Starting phenix.real_space_refine on Tue Feb 11 02:52:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irw_60823/02_2025/9irw_60823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irw_60823/02_2025/9irw_60823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9irw_60823/02_2025/9irw_60823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irw_60823/02_2025/9irw_60823.map" model { file = "/net/cci-nas-00/data/ceres_data/9irw_60823/02_2025/9irw_60823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irw_60823/02_2025/9irw_60823.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.130 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2476 2.51 5 N 650 2.21 5 O 654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3808 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3796 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 28, 'TRANS': 470} Chain breaks: 4 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.16, per 1000 atoms: 0.83 Number of scatterers: 3808 At special positions: 0 Unit cell: (73.623, 101.365, 61.886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 654 8.00 N 650 7.00 C 2476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 468.0 milliseconds 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 916 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 1 sheets defined 75.4% alpha, 0.8% 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 3 through 10 Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 144 through 171 Proline residue: A 165 - end of helix removed outlier: 3.542A pdb=" N GLY A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.912A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.628A pdb=" N VAL A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 4.445A pdb=" N ASP A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 347 through 368 Processing helix chain 'A' and resid 369 through 372 removed outlier: 3.639A pdb=" N GLN A 372 " --> pdb=" O LEU A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 378 through 403 removed outlier: 3.534A pdb=" N GLN A 382 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 424 removed outlier: 4.085A pdb=" N ILE A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 459 removed outlier: 3.508A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 488 Proline residue: A 484 - end of helix removed outlier: 3.649A pdb=" N LEU A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 495 through 512 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 526 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 248 hydrogen bonds defined for protein. 744 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: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 582 1.31 - 1.43: 1034 1.43 - 1.56: 2236 1.56 - 1.68: 0 1.68 - 1.81: 44 Bond restraints: 3896 Sorted by residual: bond pdb=" C4 URC A 701 " pdb=" N3 URC A 701 " ideal model delta sigma weight residual 1.352 1.475 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C4 URC A 701 " pdb=" N9 URC A 701 " ideal model delta sigma weight residual 1.352 1.469 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C2 URC A 701 " pdb=" N1 URC A 701 " ideal model delta sigma weight residual 1.375 1.486 -0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C2 URC A 701 " pdb=" N3 URC A 701 " ideal model delta sigma weight residual 1.376 1.485 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 URC A 701 " pdb=" C5 URC A 701 " ideal model delta sigma weight residual 1.358 1.466 -0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 3891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 5169 1.88 - 3.76: 115 3.76 - 5.64: 19 5.64 - 7.52: 7 7.52 - 9.40: 2 Bond angle restraints: 5312 Sorted by residual: angle pdb=" N LEU A 9 " pdb=" CA LEU A 9 " pdb=" C LEU A 9 " ideal model delta sigma weight residual 111.07 104.32 6.75 1.07e+00 8.73e-01 3.98e+01 angle pdb=" C GLU A 5 " pdb=" CA GLU A 5 " pdb=" CB GLU A 5 " ideal model delta sigma weight residual 110.79 103.63 7.16 1.66e+00 3.63e-01 1.86e+01 angle pdb=" N LEU A 7 " pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 113.01 108.42 4.59 1.20e+00 6.94e-01 1.47e+01 angle pdb=" N GLU A 5 " pdb=" CA GLU A 5 " pdb=" CB GLU A 5 " ideal model delta sigma weight residual 110.12 115.61 -5.49 1.47e+00 4.63e-01 1.39e+01 angle pdb=" C2 URC A 701 " pdb=" N1 URC A 701 " pdb=" C6 URC A 701 " ideal model delta sigma weight residual 129.31 119.91 9.40 3.00e+00 1.11e-01 9.81e+00 ... (remaining 5307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.86: 1993 11.86 - 23.73: 205 23.73 - 35.59: 62 35.59 - 47.46: 21 47.46 - 59.32: 8 Dihedral angle restraints: 2289 sinusoidal: 871 harmonic: 1418 Sorted by residual: dihedral pdb=" CA VAL A 117 " pdb=" C VAL A 117 " pdb=" N ASP A 118 " pdb=" CA ASP A 118 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -123.04 37.04 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CA VAL A 138 " pdb=" C VAL A 138 " pdb=" N CYS A 139 " pdb=" CA CYS A 139 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 416 0.038 - 0.075: 165 0.075 - 0.112: 39 0.112 - 0.150: 9 0.150 - 0.187: 5 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA ARG A 92 " pdb=" N ARG A 92 " pdb=" C ARG A 92 " pdb=" CB ARG A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA LEU A 9 " pdb=" N LEU A 9 " pdb=" C LEU A 9 " pdb=" CB LEU A 9 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA PHE A 91 " pdb=" N PHE