Starting phenix.real_space_refine on Wed Sep 17 04:10:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irw_60823/09_2025/9irw_60823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irw_60823/09_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_60823/09_2025/9irw_60823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irw_60823/09_2025/9irw_60823.map" model { file = "/net/cci-nas-00/data/ceres_data/9irw_60823/09_2025/9irw_60823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irw_60823/09_2025/9irw_60823.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 0.97, per 1000 atoms: 0.25 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: 0.33 Conformation dependent library (CDL) restraints added in 146.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.13 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: 0.66 Time building geometry restraints manager: 0.43 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: 1.560 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.980 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.940 ------------------------------------------------------------------------------- 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 3898 Z= 0.354 Angle : 0.721 9.396 5316 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG A 92 TYR 0.019 0.002 TYR A 275 PHE 0.019 0.002 PHE A 208 TRP 0.011 0.001 TRP A 178 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00701 ( 3896) covalent geometry : angle 0.72095 ( 5312) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.85993 ( 4) hydrogen bonds : bond 0.13568 ( 248) hydrogen bonds : angle 5.76815 ( 744) *********************** 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 : 0.128 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: 0.0706 time to fit residues: 5.8817 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 : 0.132 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3972 r_free = 0.3972 target = 0.174191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152719 restraints weight = 4470.114| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.67 r_work: 0.3608 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3898 Z= 0.169 Angle : 0.628 10.419 5316 Z= 0.305 Chirality : 0.041 0.129 634 Planarity : 0.005 0.043 656 Dihedral : 7.269 54.578 546 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.72 % Allowed : 12.16 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.38), residues: 489 helix: 0.29 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -2.56 (0.48), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 89 TYR 0.017 0.002 TYR A 275 PHE 0.018 0.002 PHE A 208 TRP 0.010 0.001 TRP A 178 HIS 0.001 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3896) covalent geometry : angle 0.62793 ( 5312) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.94453 ( 4) hydrogen bonds : bond 0.05211 ( 248) hydrogen bonds : angle 4.77776 ( 744) *********************** 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 : 0.177 Fit side-chains REVERT: A 8 ASP cc_start: 0.7272 (m-30) cc_final: 0.7020 (m-30) REVERT: A 54 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8452 (mt) REVERT: A 286 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 394 MET cc_start: 0.7817 (mmm) cc_final: 0.7286 (mtp) REVERT: A 434 ARG cc_start: 0.7127 (mmt180) cc_final: 0.6816 (mmt180) REVERT: A 458 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7258 (mt-10) outliers start: 15 outliers final: 9 residues processed: 60 average time/residue: 0.0723 time to fit residues: 5.3960 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 : 0.094 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 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 = 0.3973 r_free = 0.3973 target = 0.173858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152615 restraints weight = 4445.115| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.65 r_work: 0.3606 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3898 Z= 0.172 Angle : 0.614 8.872 5316 Z= 0.298 Chirality : 0.040 0.129 634 Planarity : 0.005 0.042 656 Dihedral : 6.793 50.631 544 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.46 % Allowed : 13.65 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.37), residues: 489 helix: 0.26 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -2.59 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.017 0.002 TYR A 275 PHE 0.017 0.002 PHE A 269 TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3896) covalent geometry : angle 0.61410 ( 5312) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.82294 ( 4) hydrogen bonds : bond 0.05023 ( 248) hydrogen bonds : angle 4.57105 ( 744) *********************** 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: 22 poor density : 43 time to evaluate : 0.101 Fit side-chains REVERT: A 8 ASP cc_start: 0.7286 (m-30) cc_final: 0.7019 (m-30) REVERT: A 286 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 394 MET cc_start: 0.7873 (mmm) cc_final: 0.7353 (mtp) REVERT: A 398 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6739 (tt) REVERT: A 425 LEU cc_start: 0.7869 (mp) cc_final: 0.7577 (mp) REVERT: A 434 ARG cc_start: 0.7195 (mmt180) cc_final: 0.6908 (mmt180) REVERT: A 458 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 518 THR cc_start: 0.8397 (m) cc_final: 0.8171 (p) outliers start: 22 outliers final: 13 residues processed: 62 average time/residue: 0.0666 time to fit residues: 5.1260 Evaluate side-chains 57 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 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 455 TYR Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 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 = 0.3982 r_free = 0.3982 target = 0.174636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153336 restraints weight = 4442.960| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.66 r_work: 0.3615 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3898 Z= 0.162 Angle : 0.600 8.915 5316 Z= 0.291 Chirality : 0.040 0.135 634 Planarity : 0.005 0.041 656 Dihedral : 6.327 46.857 542 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.96 % Allowed : 14.64 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.38), residues: 489 helix: 0.27 (0.27), residues: 367 sheet: -4.24 (1.25), residues: 10 loop : -2.62 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 487 TYR 0.016 0.002 TYR A 275 PHE 0.017 0.002 PHE A 269 TRP 0.010 0.001 TRP A 357 HIS 0.002 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3896) covalent geometry : angle 0.59938 ( 5312) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.78074 ( 4) hydrogen bonds : bond 0.04856 ( 248) hydrogen bonds : angle 4.47461 ( 744) *********************** 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 64 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.141 Fit side-chains REVERT: A 8 ASP cc_start: 0.7234 (m-30) cc_final: 0.6945 (m-30) REVERT: A 124 ARG cc_start: 0.7130 (mtm-85) cc_final: 0.6653 (mtt180) REVERT: A 286 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8060 (mt) REVERT: A 394 MET cc_start: 0.7862 (mmm) cc_final: 0.7334 (mtp) REVERT: A 398 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6729 (tt) REVERT: A 458 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7264 (mt-10) outliers start: 20 outliers final: 15 residues processed: 61 average time/residue: 0.0693 time to fit residues: 5.2779 Evaluate side-chains 60 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.178172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157341 restraints weight = 4526.114| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.66 r_work: 0.3640 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3898 Z= 0.139 Angle : 0.573 8.757 5316 Z= 0.280 Chirality : 0.039 0.126 634 Planarity : 0.004 0.041 656 Dihedral : 6.246 46.193 542 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.46 % Allowed : 14.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.38), residues: 489 helix: 0.39 (0.27), residues: 365 sheet: -4.12 (1.26), residues: 10 loop : -2.33 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 487 TYR 0.016 0.001 TYR A 275 PHE 0.017 0.002 PHE A 269 TRP 0.009 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3896) covalent geometry : angle 0.57302 ( 5312) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.77020 ( 4) hydrogen bonds : bond 0.04569 ( 248) hydrogen bonds : angle 4.33860 ( 744) *********************** 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 73 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.143 Fit side-chains REVERT: A 124 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6597 (mtt180) REVERT: A 255 VAL cc_start: 0.8480 (m) cc_final: 0.8210 (m) REVERT: A 286 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8027 (mt) REVERT: A 394 MET cc_start: 0.7835 (mmm) cc_final: 0.7324 (mtp) REVERT: A 398 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6703 (tt) REVERT: A 425 LEU cc_start: 0.7929 (mp) cc_final: 0.7714 (mp) REVERT: A 458 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7199 (mt-10) outliers start: 22 outliers final: 16 residues processed: 69 average time/residue: 0.0824 time to fit residues: 6.9486 Evaluate side-chains 66 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.177717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156863 restraints weight = 4569.889| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.67 r_work: 0.3633 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3898 Z= 0.149 Angle : 0.594 9.413 5316 Z= 0.289 Chirality : 0.041 0.198 634 Planarity : 0.004 0.040 656 Dihedral : 6.264 45.508 542 