Starting phenix.real_space_refine on Sat Apr 26 23:35:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irw_60823/04_2025/9irw_60823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irw_60823/04_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_60823/04_2025/9irw_60823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irw_60823/04_2025/9irw_60823.map" model { file = "/net/cci-nas-00/data/ceres_data/9irw_60823/04_2025/9irw_60823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irw_60823/04_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-5669/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: 2.90, per 1000 atoms: 0.76 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: 0.96 Conformation dependent library (CDL) restraints added in 553.5 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: 0.38 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: 1.03 Time building geometry restraints manager: 1.11 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: 1.130 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.790 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13568 ( 248) hydrogen bonds : angle 5.76815 ( 744) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.85993 ( 4) covalent geometry : bond 0.00701 ( 3896) covalent geometry : angle 0.72095 ( 5312) *********************** 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 : 0.397 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: 0.1747 time to fit residues: 14.5165 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 : 0.413 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151879 restraints weight = 4419.862| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.65 r_work: 0.3604 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 3898 Z= 0.180 Angle : 0.632 10.245 5316 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 Details of bonding type rmsd hydrogen bonds : bond 0.05403 ( 248) hydrogen bonds : angle 4.81660 ( 744) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.93002 ( 4) covalent geometry : bond 0.00411 ( 3896) covalent geometry : angle 0.63215 ( 5312) *********************** 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 : 0.452 Fit side-chains REVERT: A 8 ASP cc_start: 0.7302 (m-30) cc_final: 0.7033 (m-30) REVERT: A 54 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 286 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8114 (mt) REVERT: A 394 MET cc_start: 0.7822 (mmm) cc_final: 0.7295 (mtp) REVERT: A 434 ARG cc_start: 0.7104 (mmt180) cc_final: 0.6812 (mmt180) REVERT: A 458 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7275 (mt-10) outliers start: 15 outliers final: 9 residues processed: 60 average time/residue: 0.1698 time to fit residues: 12.7316 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 : 0.420 ------------------------------------------------------------------------------- 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: 0.0870 chunk 8 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.177494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156491 restraints weight = 4363.238| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.64 r_work: 0.3657 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1264 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= 0.131 Angle : 0.577 8.096 5316 Z= 0.279 Chirality : 0.038 0.126 634 Planarity : 0.004 0.042 656 Dihedral : 6.618 47.529 544 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.22 % Allowed : 12.90 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.38), residues: 489 helix: 0.45 (0.28), residues: 365 sheet: -4.15 (1.31), residues: 10 loop : -2.41 (0.52), residues: 114 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 0.016 0.002 PHE A 269 TYR 0.016 0.001 TYR A 275 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 248) hydrogen bonds : angle 4.43869 ( 744) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.93561 ( 4) covalent geometry : bond 0.00282 ( 3896) covalent geometry : angle 0.57639 ( 5312) *********************** 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 67 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.392 Fit side-chains REVERT: A 8 ASP cc_start: 0.7282 (m-30) cc_final: 0.7010 (m-30) REVERT: A 286 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 394 MET cc_start: 0.7800 (mmm) cc_final: 0.7302 (mtp) REVERT: A 425 LEU cc_start: 0.7869 (mp) cc_final: 0.7605 (mp) REVERT: A 434 ARG cc_start: 0.7143 (mmt180) cc_final: 0.6863 (mmt180) REVERT: A 458 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7244 (mt-10) outliers start: 17 outliers final: 7 residues processed: 64 average time/residue: 0.1601 time to fit residues: 13.0164 Evaluate side-chains 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 139 CYS 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 363 THR 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: 0.6980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154638 restraints weight = 4507.488| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.67 r_work: 0.3603 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3898 Z= 0.179 Angle : 0.631 9.119 5316 Z= 0.304 Chirality : 0.041 0.136 634 Planarity : 0.005 0.042 656 Dihedral : 6.263 45.785 541 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.96 % Allowed : 14.89 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.38), residues: 489 helix: 0.26 (0.27), residues: 370 sheet: -4.18 (1.24), residues: 10 loop : -2.71 (0.51), residues: 109 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 0.002 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 248) hydrogen bonds : angle 4.46275 ( 744) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.70970 ( 4) covalent geometry : bond 0.00418 ( 3896) covalent geometry : angle 0.63112 ( 5312) *********************** 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 : 0.371 Fit side-chains REVERT: A 8 ASP cc_start: 0.7223 (m-30) cc_final: 0.6966 (m-30) REVERT: A 286 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8067 (mt) REVERT: A 394 MET cc_start: 0.7911 (mmm) cc_final: 0.7346 (mtp) REVERT: A 458 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7251 (mt-10) outliers start: 20 outliers final: 16 residues processed: 61 average time/residue: 0.1621 time to fit residues: 12.5319 Evaluate side-chains 61 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.177819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.156684 restraints weight = 4575.022| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.69 r_work: 0.3630 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3898 Z= 0.145 Angle : 0.597 9.026 5316 Z= 0.287 Chirality : 0.039 0.133 634 Planarity : 0.004 0.041 656 Dihedral : 6.217 45.645 541 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.47 % Allowed : 15.38 % Favored : 80.15 % 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 (0.27), residues: 367 sheet: -4.00 (1.25), residues: 10 loop : -2.48 (0.53), 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 0.016 0.002 PHE A 208 TYR 0.016 0.001 TYR A 275 ARG 0.002 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 248) hydrogen bonds : angle 4.35351 ( 744) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.74855 ( 4) covalent geometry : bond 0.00327 ( 3896) covalent geometry : angle 0.59719 ( 5312) *********************** 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 68 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.419 Fit side-chains REVERT: A 124 ARG cc_start: 0.7061 (mtm-85) cc_final: 0.6592 (mtt180) REVERT: A 255 VAL cc_start: 0.8467 (m) cc_final: 0.8204 (m) REVERT: A 286 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 394 MET cc_start: 0.7882 (mmm) cc_final: 0.7317 (mtp) REVERT: A 425 LEU cc_start: 0.7877 (mp) cc_final: 0.7644 (mp) REVERT: A 458 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7299 (mt-10) outliers start: 18 outliers final: 14 residues processed: 65 average time/residue: 0.2022 time to fit residues: 16.3233 Evaluate side-chains 61 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 424 THR 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: 0.0470 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.177911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156936 restraints weight = 4519.844| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.67 r_work: 0.3634 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1489 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= 0.148 Angle : 0.605 9.379 5316 Z= 0.291 Chirality : 0.041 0.199 634 Planarity : 0.004 0.041 656 Dihedral : 6.223 45.102 541 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.71 % Allowed : 15.14 % Favored : 80.15 % 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: 0.32 (0.27), residues: 367 sheet: -4.05 (1.24), residues: 10 loop : -2.47 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 PHE 0.016 0.002 PHE A 208 TYR 0.016 0.001 TYR A 275 ARG 0.005 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 248) hydrogen bonds : angle 4.34341 ( 744) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.69462 ( 4) covalent geometry : bond 0.00334 ( 3896) covalent geometry : angle 0.60459 ( 5312) *********************** 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 67 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.388 Fit side-chains REVERT: A 124 ARG cc_start: 0.7066 (mtm-85) cc_final: 0.6586 (mtt180) REVERT: A 286 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8032 (mt) REVERT: A 394 MET cc_start: 0.7897 (mmm) cc_final: 0.7317 (mtp) REVERT: A 425 LEU cc_start: 0.7936 (mp) cc_final: 0.7688 (mp) REVERT: A 434 ARG cc_start: 0.7325 (mmt180) cc_final: 0.6995 (mmt180) outliers start: 19 outliers final: 15 residues processed: 63 average time/residue: 0.1734 time to fit residues: 13.7452 Evaluate side-chains 64 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.176897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155960 restraints weight = 4481.116| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.65 r_work: 0.3622 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3898 Z= 0.167 Angle : 0.627 10.097 5316 Z= 0.300 Chirality : 0.042 0.168 634 Planarity : 0.005 0.042 656 Dihedral : 6.237 44.502 541 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.47 % Allowed : 15.88 % 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: -0.74 (0.37), residues: 489 helix: 0.28 (0.27), residues: 368 sheet: -4.08 (1.24), residues: 10 loop : -2.51 (0.53), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 PHE 0.016 0.002 PHE A 208 TYR 0.017 0.002 TYR A 275 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 248) hydrogen bonds : angle 4.36899 ( 744) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.66645 ( 4) covalent geometry : bond 0.00386 ( 3896) covalent geometry : angle 0.62702 ( 5312) *********************** 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 67 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.369 Fit side-chains REVERT: A 124 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.6525 (mtt180) REVERT: A 286 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 394 MET cc_start: 0.7879 (mmm) cc_final: 0.7326 (mtp) REVERT: A 425 LEU cc_start: 0.7988 (mp) cc_final: 0.7721 (mp) REVERT: A 434 ARG cc_start: 0.7325 (mmt180) cc_final: 0.6946 (mmt180) outliers start: 18 outliers final: 14 residues processed: 64 average time/residue: 0.1621 time to fit residues: 12.9315 Evaluate side-chains 63 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 350 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 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: 1.9990 chunk 6 optimal weight: 0.0060 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.178426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157447 restraints weight = 4516.948| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.66 r_work: 0.3639 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1596 