Starting phenix.real_space_refine on Tue Feb 11 07:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ont_17000/02_2025/8ont_17000_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ont_17000/02_2025/8ont_17000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ont_17000/02_2025/8ont_17000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ont_17000/02_2025/8ont_17000.map" model { file = "/net/cci-nas-00/data/ceres_data/8ont_17000/02_2025/8ont_17000_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ont_17000/02_2025/8ont_17000_trim.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 2831 2.51 5 N 696 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4316 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "B" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 3.07, per 1000 atoms: 0.71 Number of scatterers: 4316 At special positions: 0 Unit cell: (75.516, 96.348, 78.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 762 8.00 N 696 7.00 C 2831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 498.0 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1034 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 72.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 84 through 110 removed outlier: 3.546A pdb=" N VAL A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.553A pdb=" N LEU A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 157 Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 159 through 181 removed outlier: 4.672A pdb=" N LEU A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 208 removed outlier: 3.684A pdb=" N GLU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 242 through 253 removed outlier: 4.282A pdb=" N PHE A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 252 " --> pdb=" O HIS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 300 Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.916A pdb=" N ASP A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.850A pdb=" N LEU A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 325 " --> pdb=" O MET A 321 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 362 removed outlier: 4.042A pdb=" N VAL A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 390 Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 391 through 423 Proline residue: A 411 - end of helix Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 433 through 466 removed outlier: 3.891A pdb=" N HIS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.693A pdb=" N ARG B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.398A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 939 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: 1.13 Time building geometry restraints manager: 1.33 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: 658 1.31 - 1.43: 1199 1.43 - 1.56: 2509 1.56 - 1.68: 2 1.68 - 1.81: 42 Bond restraints: 4410 Sorted by residual: bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.434 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C' PLC A 601 " pdb=" C1' PLC A 601 " ideal model delta sigma weight residual 1.503 1.569 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " ideal model delta sigma weight residual 1.634 1.689 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CB PLC A 601 " pdb=" C1B PLC A 601 " ideal model delta sigma weight residual 1.504 1.556 -0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 4405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 5947 3.19 - 6.39: 44 6.39 - 9.58: 3 9.58 - 12.77: 1 12.77 - 15.96: 1 Bond angle restraints: 5996 Sorted by residual: angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 109.58 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O1P PLC A 601 " pdb=" P PLC A 601 " pdb=" O2P PLC A 601 " ideal model delta sigma weight residual 119.61 109.11 10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C1' PLC A 601 " pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 111.19 119.79 -8.60 3.00e+00 1.11e-01 8.22e+00 angle pdb=" C1B PLC A 601 " pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 111.34 119.59 -8.25 3.00e+00 1.11e-01 7.57e+00 angle pdb=" C ALA A 300 " pdb=" CA ALA A 300 " pdb=" CB ALA A 300 " ideal model delta sigma weight residual 110.42 115.43 -5.01 1.99e+00 2.53e-01 6.34e+00 ... (remaining 5991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 2315 20.83 - 41.66: 234 41.66 - 62.48: 34 62.48 - 83.31: 5 83.31 - 104.14: 6 Dihedral angle restraints: 2594 sinusoidal: 986 harmonic: 1608 Sorted by residual: dihedral pdb=" O2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual -55.71 48.43 -104.14 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" C3 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual 67.16 168.71 -101.55 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" C2' PLC A 601 " pdb=" C' PLC A 601 " pdb=" C1' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sinusoidal sigma weight residual 169.53 79.09 90.44 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 576 0.046 - 0.093: 114 0.093 - 0.139: 20 0.139 - 0.185: 0 0.185 - 0.231: 1 Chirality restraints: 711 Sorted by residual: chirality pdb=" C2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C3 PLC A 601 " pdb=" O2 PLC A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.54 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO A 143 " pdb=" N PRO A 143 " pdb=" C PRO A 143 " pdb=" CB PRO A 143 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 708 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.307 9.50e-02 1.11e+02 1.38e-01 1.17e+01 pdb=" NE ARG B 19 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 87 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 88 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 142 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 143 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.019 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 30 2.51 - 3.10: 3511 3.10 - 3.70: 6575 3.70 - 4.30: 8905 4.30 - 4.90: 15773 Nonbonded interactions: 34794 Sorted by model distance: nonbonded pdb=" OH TYR A 82 " pdb=" OG1 THR A 296 " model vdw 1.908 3.040 nonbonded pdb=" O SER A 139 " pdb=" OG SER A 402 " model vdw 2.025 3.040 nonbonded pdb=" O VAL A 491 " pdb=" OG1 THR A 495 " model vdw 2.071 3.040 nonbonded pdb=" OD1 ASP A 66 " pdb=" OG1 THR A 346 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR A 351 " pdb=" ND2 ASN A 372 " model vdw 2.083 3.120 ... (remaining 34789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 1.160 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: 1.610 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 13.