Starting phenix.real_space_refine on Tue Feb 11 03:49:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s61_19754/02_2025/8s61_19754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s61_19754/02_2025/8s61_19754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s61_19754/02_2025/8s61_19754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s61_19754/02_2025/8s61_19754.map" model { file = "/net/cci-nas-00/data/ceres_data/8s61_19754/02_2025/8s61_19754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s61_19754/02_2025/8s61_19754.cif" } resolution = 3.53 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2647 2.51 5 N 624 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3990 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 935 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3037 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.60, per 1000 atoms: 0.90 Number of scatterers: 3990 At special positions: 0 Unit cell: (92.13, 83.83, 75.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 698 8.00 N 624 7.00 C 2647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 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: 0.96 Conformation dependent library (CDL) restraints added in 470.2 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 60.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 removed outlier: 3.851A pdb=" N THR A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.333A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.779A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 removed outlier: 4.386A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 removed outlier: 3.566A pdb=" N GLN A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.753A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 removed outlier: 4.206A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.528A pdb=" N VAL A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.179A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.571A pdb=" N TRP A 285 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 315 through 335 removed outlier: 3.529A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.844A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.621A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 426 removed outlier: 4.381A pdb=" N ILE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 removed outlier: 4.182A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.549A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.385A pdb=" N ARG B 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 600 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: 1.05 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 680 1.33 - 1.45: 1184 1.45 - 1.57: 2204 1.57 - 1.69: 1 1.69 - 1.81: 34 Bond restraints: 4103 Sorted by residual: bond pdb=" C5 VIB A 601 " pdb=" S1 VIB A 601 " ideal model delta sigma weight residual 1.721 1.511 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C4 VIB A 601 " pdb=" N3 VIB A 601 " ideal model delta sigma weight residual 1.385 1.570 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" C2A VIB A 601 " pdb=" N3A VIB A 601 " ideal model delta sigma weight residual 1.323 1.483 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C2A VIB A 601 " pdb=" N1A VIB A 601 " ideal model delta sigma weight residual 1.331 1.483 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C2 VIB A 601 " pdb=" S1 VIB A 601 " ideal model delta sigma weight residual 1.670 1.537 0.133 2.00e-02 2.50e+03 4.42e+01 ... (remaining 4098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 5564 3.30 - 6.60: 29 6.60 - 9.90: 1 9.90 - 13.20: 0 13.20 - 16.51: 1 Bond angle restraints: 5595 Sorted by residual: angle pdb=" C2 VIB A 601 " pdb=" S1 VIB A 601 " pdb=" C5 VIB A 601 " ideal model delta sigma weight residual 91.25 107.76 -16.51 3.00e+00 1.11e-01 3.03e+01 angle pdb=" N ASN A 173 " pdb=" CA ASN A 173 " pdb=" C ASN A 173 " ideal model delta sigma weight residual 112.23 105.56 6.67 1.26e+00 6.30e-01 2.80e+01 angle pdb=" N SER B 17 " pdb=" CA SER B 17 " pdb=" C SER B 17 " ideal model delta sigma weight residual 110.41 115.36 -4.95 1.23e+00 6.61e-01 1.62e+01 angle pdb=" N ILE A 449 " pdb=" CA ILE A 449 " pdb=" C ILE A 449 " ideal model delta sigma weight residual 112.80 108.41 4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N LEU A 160 " pdb=" CA LEU A 160 " pdb=" C LEU A 160 " ideal model delta sigma weight residual 113.88 109.51 4.37 1.23e+00 6.61e-01 1.26e+01 ... (remaining 5590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2033 17.85 - 35.71: 224 35.71 - 53.56: 61 53.56 - 71.41: 11 71.41 - 89.26: 4 Dihedral angle restraints: 2333 sinusoidal: 861 harmonic: 1472 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 142.97 -49.97 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR A 171 " pdb=" C TYR A 171 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 417 0.032 - 0.064: 145 0.064 - 0.095: 47 0.095 - 0.127: 17 0.127 - 0.159: 4 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA ASN B 32 " pdb=" N ASN B 32 " pdb=" C ASN B 32 " pdb=" CB ASN B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 627 not shown) Planarity restraints: 682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 87 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO B 88 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 172 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C LEU A 172 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 172 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 173 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 73 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.33e+00 pdb=" C ASP B 73 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP B 73 