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.21 % Allowed : 14.39 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.37), residues: 489 helix: 0.29 (0.27), residues: 367 sheet: -4.08 (1.26), residues: 10 loop : -2.43 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 487 TYR 0.016 0.001 TYR A 275 PHE 0.016 0.002 PHE A 208 TRP 0.008 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3896) covalent geometry : angle 0.59373 ( 5312) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.70966 ( 4) hydrogen bonds : bond 0.04642 ( 248) hydrogen bonds : angle 4.34804 ( 744) *********************** 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 69 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.136 Fit side-chains REVERT: A 124 ARG cc_start: 0.7090 (mtm-85) cc_final: 0.6596 (mtt180) REVERT: A 286 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8069 (mt) REVERT: A 394 MET cc_start: 0.7904 (mmm) cc_final: 0.7340 (mtp) REVERT: A 398 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6706 (tt) REVERT: A 425 LEU cc_start: 0.7951 (mp) cc_final: 0.7712 (mp) REVERT: A 434 ARG cc_start: 0.7424 (mmt180) cc_final: 0.7223 (mmt180) outliers start: 21 outliers final: 16 residues processed: 65 average time/residue: 0.0776 time to fit residues: 6.2191 Evaluate side-chains 65 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.174719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.153433 restraints weight = 4623.640| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.70 r_work: 0.3598 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3898 Z= 0.198 Angle : 0.651 10.427 5316 Z= 0.315 Chirality : 0.043 0.169 634 Planarity : 0.005 0.043 656 Dihedral : 6.367 45.336 542 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.71 % Allowed : 15.88 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.37), residues: 489 helix: 0.22 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -2.43 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.018 0.002 TYR A 275 PHE 0.019 0.002 PHE A 208 TRP 0.008 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 3896) covalent geometry : angle 0.65147 ( 5312) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.64395 ( 4) hydrogen bonds : bond 0.05050 ( 248) hydrogen bonds : angle 4.44994 ( 744) *********************** 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: 19 poor density : 49 time to evaluate : 0.146 Fit side-chains REVERT: A 124 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.6751 (mtt180) REVERT: A 286 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 394 MET cc_start: 0.7932 (mmm) cc_final: 0.7369 (mtp) REVERT: A 398 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6747 (tt) REVERT: A 425 LEU cc_start: 0.7989 (mp) cc_final: 0.7710 (mp) REVERT: A 434 ARG cc_start: 0.7343 (mmt180) cc_final: 0.7068 (mmt180) outliers start: 19 outliers final: 16 residues processed: 65 average time/residue: 0.0811 time to fit residues: 6.5315 Evaluate side-chains 66 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.176695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.155515 restraints weight = 4561.985| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.69 r_work: 0.3618 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3898 Z= 0.161 Angle : 0.629 10.448 5316 Z= 0.302 Chirality : 0.041 0.152 634 Planarity : 0.004 0.042 656 Dihedral : 6.352 45.571 542 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.96 % Allowed : 16.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.37), residues: 489 helix: 0.25 (0.27), residues: 366 sheet: -3.91 (1.29), residues: 10 loop : -2.51 (0.52), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.017 0.001 TYR A 275 PHE 0.017 0.002 PHE A 208 TRP 0.011 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3896) covalent geometry : angle 0.62851 ( 5312) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.69674 ( 4) hydrogen bonds : bond 0.04805 ( 248) hydrogen bonds : angle 4.37820 ( 744) *********************** 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 66 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.149 Fit side-chains REVERT: A 124 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6493 (mtt180) REVERT: A 286 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 394 MET cc_start: 0.7920 (mmm) cc_final: 0.7356 (mtp) REVERT: A 398 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6716 (tt) REVERT: A 425 LEU cc_start: 0.8030 (mp) cc_final: 0.7732 (mp) REVERT: A 434 ARG cc_start: 0.7366 (mmt180) cc_final: 0.7075 (mmt180) outliers start: 20 outliers final: 14 residues processed: 63 average time/residue: 0.0806 time to fit residues: 6.2563 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 : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 33 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.0010 