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.006 0.107 4410 Z= 0.376 Angle : 0.671 15.964 5996 Z= 0.314 Chirality : 0.038 0.231 711 Planarity : 0.006 0.138 733 Dihedral : 16.916 104.141 1554 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.87 % Allowed : 25.22 % Favored : 73.91 % 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: 1.63 (0.38), residues: 552 helix: 2.54 (0.27), residues: 360 sheet: -0.03 (0.82), residues: 47 loop : -2.54 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.003 0.001 HIS A 248 PHE 0.014 0.001 PHE A 236 TYR 0.017 0.002 TYR B 80 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.474 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.2424 time to fit residues: 15.8549 Evaluate side-chains 54 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 372 ASN A 451 ASN A 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.175600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.146027 restraints weight = 4395.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142632 restraints weight = 5337.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142881 restraints weight = 5489.676| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4410 Z= 0.295 Angle : 0.609 5.965 5996 Z= 0.311 Chirality : 0.041 0.143 711 Planarity : 0.005 0.039 733 Dihedral : 8.595 79.803 640 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.48 % Allowed : 21.96 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.37), residues: 552 helix: 2.60 (0.26), residues: 365 sheet: -0.05 (0.79), residues: 49 loop : -2.62 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.012 0.001 PHE A 236 TYR 0.014 0.001 TYR A 459 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.430 Fit side-chains REVERT: A 248 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6157 (m-70) REVERT: B 108 SER cc_start: 0.8711 (m) cc_final: 0.8463 (m) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.1983 time to fit residues: 16.4587 Evaluate side-chains 59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.0000 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.194658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3995 r_free = 0.3995 target = 0.183793 restraints weight = 4157.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.175103 restraints weight = 6520.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.174901 restraints weight = 6532.345| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4410 Z= 0.250 Angle : 0.552 6.253 5996 Z= 0.284 Chirality : 0.039 0.136 711 Planarity : 0.005 0.053 733 Dihedral : 8.174 69.584 640 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.48 % Allowed : 21.74 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.37), residues: 552 helix: 2.63 (0.26), residues: 363 sheet: 0.31 (0.79), residues: 47 loop : -2.19 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.009 0.001 PHE A 236 TYR 0.012 0.001 TYR A 459 ARG 0.004 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.441 Fit side-chains REVERT: A 339 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7866 (tt) REVERT: B 108 SER cc_start: 0.8651 (m) cc_final: 0.8377 (m) outliers start: 16 outliers final: 8 residues processed: 63 average time/residue: 0.2048 time to fit residues: 15.9209 Evaluate side-chains 57 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.178386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145290 restraints weight = 4408.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145513 restraints weight = 4300.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.145556 restraints weight = 4200.584| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4410 Z= 0.240 Angle : 0.539 6.617 5996 Z= 0.276 Chirality : 0.039 0.136 711 Planarity : 0.004 0.054 733 Dihedral : 7.852 63.486 638 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.70 % Allowed : 21.96 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.37), residues: 552 helix: 2.60 (0.26), residues: 363 sheet: 0.39 (0.78), residues: 47 loop : -2.14 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.010 0.001 PHE A 361 TYR 0.012 0.001 TYR A 335 ARG 0.004 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.477 Fit side-chains REVERT: A 248 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.6388 (m-70) REVERT: A 339 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7819 (tt) REVERT: B 108 SER cc_start: 0.8656 (m) cc_final: 0.8389 (m) outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.1867 time to fit residues: 15.2285 Evaluate side-chains 61 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.177367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143682 restraints weight = 4436.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143810 restraints weight = 4313.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143947 restraints weight = 4254.089| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4410 Z= 0.260 Angle : 0.550 6.781 5996 Z= 0.281 Chirality : 0.039 0.136 711 Planarity : 0.004 0.055 733 Dihedral : 7.779 59.678 638 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.78 % Allowed : 21.30 % Favored : 73.91 % 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: 1.87 (0.37), residues: 552 helix: 2.52 (0.26), residues: 363 sheet: 0.49 (0.79), residues: 47 loop : -2.11 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.008 0.001 PHE A 361 TYR 0.012 0.001 TYR A 335 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.432 Fit side-chains REVERT: A 140 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7499 (t0) REVERT: A 248 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.6278 (m-70) REVERT: A 285 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7742 (mp) REVERT: A 339 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7844 (tt) REVERT: B 108 SER cc_start: 0.8657 (m) cc_final: 0.8393 (m) outliers start: 22 outliers final: 14 residues processed: 72 average time/residue: 0.1753 time to fit residues: 15.9087 Evaluate side-chains 70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.179549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.153277 restraints weight = 4368.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.150169 restraints weight = 5872.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.150229 restraints weight = 6380.181| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4410 Z= 0.207 Angle : 0.541 9.653 5996 Z= 0.271 Chirality : 0.038 0.137 711 Planarity : 0.004 0.054 733 Dihedral : 7.583 57.982 638 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.78 % Allowed : 21.74 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.37), residues: 552 helix: 2.58 (0.26), residues: 362 sheet: 0.65 (0.79), residues: 47 loop : -2.06 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.011 0.001 PHE A 361 TYR 0.010 0.001 TYR A 459 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.423 Fit side-chains REVERT: A 248 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.6460 (m-70) REVERT: A 253 LEU cc_start: 0.4677 (OUTLIER) cc_final: 0.4415 (tp) REVERT: B 108 SER cc_start: 0.8626 (m) cc_final: 0.8373 (m) outliers start: 22 outliers final: 15 residues processed: 72 average time/residue: 0.1861 time to fit residues: 16.7235 Evaluate side-chains 66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** 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 = 0.3911 r_free = 0.3911 target = 0.179317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.154007 restraints weight = 4389.