Starting phenix.real_space_refine on Tue Feb 3 14:27:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unx_64368/02_2026/9unx_64368.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unx_64368/02_2026/9unx_64368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9unx_64368/02_2026/9unx_64368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unx_64368/02_2026/9unx_64368.map" model { file = "/net/cci-nas-00/data/ceres_data/9unx_64368/02_2026/9unx_64368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unx_64368/02_2026/9unx_64368.cif" } resolution = 3.45 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= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 29 5.16 5 C 2375 2.51 5 N 620 2.21 5 O 622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3647 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3613 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' BR': 1, 'OLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.65, per 1000 atoms: 0.18 Number of scatterers: 3647 At special positions: 0 Unit cell: (96.5016, 59.3856, 71.7576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 29 16.00 O 622 8.00 N 620 7.00 C 2375 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 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " 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: 0.18 Conformation dependent library (CDL) restraints added in 92.3 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 862 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 81.4% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.986A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 159 removed outlier: 4.026A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 removed outlier: 3.727A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.536A pdb=" N TYR A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.566A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.589A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.919A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.555A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.921A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.878A pdb=" N GLY A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 448 removed outlier: 3.750A pdb=" N GLY A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 492 through 504 removed outlier: 4.164A pdb=" N ALA A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 243 hydrogen bonds defined for protein. 720 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: 0.49 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1122 1.34 - 1.45: 523 1.45 - 1.57: 2043 1.57 - 1.69: 2 1.69 - 1.81: 45 Bond restraints: 3735 Sorted by residual: bond pdb=" C15 OLM A 602 " pdb=" C18 OLM A 602 " ideal model delta sigma weight residual 1.491 1.583 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C5 OLM A 602 " pdb=" C8 OLM A 602 " ideal model delta sigma weight residual 1.479 1.567 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C13 OLM A 602 " pdb=" C14 OLM A 602 " ideal model delta sigma weight residual 1.463 1.509 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" C ILE A 269 " pdb=" N GLU A 270 " ideal model delta sigma weight residual 1.330 1.300 0.029 1.31e-02 5.83e+03 5.05e+00 bond pdb=" C16 OLM A 602 " pdb=" N6 OLM A 602 " ideal model delta sigma weight residual 1.368 1.325 0.043 2.00e-02 2.50e+03 4.69e+00 ... (remaining 3730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 4981 1.46 - 2.92: 68 2.92 - 4.38: 22 4.38 - 5.84: 12 5.84 - 7.30: 1 Bond angle restraints: 5084 Sorted by residual: angle pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" CD PRO A 333 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.82e+00 angle pdb=" O1 OLM A 602 " pdb=" C21 OLM A 602 " pdb=" O2 OLM A 602 " ideal model delta sigma weight residual 127.27 119.97 7.30 3.00e+00 1.11e-01 5.92e+00 angle pdb=" CA MET A 452 " pdb=" CB MET A 452 " pdb=" CG MET A 452 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.63e+00 angle pdb=" N PRO A 333 " pdb=" CD PRO A 333 " pdb=" CG PRO A 333 " ideal model delta sigma weight residual 103.20 100.27 2.93 1.50e+00 4.44e-01 3.83e+00 angle pdb=" C16 OLM A 602 " pdb=" C17 OLM A 602 " pdb=" C21 OLM A 602 " ideal model delta sigma weight residual 132.53 127.13 5.40 3.00e+00 1.11e-01 3.24e+00 ... (remaining 5079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 2055 28.14 - 56.29: 126 56.29 - 84.43: 15 84.43 - 112.58: 0 112.58 - 140.72: 1 Dihedral angle restraints: 2197 sinusoidal: 856 harmonic: 1341 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -166.36 80.36 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" C3 OLM A 602 " pdb=" C1 OLM A 602 " pdb=" C2 OLM A 602 " pdb=" N1 OLM A 602 " ideal model delta sinusoidal sigma weight residual -125.43 15.29 -140.72 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CG ARG A 454 " pdb=" CD ARG A 454 " pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sinusoidal sigma weight residual 90.00 134.97 -44.97 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 2194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 385 0.026 - 0.052: 131 0.052 - 0.078: 45 0.078 - 0.104: 20 0.104 - 0.130: 6 Chirality restraints: 587 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL A 365 " pdb=" N VAL A 365 " pdb=" C VAL A 365 " pdb=" CB VAL A 365 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 584 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 332 " 0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 333 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 67 " 0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 68 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 116 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 117 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.024 5.00e-02 4.00e+02 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 892 2.79 - 3.32: 3525 3.32 - 3.84: 6028 3.84 - 4.37: 6950 4.37 - 4.90: 12102 Nonbonded interactions: 29497 Sorted by model distance: nonbonded pdb=" OG SER A 175 " pdb=" O PHE A 191 " model vdw 2.262 3.040 nonbonded pdb=" O ARG A 273 " pdb=" OG SER A 276 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 278 " pdb=" OG SER A 278 " model vdw 2.368 3.040 nonbonded pdb=" OE2 GLU A 506 " pdb=" N LEU A 508 " model vdw 2.417 3.120 nonbonded pdb=" O GLY A 446 " pdb=" NE ARG A 454 " model vdw 2.432 3.120 ... (remaining 29492 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.670 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.004 0.092 3737 Z= 0.195 Angle : 0.528 7.300 5088 Z= 0.251 Chirality : 0.035 0.130 587 Planarity : 0.005 0.085 633 Dihedral : 16.726 140.721 1329 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 23.71 % Favored : 76.29 % 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 are not related in a simple way. whole: 0.04 (0.39), residues: 459 helix: 0.17 (0.28), residues: 341 sheet: 0.23 (1.90), residues: 10 loop : 0.02 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.006 0.001 TYR A 353 PHE 0.013 0.001 PHE A 262 TRP 0.006 0.001 TRP A 274 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3735) covalent geometry : angle 0.52783 ( 5084) SS BOND : bond 0.00325 ( 2) SS BOND : angle 0.34475 ( 4) hydrogen bonds : bond 0.26387 ( 243) hydrogen bonds : angle 8.15495 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.133 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0634 time to fit residues: 5.0638 Evaluate side-chains 59 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122294 restraints weight = 4337.479| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.99 r_work: 0.3250 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3737 Z= 0.158 Angle : 0.574 5.534 5088 Z= 0.292 Chirality : 0.039 0.127 587 Planarity : 0.005 0.056 633 Dihedral : 8.799 136.380 520 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.87 % Allowed : 20.36 % Favored : 75.77 % 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 are not related in a simple way. whole: 1.04 (0.40), residues: 459 helix: 1.03 (0.28), residues: 352 sheet: -0.07 (1.86), residues: 10 loop : -0.16 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.014 0.001 TYR A 264 PHE 0.018 0.002 PHE A 258 TRP 0.012 0.001 TRP A 247 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3735) covalent geometry : angle 0.57436 ( 5084) SS BOND : bond 0.00749 ( 2) SS BOND : angle 0.63474 ( 4) hydrogen bonds : bond 0.05303 ( 243) hydrogen bonds : angle 4.88129 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.130 Fit side-chains REVERT: A 81 PHE cc_start: 0.8018 (m-80) cc_final: 0.7692 (m-80) REVERT: A 236 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7288 (tt) REVERT: A 359 ASP cc_start: 0.8346 (t0) cc_final: 0.7965 (m-30) REVERT: A 454 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7258 (ttm170) REVERT: A 506 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7722 (tp30) outliers start: 15 outliers final: 10 residues processed: 79 average time/residue: 0.0523 time to fit residues: 5.4309 Evaluate side-chains 73 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 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 = 0.3628 r_free = 0.3628 target = 0.148062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121430 restraints weight = 4323.551| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.01 r_work: 0.3232 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3737 Z= 0.152 Angle : 0.590 7.962 5088 Z= 0.283 Chirality : 0.039 0.133 587 Planarity : 0.004 0.051 633 Dihedral : 8.244 134.936 520 