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= 0.145 Angle : 0.618 9.759 5316 Z= 0.293 Chirality : 0.041 0.147 634 Planarity : 0.004 0.042 656 Dihedral : 5.931 43.270 539 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.47 % Allowed : 16.38 % 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 (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: -0.67 (0.38), residues: 489 helix: 0.32 (0.27), residues: 367 sheet: -4.00 (1.28), residues: 10 loop : -2.45 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 PHE 0.015 0.002 PHE A 208 TYR 0.017 0.001 TYR A 275 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 248) hydrogen bonds : angle 4.31984 ( 744) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.69049 ( 4) covalent geometry : bond 0.00325 ( 3896) covalent geometry : angle 0.61809 ( 5312) *********************** 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 67 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.426 Fit side-chains REVERT: A 124 ARG cc_start: 0.7102 (mtm-85) cc_final: 0.6483 (mtt180) REVERT: A 168 ASP cc_start: 0.7687 (m-30) cc_final: 0.7456 (m-30) REVERT: A 286 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8021 (mt) REVERT: A 394 MET cc_start: 0.7874 (mmm) cc_final: 0.7325 (mtp) REVERT: A 425 LEU cc_start: 0.8010 (mp) cc_final: 0.7733 (mp) REVERT: A 434 ARG cc_start: 0.7409 (mmt180) cc_final: 0.7065 (mmt180) outliers start: 18 outliers final: 15 residues processed: 64 average time/residue: 0.1760 time to fit residues: 14.1459 Evaluate side-chains 64 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.171069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150086 restraints weight = 4490.208| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.68 r_work: 0.3603 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 0.031 3898 Z= 0.142 Angle : 0.609 9.580 5316 Z= 0.291 Chirality : 0.041 0.143 634 Planarity : 0.004 0.042 656 Dihedral : 5.897 43.572 539 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.22 % Allowed : 16.87 % 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: -0.63 (0.38), residues: 489 helix: 0.34 (0.27), residues: 368 sheet: -3.87 (1.29), residues: 10 loop : -2.43 (0.54), residues: 111 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 0.002 PHE A 208 TYR 0.016 0.001 TYR A 275 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 248) hydrogen bonds : angle 4.28884 ( 744) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.67974 ( 4) covalent geometry : bond 0.00319 ( 3896) covalent geometry : angle 0.60907 ( 5312) *********************** 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: 17 poor density : 47 time to evaluate : 0.374 Fit side-chains REVERT: A 124 ARG cc_start: 0.7102 (mtm-85) cc_final: 0.6466 (mtt180) REVERT: A 286 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7964 (mt) REVERT: A 394 MET cc_start: 0.7883 (mmm) cc_final: 0.7317 (mtp) REVERT: A 434 ARG cc_start: 0.7324 (mmt180) cc_final: 0.6965 (mmt180) outliers start: 17 outliers final: 14 residues processed: 61 average time/residue: 0.1727 time to fit residues: 13.1053 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 : 0.404 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 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 = 0.3933 r_free = 0.3933 target = 0.170516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149831 restraints weight = 4566.807| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.69 r_work: 0.3587 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1682 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= 0.163 Angle : 0.640 11.669 5316 Z= 0.304 Chirality : 0.042 0.164 634 Planarity : 0.004 0.043 656 Dihedral : 5.974 43.626 539 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: -0.67 (0.38), residues: 489 helix: 0.31 (0.27), residues: 367 sheet: -3.79 (1.33), residues: 10 loop : -2.44 (0.53), 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 0.017 0.002 PHE A 208 TYR 0.017 0.002 TYR A 275 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 248) hydrogen bonds : angle 4.34680 ( 744) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.66537 ( 4) covalent geometry : bond 0.00375 ( 3896) covalent geometry : angle 0.64002 ( 5312) ********************** 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 62 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.371 Fit side-chains REVERT: A 124 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6484 (mtt180) REVERT: A 286 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7949 (mt) REVERT: A 394 MET cc_start: 0.7892 (mmm) cc_final: 0.7329 (mtp) REVERT: A 434 ARG cc_start: 0.7232 (mmt180) cc_final: 0.7007 (mmt180) outliers start: 16 outliers final: 14 residues processed: 59 average time/residue: 0.1793 time to fit residues: 13.2489 Evaluate side-chains 60 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.159092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144478 restraints weight = 4406.083| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.10 r_work: 0.3488 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3898 Z= 0.187 Angle : 0.665 12.366 5316 Z= 0.317 Chirality : 0.043 0.172 634 Planarity : 0.005 0.043 656 Dihedral : 6.053 44.133 539 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.72 % Allowed : 16.87 % 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 (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: 366 sheet: None (None), residues: 0 loop : -2.47 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.002 0.001 HIS A 428 PHE 0.019 0.002 PHE A 208 TYR 0.017 0.002 TYR A 275 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 248) hydrogen bonds : angle 4.44519 ( 744) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.69239 ( 4) covalent geometry : bond 0.00438 ( 3896) covalent geometry : angle 0.66527 ( 5312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.10 seconds wall clock time: 41 minutes 10.35 seconds (2470.35 seconds total)