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.149410 restraints weight = 5121.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.149507 restraints weight = 6231.491| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4410 Z= 0.237 Angle : 0.550 8.471 5996 Z= 0.278 Chirality : 0.039 0.137 711 Planarity : 0.004 0.055 733 Dihedral : 7.351 57.554 638 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.13 % Allowed : 22.83 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.37), residues: 552 helix: 2.56 (0.26), residues: 362 sheet: 0.74 (0.81), residues: 47 loop : -2.05 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.013 0.001 PHE A 64 TYR 0.010 0.001 TYR A 335 ARG 0.007 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.446 Fit side-chains REVERT: A 140 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 248 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6603 (m-70) REVERT: A 253 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4825 (tp) REVERT: A 285 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7803 (mp) outliers start: 19 outliers final: 13 residues processed: 66 average time/residue: 0.2156 time to fit residues: 17.3911 Evaluate side-chains 64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.173671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142488 restraints weight = 4430.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.138211 restraints weight = 6389.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138914 restraints weight = 6543.570| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4410 Z= 0.265 Angle : 0.565 8.205 5996 Z= 0.284 Chirality : 0.039 0.136 711 Planarity : 0.004 0.055 733 Dihedral : 6.836 55.073 636 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.35 % Allowed : 23.26 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.37), residues: 552 helix: 2.49 (0.26), residues: 362 sheet: 0.82 (0.81), residues: 47 loop : -2.03 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.009 0.001 PHE A 361 TYR 0.011 0.001 TYR A 335 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.486 Fit side-chains REVERT: A 140 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7597 (t0) REVERT: A 248 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6547 (m-70) REVERT: A 253 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4825 (tp) REVERT: A 285 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7761 (mp) outliers start: 20 outliers final: 14 residues processed: 66 average time/residue: 0.1939 time to fit residues: 15.9097 Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.173793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.140771 restraints weight = 4437.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137529 restraints weight = 6521.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138268 restraints weight = 6380.753| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4410 Z= 0.254 Angle : 0.574 8.060 5996 Z= 0.285 Chirality : 0.039 0.137 711 Planarity : 0.004 0.055 733 Dihedral : 6.586 56.097 636 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.13 % Allowed : 23.26 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.37), residues: 552 helix: 2.47 (0.26), residues: 362 sheet: 0.88 (0.81), residues: 47 loop : -2.03 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.009 0.001 PHE A 361 TYR 0.011 0.001 TYR A 335 ARG 0.007 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.435 Fit side-chains REVERT: A 140 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7577 (t0) REVERT: A 248 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6510 (m-70) REVERT: A 253 LEU cc_start: 0.5126 (OUTLIER) cc_final: 0.4853 (tp) REVERT: A 285 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7761 (mp) outliers start: 19 outliers final: 14 residues processed: 63 average time/residue: 0.1652 time to fit residues: 13.4471 Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.181351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.155278 restraints weight = 4310.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.151011 restraints weight = 5025.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.150764 restraints weight = 5681.197| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4410 Z= 0.194 Angle : 0.552 8.010 5996 Z= 0.273 Chirality : 0.038 0.142 711 Planarity : 0.004 0.055 733 Dihedral : 6.267 56.642 636 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.26 % Allowed : 24.35 % Favored : 72.39 % 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: 2.01 (0.37), residues: 552 helix: 2.57 (0.26), residues: 364 sheet: 1.04 (0.80), residues: 47 loop : -2.10 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.001 0.001 HIS A 248 PHE 0.013 0.001 PHE A 361 TYR 0.009 0.001 TYR A 459 ARG 0.007 0.000 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.444 Fit side-chains REVERT: A 140 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7482 (t0) REVERT: A 248 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.6367 (m-70) REVERT: A 253 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4845 (tp) outliers start: 15 outliers final: 10 residues processed: 59 average time/residue: 0.1914 time to fit residues: 14.1534 Evaluate side-chains 56 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.178241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.144016 restraints weight = 4416.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.144022 restraints weight = 4239.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.144022 restraints weight = 4221.065| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4410 Z= 0.273 Angle : 0.591 7.940 5996 Z= 0.294 Chirality : 0.041 0.279 711 Planarity : 0.005 0.056 733 Dihedral : 5.767 47.191 633 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.26 % Allowed : 24.35 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.37), residues: 552 helix: 2.46 (0.26), residues: 362 sheet: 1.16 (0.81), residues: 47 loop : -2.01 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.009 0.001 PHE A 361 TYR 0.010 0.001 TYR A 459 ARG 0.007 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1524.48 seconds wall clock time: 28 minutes 3.21 seconds (1683.21 seconds total)