Starting phenix.real_space_refine on Wed Mar 5 18:59:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq0_33387/03_2025/7xq0_33387_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq0_33387/03_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_33387/03_2025/7xq0_33387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq0_33387/03_2025/7xq0_33387.map" model { file = "/net/cci-nas-00/data/ceres_data/7xq0_33387/03_2025/7xq0_33387_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq0_33387/03_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-5624/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: 3.40, per 1000 atoms: 1.02 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: 0.81 Conformation dependent library (CDL) restraints added in 405.9 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: 0.34 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: 0.93 Time building geometry restraints manager: 0.99 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: 2.650 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: 0.020 Set scattering table: 0.040 Process input model: 14.190 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:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- 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 : 0.351 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: 0.8713 time to fit residues: 50.8584 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 : 0.346 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.110783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.093432 restraints weight = 3914.732| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.78 r_work: 0.2880 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.371 Fit side-chains REVERT: A 26 ARG cc_start: 0.7433 (mtp85) cc_final: 0.6580 (mmp-170) REVERT: A 62 GLU cc_start: 0.7748 (pp20) cc_final: 0.6777 (pm20) REVERT: A 333 ARG cc_start: 0.7584 (tmt170) cc_final: 0.7001 (tpt-90) REVERT: A 416 PHE cc_start: 0.8534 (t80) cc_final: 0.8262 (t80) REVERT: A 451 MET cc_start: 0.6806 (mmt) cc_final: 0.6452 (mpp) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.6545 time to fit residues: 39.4728 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 : 0.336 ------------------------------------------------------------------------------- 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: 0.4980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.089943 restraints weight = 3834.079| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.83 r_work: 0.2827 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3421 Z= 0.244 Angle : 0.559 7.824 4681 Z= 0.281 Chirality : 0.039 0.112 542 Planarity : 0.004 0.028 552 Dihedral : 5.718 23.518 574 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.17 % Allowed : 12.97 % Favored : 83.86 % 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 (0.39), residues: 398 helix: -0.17 (0.27), residues: 317 sheet: None (None), residues: 0 loop : -2.07 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.010 0.001 PHE A 125 TYR 0.011 0.001 TYR A 438 ARG 0.001 0.000 ARG A 303 *********************** 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.328 Fit side-chains REVERT: A 26 ARG cc_start: 0.7380 (mtp85) cc_final: 0.6488 (mmp-170) REVERT: A 62 GLU cc_start: 0.7855 (pp20) cc_final: 0.6900 (pm20) REVERT: A 333 ARG cc_start: 0.7492 (tmt170) cc_final: 0.6923 (tpt-90) REVERT: A 416 PHE cc_start: 0.8539 (t80) cc_final: 0.8197 (t80) REVERT: A 451 MET cc_start: 0.6679 (mmt) cc_final: 0.6415 (mpp) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.7359 time to fit residues: 37.1998 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 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 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.091808 restraints weight = 3917.943| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.79 r_work: 0.2856 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2424 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= 0.194 Angle : 0.523 8.503 4681 Z= 0.261 Chirality : 0.038 0.127 542 Planarity : 0.003 0.027 552 Dihedral : 5.557 24.148 574 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.17 % Allowed : 14.41 % Favored : 82.42 % 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: 0.05 (0.41), residues: 398 helix: 0.53 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.73 (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 114 PHE 0.015 0.001 PHE A 84 TYR 0.009 0.001 TYR A 438 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 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.384 Fit side-chains REVERT: A 26 ARG cc_start: 0.7372 (mtp85) cc_final: 0.6501 (mmp-170) REVERT: A 62 GLU cc_start: 0.7878 (pp20) cc_final: 0.6899 (pm20) REVERT: A 333 ARG cc_start: 0.7454 (tmt170) cc_final: 0.6894 (tpt-90) REVERT: A 416 PHE cc_start: 0.8581 (t80) cc_final: 0.8254 (t80) outliers start: 11 outliers final: 5 residues processed: 47 average time/residue: 0.8549 time to fit residues: 42.3453 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 : 0.313 ------------------------------------------------------------------------------- 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: 0.4980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.109524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.091724 restraints weight = 