Starting phenix.real_space_refine on Thu Mar 6 02:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ont_17000/03_2025/8ont_17000_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ont_17000/03_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_17000/03_2025/8ont_17000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ont_17000/03_2025/8ont_17000.map" model { file = "/net/cci-nas-00/data/ceres_data/8ont_17000/03_2025/8ont_17000_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ont_17000/03_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-5624/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: 3.36, per 1000 atoms: 0.78 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: 1.28 Conformation dependent library (CDL) restraints added in 557.7 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: 0.42 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: 1.24 Time building geometry restraints manager: 1.40 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: 0.490 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.510 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- 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 : 0.422 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.2425 time to fit residues: 15.7358 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 : 0.470 ------------------------------------------------------------------------------- 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 = 0.146021 restraints weight = 4395.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142634 restraints weight = 5326.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142893 restraints weight = 5485.209| |-----------------------------------------------------------------------------| 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 : 0.449 Fit side-chains REVERT: A 248 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6156 (m-70) REVERT: B 108 SER cc_start: 0.8712 (m) cc_final: 0.8463 (m) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.2021 time to fit residues: 16.7832 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 : 0.467 ------------------------------------------------------------------------------- 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: 0.5980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.193074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.177229 restraints weight = 4219.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175535 restraints weight = 7239.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.175730 restraints weight = 7271.053| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1609 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= 0.212 Angle : 0.538 6.459 5996 Z= 0.275 Chirality : 0.038 0.137 711 Planarity : 0.005 0.053 733 Dihedral : 8.081 68.408 640 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.70 % Allowed : 20.65 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.37), residues: 552 helix: 2.71 (0.26), residues: 363 sheet: 0.32 (0.79), residues: 47 loop : -2.16 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.001 0.000 HIS A 248 PHE 0.010 0.001 PHE A 361 TYR 0.011 0.001 TYR A 459 ARG 0.005 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 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.458 Fit side-chains REVERT: A 248 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6218 (m-70) REVERT: B 108 SER cc_start: 0.8713 (m) cc_final: 0.8464 (m) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 0.2058 time to fit residues: 16.1138 Evaluate side-chains 58 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 248 HIS 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 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: 0.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.178520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144993 restraints weight = 4412.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145148 restraints weight = 4285.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145148 restraints weight = 4204.570| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1722 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= 0.245 Angle : 0.542 6.718 5996 Z= 0.278 Chirality : 0.039 0.136 711 Planarity : 0.004 0.054 733 Dihedral : 7.760 62.745 638 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.04 % Allowed : 21.74 % Favored : 75.22 % 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: 1.97 (0.37), residues: 552 helix: 2.63 (0.26), residues: 363 sheet: 0.45 (0.79), residues: 47 loop : -2.13 (0.52), residues: 142 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 459 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 64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.482 Fit side-chains REVERT: B 108 SER cc_start: 0.8658 (m) cc_final: 0.8393 (m) outliers start: 14 outliers final: 11 residues processed: 63 average time/residue: 0.1999 time to fit residues: 15.8819 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 : 0.470 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.179035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.152898 restraints weight = 4415.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.149505 restraints weight = 5942.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.149733 restraints weight = 6149.614| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4410 Z= 0.223 Angle : 0.528 6.001 5996 Z= 0.270 Chirality : 0.038 0.136 711 Planarity : 0.004 0.055 733 Dihedral : 7.563 57.876 638 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.78 % Allowed : 20.22 % Favored : 75.00 % 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: 2.02 (0.37), residues: 552 helix: 2.62 (0.26), residues: 364 sheet: 0.56 (0.79), residues: 47 loop : -2.04 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.001 HIS A 112 PHE 0.009 0.001 PHE A 361 TYR 0.011 0.001 TYR A 459 ARG 0.005 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 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.483 Fit side-chains REVERT: A 248 HIS cc_start: 0.6753 (OUTLIER) cc_final: 0.6251 (m-70) REVERT: B 108 SER cc_start: 0.8629 (m) cc_final: 0.8378 (m) outliers start: 22 outliers final: 14 residues processed: 68 average time/residue: 0.1872 time to fit residues: 15.8363 Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 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 = 0.4135 r_free = 0.4135 target = 0.197904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.188738 restraints weight = 4200.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.187583 restraints weight = 6691.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.179102 restraints weight = 7351.802| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4410 Z= 0.222 Angle : 0.544 10.205 5996 Z= 0.273 Chirality : 0.038 0.135 711 Planarity : 0.004 0.055 733 Dihedral : 7.376 57.247 638 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.91 % Allowed : 20.87 % Favored : 75.22 % 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: 2.05 (0.37), residues: 552 helix: 2.62 (0.26), residues: 363 sheet: 0.77 (0.80), residues: 47 loop : -2.00 (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 0.011 0.001 PHE A 64 TYR 0.010 0.001 TYR A 335 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 73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.460 Fit side-chains REVERT: A 140 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7485 (t0) REVERT: A 248 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6502 (m-70) REVERT: A 253 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.4404 (tp) REVERT: A 285 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7755 (mp) REVERT: B 108 SER cc_start: 0.8639 (m) cc_final: 0.8375 (m) outliers start: 18 outliers final: 12 residues processed: 71 average time/residue: 0.1868 time to fit residues: 16.5860 Evaluate side-chains 66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.178849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144927 restraints weight = 4406.