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.38 % Allowed : 21.65 % Favored : 73.97 % 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 are not related in a simple way. whole: 1.35 (0.40), residues: 459 helix: 1.29 (0.28), residues: 347 sheet: -0.06 (1.87), residues: 10 loop : -0.12 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 454 TYR 0.015 0.001 TYR A 264 PHE 0.014 0.001 PHE A 258 TRP 0.009 0.001 TRP A 247 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3735) covalent geometry : angle 0.59016 ( 5084) SS BOND : bond 0.00792 ( 2) SS BOND : angle 0.78125 ( 4) hydrogen bonds : bond 0.04548 ( 243) hydrogen bonds : angle 4.48845 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.130 Fit side-chains REVERT: A 81 PHE cc_start: 0.8013 (m-80) cc_final: 0.7662 (m-80) REVERT: A 338 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6974 (tt) REVERT: A 359 ASP cc_start: 0.8404 (t0) cc_final: 0.8153 (t0) REVERT: A 448 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8596 (tp) REVERT: A 454 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7324 (ttm170) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 0.0527 time to fit residues: 4.9171 Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.0040 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.152554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126750 restraints weight = 4176.977| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.81 r_work: 0.3295 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3737 Z= 0.117 Angle : 0.572 12.564 5088 Z= 0.268 Chirality : 0.038 0.140 587 Planarity : 0.004 0.043 633 Dihedral : 7.766 132.194 520 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.41 % Allowed : 22.42 % Favored : 72.16 % 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 are not related in a simple way. whole: 1.68 (0.40), residues: 459 helix: 1.55 (0.29), residues: 347 sheet: -0.06 (1.82), residues: 10 loop : -0.07 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.011 0.001 TYR A 264 PHE 0.012 0.001 PHE A 258 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3735) covalent geometry : angle 0.57217 ( 5084) SS BOND : bond 0.00587 ( 2) SS BOND : angle 0.64920 ( 4) hydrogen bonds : bond 0.03836 ( 243) hydrogen bonds : angle 4.23765 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.077 Fit side-chains REVERT: A 140 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 236 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7359 (tt) REVERT: A 338 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6797 (tt) REVERT: A 359 ASP cc_start: 0.8401 (t0) cc_final: 0.8117 (t0) REVERT: A 448 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8558 (tp) outliers start: 21 outliers final: 13 residues processed: 71 average time/residue: 0.0325 time to fit residues: 3.0462 Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.0370 chunk 26 optimal weight: 0.4980 chunk 31 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128410 restraints weight = 4204.771| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.79 r_work: 0.3312 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3737 Z= 0.110 Angle : 0.546 9.999 5088 Z= 0.257 Chirality : 0.037 0.129 587 Planarity : 0.004 0.039 633 Dihedral : 7.504 131.357 520 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.67 % Allowed : 22.42 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.40), residues: 459 helix: 1.72 (0.29), residues: 349 sheet: 0.09 (1.84), residues: 10 loop : -0.06 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.011 0.001 TYR A 264 PHE 0.010 0.001 PHE A 258 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3735) covalent geometry : angle 0.54622 ( 5084) SS BOND : bond 0.00543 ( 2) SS BOND : angle 0.61838 ( 4) hydrogen bonds : bond 0.03611 ( 243) hydrogen bonds : angle 4.10573 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.126 Fit side-chains REVERT: A 81 PHE cc_start: 0.8184 (m-80) cc_final: 0.7918 (m-80) REVERT: A 338 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6682 (tt) REVERT: A 359 ASP cc_start: 0.8397 (t0) cc_final: 0.7954 (m-30) REVERT: A 448 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8454 (tp) outliers start: 22 outliers final: 16 residues processed: 69 average time/residue: 0.0471 time to fit residues: 4.2843 Evaluate side-chains 66 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.152604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126741 restraints weight = 4245.578| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.83 r_work: 0.3296 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3737 Z= 0.122 Angle : 0.537 8.717 5088 Z= 0.258 Chirality : 0.038 0.130 587 Planarity : 0.004 0.037 633 Dihedral : 7.423 131.017 520 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 