3896.806| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.87 r_work: 0.2850 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2559 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= 0.206 Angle : 0.520 8.003 4681 Z= 0.263 Chirality : 0.039 0.168 542 Planarity : 0.003 0.027 552 Dihedral : 5.564 24.664 574 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 4.90 % Allowed : 14.12 % Favored : 80.98 % 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: 0.52 (0.42), residues: 398 helix: 0.90 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.70 (0.60), residues: 80 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 0.018 0.001 PHE A 447 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.332 Fit side-chains REVERT: A 26 ARG cc_start: 0.7368 (mtp85) cc_final: 0.6421 (mmp-170) REVERT: A 62 GLU cc_start: 0.7743 (pp20) cc_final: 0.6727 (pm20) REVERT: A 114 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7089 (m-70) REVERT: A 333 ARG cc_start: 0.7439 (tmt170) cc_final: 0.6890 (tpt-90) REVERT: A 395 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7589 (tm) REVERT: A 416 PHE cc_start: 0.8501 (t80) cc_final: 0.8208 (t80) outliers start: 17 outliers final: 7 residues processed: 49 average time/residue: 0.6755 time to fit residues: 34.9725 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 13 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 = 0.3200 r_free = 0.3200 target = 0.108854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.091370 restraints weight = 3975.951| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.82 r_work: 0.2849 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 0.027 3421 Z= 0.218 Angle : 0.523 9.045 4681 Z= 0.262 Chirality : 0.039 0.156 542 Planarity : 0.003 0.028 552 Dihedral : 5.588 25.454 574 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.03 % Allowed : 15.85 % 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: 0.83 (0.42), residues: 398 helix: 1.11 (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 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 PHE 0.018 0.001 PHE A 84 TYR 0.010 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.319 Fit side-chains REVERT: A 26 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6421 (mmp-170) REVERT: A 62 GLU cc_start: 0.7716 (pp20) cc_final: 0.6724 (pm20) REVERT: A 114 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7069 (m-70) REVERT: A 303 ARG cc_start: 0.7008 (mtp180) cc_final: 0.6622 (ptp90) REVERT: A 333 ARG cc_start: 0.7430 (tmt170) cc_final: 0.6886 (tpt-90) REVERT: A 395 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7570 (tm) REVERT: A 416 PHE cc_start: 0.8499 (t80) cc_final: 0.8204 (t80) REVERT: A 451 MET cc_start: 0.6789 (mmt) cc_final: 0.6466 (mpp) outliers start: 14 outliers final: 6 residues processed: 51 average time/residue: 0.7857 time to fit residues: 42.0001 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.109020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091335 restraints weight = 3870.569| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.84 r_work: 0.2848 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2694 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= 0.211 Angle : 0.519 8.608 4681 Z= 0.261 Chirality : 0.039 0.142 542 Planarity : 0.003 0.029 552 Dihedral : 5.594 25.959 574 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.31 % Allowed : 18.16 % Favored : 79.54 % 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: 0.98 (0.42), residues: 398 helix: 1.22 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.62 (0.63), 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 0.008 0.001 PHE A 372 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 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.360 Fit side-chains REVERT: A 26 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6420 (mmp-170) REVERT: A 62 GLU cc_start: 0.7701 (pp20) cc_final: 0.6707 (pm20) REVERT: A 114 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7141 (m-70) REVERT: A 303 ARG cc_start: 0.7073 (mtp180) cc_final: 0.6668 (ptp90) REVERT: A 333 ARG cc_start: 0.7426 (tmt170) cc_final: 0.6883 (tpt-90) REVERT: A 395 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7578 (tm) REVERT: A 416 PHE cc_start: 0.8474 (t80) cc_final: 0.8184 (t80) REVERT: A 451 MET cc_start: 0.6768 (mmt) cc_final: 0.6443 (mpp) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.8258 time to fit residues: 39.8197 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 : 0.362 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.107991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.090495 restraints weight = 3958.424| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.83 r_work: 0.2838 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3421 Z= 0.243 Angle : 0.533 9.605 4681 Z= 0.267 Chirality : 0.040 0.141 542 Planarity : 0.003 0.030 552 Dihedral : 5.669 26.644 574 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.17 % Allowed : 17.29 % Favored : 79.54 % 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: 1.09 (0.42), residues: 398 helix: 1.30 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.62 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.001 HIS A 114 PHE 0.020 0.001 PHE A 84 TYR 0.011 0.001 TYR A 438 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 