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.145393 restraints weight = 4297.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.145393 restraints weight = 4186.372| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2101 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= 0.245 Angle : 0.549 8.221 5996 Z= 0.277 Chirality : 0.038 0.136 711 Planarity : 0.004 0.056 733 Dihedral : 7.199 59.008 636 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.91 % Allowed : 21.52 % 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: 2.00 (0.37), residues: 552 helix: 2.59 (0.26), residues: 362 sheet: 0.86 (0.80), residues: 47 loop : -2.06 (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 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 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.489 Fit side-chains REVERT: A 140 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7507 (t0) REVERT: A 253 LEU cc_start: 0.5012 (OUTLIER) cc_final: 0.4772 (tp) REVERT: A 285 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7736 (mp) REVERT: B 108 SER cc_start: 0.8645 (m) cc_final: 0.8392 (m) outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.1910 time to fit residues: 15.9343 Evaluate side-chains 63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.174744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142229 restraints weight = 4420.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.139884 restraints weight = 6403.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140265 restraints weight = 6536.742| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4410 Z= 0.237 Angle : 0.549 8.200 5996 Z= 0.277 Chirality : 0.038 0.137 711 Planarity : 0.004 0.056 733 Dihedral : 6.884 55.289 636 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.35 % Allowed : 21.30 % 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: 2.02 (0.37), residues: 552 helix: 2.59 (0.26), residues: 362 sheet: 0.90 (0.81), residues: 47 loop : -2.00 (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 0.010 0.001 PHE A 361 TYR 0.011 0.001 TYR A 335 ARG 0.007 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 : 0.457 Fit side-chains REVERT: A 140 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7493 (t0) REVERT: A 248 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6544 (m-70) REVERT: A 253 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4833 (tp) REVERT: A 285 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7780 (mp) outliers start: 20 outliers final: 13 residues processed: 68 average time/residue: 0.1973 time to fit residues: 16.5523 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 : 0.455 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 40 optimal weight: 0.0170 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.180263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146277 restraints weight = 4375.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.146445 restraints weight = 4358.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.146452 restraints weight = 4262.547| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.003 0.040 4410 Z= 0.221 Angle : 0.548 8.033 5996 Z= 0.275 Chirality : 0.038 0.138 711 Planarity : 0.004 0.055 733 Dihedral : 6.529 55.809 636 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.48 % Allowed : 22.39 % Favored : 74.13 % 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: 2.06 (0.37), residues: 552 helix: 2.62 (0.26), residues: 362 sheet: 0.98 (0.80), residues: 47 loop : -2.02 (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 0.011 0.001 PHE A 361 TYR 0.009 0.001 TYR A 459 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: 16 poor density : 49 time to evaluate : 0.456 Fit side-chains REVERT: A 140 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7479 (t0) REVERT: A 193 MET cc_start: 0.8329 (tpp) cc_final: 0.8098 (tpp) REVERT: A 248 HIS cc_start: 0.6797 (OUTLIER) cc_final: 0.6329 (m-70) REVERT: A 253 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4799 (tp) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.2038 time to fit residues: 16.0751 Evaluate side-chains 63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.0470 chunk 48 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.177869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.142432 restraints weight = 4348.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142867 restraints weight = 4221.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143174 restraints weight = 4056.847| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4410 Z= 0.184 Angle : 0.537 7.948 5996 Z= 0.266 Chirality : 0.038 0.143 711 Planarity : 0.004 0.056 733 Dihedral : 6.121 55.601 636 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.83 % Allowed : 23.26 % 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: 2.18 (0.37), residues: 552 helix: 2.74 (0.26), residues: 361 sheet: 0.33 (0.75), residues: 57 loop : -1.91 (0.54), residues: 134 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 0.008 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: 13 poor density : 46 time to evaluate : 0.443 Fit side-chains REVERT: A 248 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.6217 (m-70) REVERT: A 410 MET cc_start: 0.8091 (tmm) cc_final: 0.7870 (tmm) outliers start: 13 outliers final: 10 residues processed: 59 average time/residue: 0.2393 time to fit residues: 17.2262 Evaluate side-chains 56 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 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 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.177549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.142028 restraints weight = 4421.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.142029 restraints weight = 4259.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.142029 restraints weight = 4258.385| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4410 Z= 0.247 Angle : 1.174 59.187 5996 Z= 0.705 Chirality : 0.039 0.156 711 Planarity : 0.005 0.056 733 Dihedral : 5.697 45.163 633 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 3.04 % Allowed : 23.04 % Favored : 73.91 % Cbeta Deviations : 0.19 % 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: 2.18 (0.37), residues: 552 helix: 2.72 (0.26), residues: 361 sheet: 0.60 (0.75), residues: 55 loop : -1.95 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.009 0.002 HIS A 467 PHE 0.011 0.001 PHE A 361 TYR 0.008 0.001 TYR A 459 ARG 0.006 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.98 seconds wall clock time: 27 minutes 57.35 seconds (1677.35 seconds total)