7.47 % Allowed : 21.91 % Favored : 70.62 % 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 are not related in a simple way. whole: 1.97 (0.40), residues: 459 helix: 1.76 (0.29), residues: 348 sheet: -0.02 (1.80), residues: 10 loop : -0.02 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.013 0.001 TYR A 264 PHE 0.021 0.001 PHE A 347 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3735) covalent geometry : angle 0.53715 ( 5084) SS BOND : bond 0.00639 ( 2) SS BOND : angle 0.69392 ( 4) hydrogen bonds : bond 0.03649 ( 243) hydrogen bonds : angle 4.08228 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.076 Fit side-chains REVERT: A 131 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7733 (mtm-85) REVERT: A 140 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7766 (mt) REVERT: A 236 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7406 (tt) REVERT: A 338 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6739 (tt) REVERT: A 359 ASP cc_start: 0.8497 (t0) cc_final: 0.8027 (m-30) REVERT: A 444 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 448 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8387 (tp) outliers start: 29 outliers final: 18 residues processed: 75 average time/residue: 0.0398 time to fit residues: 3.8447 Evaluate side-chains 76 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.125589 restraints weight = 4331.744| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.87 r_work: 0.3282 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3737 Z= 0.133 Angle : 0.571 11.294 5088 Z= 0.271 Chirality : 0.038 0.129 587 Planarity : 0.004 0.035 633 Dihedral : 7.400 130.358 520 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 6.96 % Allowed : 22.42 % Favored : 70.62 % 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 are not related in a simple way. whole: 1.95 (0.40), residues: 459 helix: 1.78 (0.29), residues: 347 sheet: 0.03 (1.81), residues: 10 loop : -0.14 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.014 0.001 TYR A 264 PHE 0.012 0.001 PHE A 152 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3735) covalent geometry : angle 0.57130 ( 5084) SS BOND : bond 0.00679 ( 2) SS BOND : angle 0.71510 ( 4) hydrogen bonds : bond 0.03763 ( 243) hydrogen bonds : angle 4.11932 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.075 Fit side-chains REVERT: A 81 PHE cc_start: 0.8184 (m-80) cc_final: 0.7908 (m-80) REVERT: A 131 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7732 (mtm-85) REVERT: A 140 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7799 (mt) REVERT: A 236 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7385 (tt) REVERT: A 338 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6793 (tt) REVERT: A 444 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7415 (t80) REVERT: A 448 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8328 (tp) outliers start: 27 outliers final: 18 residues processed: 80 average time/residue: 0.0466 time to fit residues: 4.8020 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.152550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127215 restraints weight = 4209.417| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.81 r_work: 0.3300 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3737 Z= 0.118 Angle : 0.582 14.882 5088 Z= 0.270 Chirality : 0.038 0.128 587 Planarity : 0.004 0.033 633 Dihedral : 7.380 129.597 520 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 7.22 % Allowed : 23.45 % Favored : 69.33 % 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 are not related in a simple way. whole: 1.98 (0.40), residues: 459 helix: 1.77 (0.29), residues: 348 sheet: 0.01 (1.81), residues: 10 loop : -0.04 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.012 0.001 TYR A 264 PHE 0.024 0.001 PHE A 347 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3735) covalent geometry : angle 0.58154 ( 5084) SS BOND : bond 0.00595 ( 2) SS BOND : angle 0.65322 ( 4) hydrogen bonds : bond 0.03597 ( 243) hydrogen bonds : angle 4.08101 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.078 Fit side-chains REVERT: A 131 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7714 (mtm-85) REVERT: A 140 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7785 (mt) REVERT: A 236 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7386 (tt) REVERT: A 338 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6613 (tt) REVERT: A 342 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7423 (mp) REVERT: A 359 ASP cc_start: 0.8368 (t0) cc_final: 0.7940 (m-30) REVERT: A 444 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7383 (t80) outliers start: 28 outliers final: 20 residues processed: 77 average time/residue: 0.0476 time to fit residues: 