A 91 " pdb=" C PHE A 91 " pdb=" CB PHE A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 631 not shown) Planarity restraints: 656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 390 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO A 391 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 6 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LEU A 6 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 6 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 7 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 160 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C ALA A 160 " -0.027 2.00e-02 2.50e+03 pdb=" O ALA A 160 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 161 " 0.009 2.00e-02 2.50e+03 ... (remaining 653 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 787 2.77 - 3.30: 3824 3.30 - 3.84: 6623 3.84 - 4.37: 7827 4.37 - 4.90: 13423 Nonbonded interactions: 32484 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" O PRO A 516 " model vdw 2.239 3.040 nonbonded pdb=" NH1 ARG A 325 " pdb=" OD2 ASP A 525 " model vdw 2.253 3.120 nonbonded pdb=" O GLY A 212 " pdb=" ND2 ASN A 216 " model vdw 2.314 3.120 nonbonded pdb=" NH1 ARG A 172 " pdb=" OE2 GLU A 223 " model vdw 2.328 3.120 nonbonded pdb=" O ILE A 126 " pdb=" NH1 ARG A 256 " model vdw 2.334 3.120 ... (remaining 32479 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.007 0.123 3896 Z= 0.427 Angle : 0.721 9.396 5312 Z= 0.391 Chirality : 0.044 0.187 634 Planarity : 0.005 0.047 656 Dihedral : 11.884 59.320 1367 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.47 % Allowed : 9.18 % Favored : 87.34 % 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 (0.38), residues: 489 helix: 0.19 (0.28), residues: 348 sheet: -4.43 (1.27), residues: 10 loop : -2.40 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 178 HIS 0.002 0.001 HIS A 47 PHE 0.019 0.002 PHE A 208 TYR 0.019 0.002 TYR A 275 ARG 0.002 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.407 Fit side-chains REVERT: A 54 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 286 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7742 (mt) REVERT: A 394 MET cc_start: 0.6993 (mmm) cc_final: 0.6664 (mtp) REVERT: A 458 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6792 (mt-10) REVERT: A 518 THR cc_start: 0.8434 (m) cc_final: 0.8067 (p) outliers start: 14 outliers final: 6 residues processed: 67 average time/residue: 0.1776 time to fit residues: 14.7584 Evaluate side-chains 49 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.173265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151893 restraints weight = 4419.862| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.65 r_work: 0.3604 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3896 Z= 0.271 Angle : 0.632 10.245 5312 Z= 0.308 Chirality : 0.041 0.130 634 Planarity : 0.005 0.043 656 Dihedral : 7.294 55.940 546 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.72 % Allowed : 11.91 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.66 (0.38), residues: 489 helix: 0.33 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -2.53 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 178 HIS 0.001 0.001 HIS A 47 PHE 0.018 0.002 PHE A 208 TYR 0.017 0.002 TYR A 275 ARG 0.003 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.722 Fit side-chains REVERT: A 8 ASP cc_start: 0.7294 (m-30) cc_final: 0.7024 (m-30) REVERT: A 54 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 286 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 394 MET cc_start: 0.7818 (mmm) cc_final: 0.7293 (mtp) REVERT: A 434 ARG cc_start: 0.7102 (mmt180) cc_final: 0.6812 (mmt180) REVERT: A 458 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7271 (mt-10) outliers start: 15 outliers final: 9 residues processed: 60 average time/residue: 0.1718 time to fit residues: 13.0205 Evaluate side-chains 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.0970 chunk 8 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.175844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154797 restraints weight = 4364.682| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.64 r_work: 0.3641 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3896 Z= 0.196 Angle : 0.586 8.474 5312 Z= 0.284 Chirality : 0.039 0.126 634 Planarity : 0.004 0.042 656 Dihedral : 6.711 50.087 544 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.22 % Allowed : 13.15 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.38), residues: 489 helix: 0.38 (0.28), residues: 365 sheet: -4.19 (1.31), residues: 10 loop : -2.44 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 PHE 0.016 0.002 PHE A 269 TYR 0.016 0.001 TYR A 275 ARG 0.003 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.423 Fit side-chains REVERT: A 8 ASP cc_start: 0.7302 (m-30) cc_final: 0.7028 (m-30) REVERT: A 286 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8035 (mt) REVERT: A 394 MET cc_start: 0.7813 (mmm) cc_final: 0.7302 (mtp) REVERT: A 398 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6708 (tt) REVERT: A 434 ARG cc_start: 0.7134 (mmt180) cc_final: 0.6873 (mmt180) REVERT: A 458 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7250 (mt-10) outliers start: 17 outliers final: 8 residues processed: 63 average time/residue: 0.1660 time to fit residues: 13.1732 Evaluate side-chains 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.175664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154416 