chunk 6 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.3144 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.172417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151673 restraints weight = 4568.292| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.70 r_work: 0.3606 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3898 Z= 0.132 Angle : 0.619 9.256 5316 Z= 0.297 Chirality : 0.041 0.196 634 Planarity : 0.004 0.041 656 Dihedral : 6.079 44.747 541 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.47 % Allowed : 17.12 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.38), residues: 489 helix: 0.38 (0.27), residues: 366 sheet: -3.88 (1.31), residues: 10 loop : -2.55 (0.52), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.015 0.001 TYR A 275 PHE 0.014 0.002 PHE A 208 TRP 0.010 0.001 TRP A 357 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3896) covalent geometry : angle 0.61518 ( 5312) SS BOND : bond 0.00350 ( 2) SS BOND : angle 2.41725 ( 4) hydrogen bonds : bond 0.04522 ( 248) hydrogen bonds : angle 4.25752 ( 744) *********************** 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 62 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.087 Fit side-chains REVERT: A 124 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6483 (mtt180) REVERT: A 286 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 394 MET cc_start: 0.7904 (mmm) cc_final: 0.7311 (mtp) REVERT: A 398 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6594 (tt) REVERT: A 425 LEU cc_start: 0.8001 (mp) cc_final: 0.7712 (mp) REVERT: A 434 ARG cc_start: 0.7157 (mmt180) cc_final: 0.6911 (mmt180) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.0837 time to fit residues: 6.1870 Evaluate side-chains 56 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP 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 363 THR 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 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.163911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142949 restraints weight = 4612.311| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.84 r_work: 0.3515 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3898 Z= 0.138 Angle : 0.635 10.653 5316 Z= 0.303 Chirality : 0.041 0.174 634 Planarity : 0.004 0.042 656 Dihedral : 5.705 42.182 538 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.48 % Allowed : 18.36 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.38), residues: 489 helix: 0.39 (0.27), residues: 369 sheet: -3.66 (1.34), residues: 10 loop : -2.64 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 487 TYR 0.016 0.001 TYR A 275 PHE 0.013 0.002 PHE A 208 TRP 0.009 0.001 TRP A 357 HIS 0.001 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3896) covalent geometry : angle 0.63158 ( 5312) SS BOND : bond 0.00465 ( 2) SS BOND : angle 2.31707 ( 4) hydrogen bonds : bond 0.04538 ( 248) hydrogen bonds : angle 4.26579 ( 744) ********************** 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 59 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.148 Fit side-chains REVERT: A 124 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6376 (mtt180) REVERT: A 286 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7753 (mt) REVERT: A 394 MET cc_start: 0.7895 (mmm) cc_final: 0.7175 (mtp) REVERT: A 398 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6320 (tt) REVERT: A 434 ARG cc_start: 0.6970 (mmt180) cc_final: 0.6692 (mmt180) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.0801 time to fit residues: 5.6303 Evaluate side-chains 59 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 286 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.0370 chunk 17 optimal weight: 0.5980 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.164951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143308 restraints weight = 4588.318| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.87 r_work: 0.3519 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3898 Z= 0.143 Angle : 0.617 9.547 5316 Z= 0.298 Chirality : 0.041 0.174 634 Planarity : 0.004 0.042 656 Dihedral : 5.732 42.255 538 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.98 % Allowed : 17.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.38), residues: 489 helix: 0.42 (0.27), residues: 367 sheet: -3.65 (1.35), residues: 10 loop : -2.53 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 487 TYR 0.016 0.001 TYR A 275 PHE 0.016 0.002 PHE A 208 TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3896) covalent geometry : angle 0.61464 ( 5312) SS BOND : bond 0.00412 ( 2) SS BOND : angle 2.16614 ( 4) hydrogen bonds : bond 0.04555 ( 248) hydrogen bonds : angle 4.25907 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1118.07 seconds wall clock time: 19 minutes 53.61 seconds (1193.61 seconds total)