4.7071 Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.151476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126383 restraints weight = 4233.373| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.79 r_work: 0.3291 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3737 Z= 0.130 Angle : 0.599 14.844 5088 Z= 0.282 Chirality : 0.038 0.132 587 Planarity : 0.004 0.032 633 Dihedral : 7.383 129.452 520 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 7.99 % Allowed : 23.20 % Favored : 68.81 % 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 are not related in a simple way. whole: 1.92 (0.40), residues: 459 helix: 1.71 (0.29), residues: 351 sheet: -0.00 (1.80), residues: 10 loop : 0.00 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.013 0.001 TYR A 264 PHE 0.011 0.001 PHE A 152 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3735) covalent geometry : angle 0.59907 ( 5084) SS BOND : bond 0.00650 ( 2) SS BOND : angle 0.66872 ( 4) hydrogen bonds : bond 0.03700 ( 243) hydrogen bonds : angle 4.10517 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.075 Fit side-chains REVERT: A 140 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7822 (mt) REVERT: A 236 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7383 (tt) REVERT: A 338 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6650 (tt) REVERT: A 342 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7415 (mp) REVERT: A 359 ASP cc_start: 0.8460 (t0) cc_final: 0.8017 (m-30) REVERT: A 444 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7405 (t80) outliers start: 31 outliers final: 23 residues processed: 84 average time/residue: 0.0468 time to fit residues: 5.0834 Evaluate side-chains 86 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 overall best weight: 0.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129239 restraints weight = 4240.743| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.84 r_work: 0.3328 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3737 Z= 0.108 Angle : 0.589 15.038 5088 Z= 0.275 Chirality : 0.037 0.128 587 Planarity : 0.004 0.032 633 Dihedral : 7.336 128.462 520 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.41 % Allowed : 25.26 % Favored : 69.33 % 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 are not related in a simple way. whole: 2.10 (0.40), residues: 459 helix: 1.84 (0.29), residues: 349 sheet: 0.01 (1.82), residues: 10 loop : 0.04 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.008 0.001 TYR A 264 PHE 0.029 0.001 PHE A 347 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.000 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3735) covalent geometry : angle 0.58885 ( 5084) SS BOND : bond 0.00488 ( 2) SS BOND : angle 0.61143 ( 4) hydrogen bonds : bond 0.03400 ( 243) hydrogen bonds : angle 4.00841 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.143 Fit side-chains REVERT: A 9 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: A 140 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7795 (mt) REVERT: A 280 ARG cc_start: 0.6899 (mmm160) cc_final: 0.6572 (mmm160) REVERT: A 338 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6669 (tt) REVERT: A 342 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 359 ASP cc_start: 0.8329 (t0) cc_final: 0.7889 (m-30) REVERT: A 444 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7366 (t80) outliers start: 21 outliers final: 16 residues processed: 73 average time/residue: 0.0417 time to fit residues: 4.0238 Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 15 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.154754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128595 restraints weight = 4085.609| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.80 r_work: 0.3325 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3737 Z= 0.117 Angle : 0.590 14.838 5088 Z= 0.278 Chirality : 0.038 0.130 587 Planarity : 0.004 0.032 633 Dihedral : 7.350 128.664 520 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.15 % Allowed : 26.55 % Favored : 68.30 % 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 are not related in a simple way. whole: 2.11 (0.40), residues: 459 helix: 1.85 (0.29), residues: 349 sheet: -0.01 (1.81), residues: 10 loop : 0.10 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.010 0.001 TYR A 264 PHE 0.011 0.001 PHE A 152 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.000 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3735) covalent geometry : angle 0.58960 ( 5084) SS BOND : bond 0.00519 ( 2) SS BOND : angle 0.58634 ( 4) hydrogen bonds : bond 0.03449 ( 243) hydrogen bonds : angle 3.99983 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 838.95 seconds wall clock time: 15 minutes 5.67 seconds (905.67 seconds total)