 0.8053 (m100) cc_final: 0.6545 (p-90) REVERT: A 416 PHE cc_start: 0.8477 (t80) cc_final: 0.8240 (t80) REVERT: A 451 MET cc_start: 0.7136 (mmt) cc_final: 0.6846 (mmt) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.8877 time to fit residues: 39.9063 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.110068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.092741 restraints weight = 3907.013| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.84 r_work: 0.2884 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3421 Z= 0.195 Angle : 0.546 8.875 4681 Z= 0.264 Chirality : 0.039 0.150 542 Planarity : 0.003 0.028 552 Dihedral : 5.545 26.880 574 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.02 % Allowed : 18.16 % Favored : 79.83 % 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: 1.38 (0.42), residues: 398 helix: 1.52 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.55 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.023 0.001 PHE A 84 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.51 seconds wall clock time: 40 minutes 59.26 seconds (2459.26 seconds total)