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.354 Fit side-chains REVERT: A 26 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6449 (mmp-170) REVERT: A 62 GLU cc_start: 0.7787 (pp20) cc_final: 0.6777 (pm20) REVERT: A 114 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7130 (m-70) REVERT: A 303 ARG cc_start: 0.7141 (mtp180) cc_final: 0.6703 (ptp90) REVERT: A 333 ARG cc_start: 0.7491 (tmt170) cc_final: 0.6944 (tpt-90) REVERT: A 395 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7659 (tm) REVERT: A 416 PHE cc_start: 0.8513 (t80) cc_final: 0.8243 (t80) REVERT: A 451 MET cc_start: 0.6796 (mmt) cc_final: 0.6463 (mpp) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.7570 time to fit residues: 38.2658 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 : 0.347 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.110253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092950 restraints weight = 3918.125| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.83 r_work: 0.2879 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2761 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= 0.182 Angle : 0.509 9.549 4681 Z= 0.254 Chirality : 0.038 0.139 542 Planarity : 0.003 0.029 552 Dihedral : 5.514 26.498 574 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.31 % Allowed : 18.16 % Favored : 79.54 % 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: 1.25 (0.42), residues: 398 helix: 1.44 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.62 (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 114 PHE 0.021 0.001 PHE A 84 TYR 0.009 0.001 TYR A 438 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 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.352 Fit side-chains REVERT: A 26 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6456 (mmp-170) REVERT: A 62 GLU cc_start: 0.7769 (pp20) cc_final: 0.6747 (pm20) REVERT: A 114 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7122 (m-70) REVERT: A 289 HIS cc_start: 0.8742 (m-70) cc_final: 0.8337 (m170) REVERT: A 303 ARG cc_start: 0.7105 (mtp180) cc_final: 0.6687 (ptp90) REVERT: A 333 ARG cc_start: 0.7422 (tmt170) cc_final: 0.6908 (tpt-90) REVERT: A 363 TRP cc_start: 0.8078 (m100) cc_final: 0.6556 (p-90) REVERT: A 416 PHE cc_start: 0.8472 (t80) cc_final: 0.8222 (t80) REVERT: A 451 MET cc_start: 0.6757 (mmt) cc_final: 0.6471 (mpp) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.8641 time to fit residues: 40.6498 Evaluate side-chains 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 299 THR 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: 0.4980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 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 = 0.3206 r_free = 0.3206 target = 0.109219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091627 restraints weight = 3895.446| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.84 r_work: 0.2852 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2794 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= 0.230 Angle : 0.543 9.567 4681 Z= 0.268 Chirality : 0.040 0.145 542 Planarity : 0.003 0.030 552 Dihedral : 5.628 27.010 574 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.73 % Allowed : 19.31 % Favored : 78.96 % 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: 1.25 (0.42), residues: 398 helix: 1.43 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.61 (0.62), residues: 78 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 0.008 0.001 PHE A 372 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 303 ********************** 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: 6 poor density : 38 time to evaluate : 0.342 Fit side-chains REVERT: A 26 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6424 (mmp-170) REVERT: A 62 GLU cc_start: 0.7730 (pp20) cc_final: 0.6703 (pm20) REVERT: A 114 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7084 (m-70) REVERT: A 289 HIS cc_start: 0.8720 (m-70) cc_final: 0.8316 (m170) REVERT: A 303 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6682 (ptp90) REVERT: A 333 ARG cc_start: 0.7371 (tmt170) cc_final: 0.6870 (tpt-90) REVERT: A 416 PHE cc_start: 0.8464 (t80) cc_final: 0.8203 (t80) REVERT: A 451 MET cc_start: 0.6640 (mmt) cc_final: 0.6351 (mpp) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.8427 time to fit residues: 37.9570 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 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 = 0.3214 r_free = 0.3214 target = 0.109713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.092132 restraints weight = 3922.346| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.84 r_work: 0.2858 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2790 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= 0.213 Angle : 0.534 9.605 4681 Z= 0.263 Chirality : 0.039 0.134 542 Planarity : 0.003 0.029 552 Dihedral : 5.605 27.106 574 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.02 % Allowed : 19.02 % Favored : 78.96 % 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: 1.29 (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 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.008 0.001 PHE A 372 TYR 0.010 0.001 TYR A 438 ARG 0.001 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.31 seconds wall clock time: 39 minutes 48.54 seconds (2388.54 seconds total)