restraints weight = 4433.659| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.66 r_work: 0.3630 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3896 Z= 0.230 Angle : 0.599 8.882 5312 Z= 0.289 Chirality : 0.040 0.128 634 Planarity : 0.004 0.041 656 Dihedral : 6.279 46.125 542 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.96 % Allowed : 14.39 % Favored : 80.65 % 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: -0.71 (0.38), residues: 489 helix: 0.33 (0.27), residues: 367 sheet: -4.19 (1.26), residues: 10 loop : -2.58 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 PHE 0.017 0.002 PHE A 269 TYR 0.017 0.001 TYR A 275 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.377 Fit side-chains REVERT: A 8 ASP cc_start: 0.7199 (m-30) cc_final: 0.6945 (m-30) REVERT: A 234 MET cc_start: 0.8319 (mmm) cc_final: 0.7807 (mmm) REVERT: A 286 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 394 MET cc_start: 0.7833 (mmm) cc_final: 0.7320 (mtp) REVERT: A 398 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6717 (tt) REVERT: A 425 LEU cc_start: 0.7888 (mp) cc_final: 0.7610 (mp) REVERT: A 434 ARG cc_start: 0.7218 (mmt180) cc_final: 0.6894 (mmt180) REVERT: A 458 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7237 (mt-10) outliers start: 20 outliers final: 14 residues processed: 62 average time/residue: 0.1612 time to fit residues: 12.6002 Evaluate side-chains 60 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.182034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.161240 restraints weight = 4558.882| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.66 r_work: 0.3679 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3896 Z= 0.160 Angle : 0.558 8.317 5312 Z= 0.269 Chirality : 0.038 0.125 634 Planarity : 0.004 0.041 656 Dihedral : 6.110 44.733 542 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.97 % Allowed : 16.38 % Favored : 79.65 % 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: -0.42 (0.38), residues: 489 helix: 0.51 (0.27), residues: 367 sheet: -4.08 (1.26), residues: 10 loop : -2.40 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 PHE 0.015 0.001 PHE A 269 TYR 0.015 0.001 TYR A 275 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.380 Fit side-chains REVERT: A 124 ARG cc_start: 0.7036 (mtm-85) cc_final: 0.6420 (mtt180) REVERT: A 255 VAL cc_start: 0.8408 (m) cc_final: 0.8143 (m) REVERT: A 286 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7968 (mt) REVERT: A 394 MET cc_start: 0.7800 (mmm) cc_final: 0.7290 (mtp) REVERT: A 398 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6609 (tt) REVERT: A 425 LEU cc_start: 0.7930 (mp) cc_final: 0.7669 (mp) REVERT: A 434 ARG cc_start: 0.7203 (mmt180) cc_final: 0.6944 (mmt180) outliers start: 16 outliers final: 11 residues processed: 64 average time/residue: 0.1974 time to fit residues: 15.2572 Evaluate side-chains 60 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 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 = 0.3995 r_free = 0.3995 target = 0.176336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154785 restraints weight = 4484.601| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.68 r_work: 0.3622 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3896 Z= 0.257 Angle : 0.619 11.496 5312 Z= 0.299 Chirality : 0.042 0.198 634 Planarity : 0.005 0.041 656 Dihedral : 5.909 43.342 539 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.97 % Allowed : 16.13 % Favored : 79.90 % 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: -0.65 (0.38), residues: 489 helix: 0.33 (0.27), residues: 368 sheet: -4.06 (1.25), residues: 10 loop : -2.44 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 178 HIS 0.001 0.000 HIS A 47 PHE 0.017 0.002 PHE A 208 TYR 0.017 0.001 TYR A 275 ARG 0.002 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.402 Fit side-chains REVERT: A 124 ARG cc_start: 0.7097 (mtm-85) cc_final: 0.6606 (mtt180) REVERT: A 255 VAL cc_start: 0.8442 (m) cc_final: 0.8228 (m) REVERT: A 394 MET cc_start: 0.7947 (mmm) cc_final: 0.7357 (mtp) REVERT: A 398 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6737 (tt) REVERT: A 434 ARG cc_start: 0.7282 (mmt180) cc_final: 0.6967 (mmt180) outliers start: 16 outliers final: 13 residues processed: 58 average time/residue: 0.1674 time to fit residues: 12.0294 Evaluate side-chains 60 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.175325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.154312 restraints weight = 4491.638| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.66 r_work: 0.3606 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3896 Z= 0.301 Angle : 0.645 9.973 5312 Z= 0.311 Chirality : 0.043 0.163 634 Planarity : 0.005 0.043 656 Dihedral : 5.615 43.142 537 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.21 % Allowed : 16.13 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.37), residues: 489 helix: 0.26 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -2.45 (0.49), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.001 0.001 HIS A 47 PHE 0.018 0.002 PHE A 208 TYR 0.019 0.002 TYR A 275 ARG 0.005 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.386 Fit side-chains REVERT: A 124 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6549 (mtt180) REVERT: A 286 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 394 MET cc_start: 0.7899 (mmm) cc_final: 0.7347 (mtp) REVERT: A 398 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6743 (tt) REVERT: A 434 ARG cc_start: 0.7350 (mmt180) cc_final: 0.7090 (mmt180) outliers start: 21 outliers final: 16 residues processed: 65 average time/residue: 0.1699 time to fit residues: 13.6985 Evaluate side-chains 64 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.178444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157683 restraints weight = 4521.163| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.65 r_work: 0.3645 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3896 Z= 0.206 Angle : 0.606 9.348 5312 Z= 0.290 Chirality : 0.040 0.151 634 Planarity : 0.004 0.042 656 Dihedral : 5.531 43.451 537 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.71 % Allowed : 16.87 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.38), residues: 489 helix: 0.33 (0.27), residues: 367 sheet: -3.89 (1.29), residues: 10 loop : -2.45 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 PHE 0.015 0.002 PHE A 208 TYR 0.017 0.001 TYR A 275 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.422 Fit side-chains REVERT: A 124 ARG cc_start: 0.7093 (mtm-85) cc_final: 0.6484 (mtt180) REVERT: A 286 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8047 (mt) REVERT: A 394 MET cc_start: 0.7847 (mmm) cc_final: 0.7307 (mtp) REVERT: A 398 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6635 (tt) REVERT: A 434 ARG cc_start: 0.7216 (mmt180) cc_final: 0.6949 (mmt180) outliers start: 19 outliers final: 16 residues processed: 62 average time/residue: 0.1783 time to fit residues: 13.6567 Evaluate side-chains 62 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.163037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141463 restraints weight = 4547.768| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.86 r_work: 0.3500 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3896 Z= 0.208 Angle : 0.604 9.639 5312 Z= 0.288 Chirality : 0.040 0.141 634 Planarity : 0.004 0.042 656 Dihedral : 5.486 43.808 537 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.71 % Allowed : 16.38 % Favored : 78.91 % 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: -0.59 (0.38), residues: 489 helix: 0.38 (0.27), residues: 367 sheet: -3.84 (1.28), residues: 10 loop : -2.45 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 PHE 0.014 0.002 PHE A 208 TYR 0.016 0.001 TYR A 275 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.412 Fit side-chains REVERT: A 124 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6356 (mtt180) REVERT: A 286 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7785 (mt) REVERT: A 394 MET cc_start: 0.7881 (mmm) cc_final: 0.7165 (mtp) REVERT: A 398 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6420 (tt) REVERT: A 434 ARG cc_start: 0.6925 (mmt180) cc_final: 0.6600 (mmt180) outliers start: 19 outliers final: 16 residues processed: 61 average time/residue: 0.1907 time to fit residues: 14.3973 Evaluate side-chains 62 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 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 = 0.3829 r_free = 0.3829 target = 0.160910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139248 restraints weight = 4589.673| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.86 r_work: 0.3474 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3896 Z= 0.258 Angle : 0.625 9.917 5312 Z= 0.300 Chirality : 0.041 0.150 634 Planarity : 0.005 0.043 656 Dihedral : 5.548 43.853 537 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.71 % Allowed : 17.12 % Favored : 78.16 % 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 (0.37), residues: 489 helix: 0.31 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -2.46 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.001 0.000 HIS A 428 PHE 0.017 0.002 PHE A 208 TYR 0.017 0.002 TYR A 275 ARG 0.003 0.000 ARG A 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.429 Fit side-chains REVERT: A 124 ARG cc_start: 0.7045 (mtm-85) cc_final: 0.6204 (mtt180) REVERT: A 286 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 394 MET cc_start: 0.7882 (mmm) cc_final: 0.7178 (mtp) REVERT: A 398 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6570 (tt) REVERT: A 434 ARG cc_start: 0.7072 (mmt180) cc_final: 0.6751 (mmt180) outliers start: 19 outliers final: 16 residues processed: 62 average time/residue: 0.1786 time to fit residues: 13.7874 Evaluate side-chains 64 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 455 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.164729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143548 restraints weight = 4538.042| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.79 r_work: 0.3508 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3896 Z= 0.266 Angle : 0.630 9.949 5312 Z= 0.302 Chirality : 0.042 0.149 634 Planarity : 0.005 0.043 656 Dihedral : 5.578 44.081 537 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.96 % Allowed : 17.12 % Favored : 77.92 % 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: -0.63 (0.37), residues: 489 helix: 0.29 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -2.47 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS A 428 PHE 0.018 0.002 PHE A 208 TYR 0.017 0.002 TYR A 275 ARG 0.003 0.000 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.47 seconds wall clock time: 40 minutes 57.16 seconds (2457.16 seconds total)