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 74 " -0.010 2.00e-02 2.50e+03 ... (remaining 679 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 23 2.57 - 3.16: 3363 3.16 - 3.74: 5880 3.74 - 4.32: 8341 4.32 - 4.90: 14385 Nonbonded interactions: 31992 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" O1 VIB A 601 " model vdw 1.994 3.040 nonbonded pdb=" OE1 GLN A 159 " pdb=" OG SER A 163 " model vdw 2.200 3.040 nonbonded pdb=" O TYR A 76 " pdb=" NE2 HIS A 200 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 277 " pdb=" O GLN A 393 " model vdw 2.328 3.120 nonbonded pdb=" OE1 GLU A 110 " pdb=" N4A VIB A 601 " model vdw 2.364 3.120 ... (remaining 31987 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.240 Find NCS groups from input model: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.008 0.210 4103 Z= 0.603 Angle : 0.625 16.505 5595 Z= 0.349 Chirality : 0.039 0.159 630 Planarity : 0.004 0.066 682 Dihedral : 16.574 89.265 1394 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 19.48 % Favored : 80.52 % 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 (0.38), residues: 496 helix: -1.07 (0.31), residues: 280 sheet: -2.36 (0.77), residues: 52 loop : -0.96 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS A 135 PHE 0.014 0.001 PHE A 198 TYR 0.005 0.001 TYR B 47 ARG 0.002 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.401 Fit side-chains REVERT: A 198 PHE cc_start: 0.7743 (m-80) cc_final: 0.5705 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1808 time to fit residues: 11.1013 Evaluate side-chains 47 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.138178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127956 restraints weight = 4609.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128778 restraints weight = 3972.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.129474 restraints weight = 3500.458| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4103 Z= 0.360 Angle : 0.645 6.117 5595 Z= 0.339 Chirality : 0.043 0.168 630 Planarity : 0.005 0.058 682 Dihedral : 5.867 64.069 556 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.61 % Allowed : 19.24 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.39), residues: 496 helix: -0.10 (0.32), residues: 282 sheet: -1.48 (0.97), residues: 37 loop : -1.33 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 284 HIS 0.003 0.002 HIS A 364 PHE 0.016 0.002 PHE A 439 TYR 0.013 0.002 TYR A 280 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.389 Fit side-chains REVERT: A 198 PHE cc_start: 0.7848 (m-80) cc_final: 0.6482 (t80) outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 0.1449 time to fit residues: 9.2513 Evaluate side-chains 44 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain A residue 167 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.0670 chunk 34 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 overall best weight: 0.2634 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.138509 restraints weight = 4474.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139633 restraints weight = 3597.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.140497 restraints weight = 3065.845| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4103 Z= 0.168 Angle : 0.508 5.284 5595 Z= 0.270 Chirality : 0.039 0.163 630 Planarity : 0.004 0.057 682 Dihedral : 5.573 69.406 556 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.56 % Allowed : 18.53 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.39), residues: 496 helix: 0.42 (0.33), residues: 282 sheet: -0.92 (0.94), residues: 37 loop : -1.18 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 135 PHE 0.009 0.001 PHE A 90 TYR 0.011 0.001 TYR A 14 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.407 Fit side-chains REVERT: A 18 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 198 PHE cc_start: 0.7795 (m-80) cc_final: 0.6317 (t80) outliers start: 15 outliers final: 8 residues processed: 54 average time/residue: 0.1625 time to fit residues: 11.4760 Evaluate side-chains 49 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.143804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133669 restraints weight = 4549.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133523 restraints weight = 4585.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134082 restraints weight = 4753.676| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4103 Z= 0.257 Angle : 0.574 9.252 5595 Z= 0.293 Chirality : 0.041 0.165 630 Planarity : 0.004 0.057 682 Dihedral : 5.701 68.466 556 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.80 % Allowed : 19.71 % Favored : 76.48 % 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: -0.43 (0.39), residues: 496 helix: 0.40 (0.33), residues: 282 sheet: -0.68 (0.94), residues: 35 loop : -1.20 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE A 439 TYR 0.016 0.001 TYR A 336 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.385 Fit side-chains REVERT: A 18 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 198 PHE cc_start: 0.7915 (m-80) cc_final: 0.6569 (t80) REVERT: A 421 MET cc_start: 0.8430 (ttp) cc_final: 0.8096 (ptt) outliers start: 16 outliers final: 12 residues processed: 56 average time/residue: 0.1436 time to fit residues: 10.4711 Evaluate side-chains 55 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 366 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 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 = 0.3413 r_free = 0.3413 target = 0.135066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.124810 restraints weight = 4740.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.125406 restraints weight = 3990.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.126302 restraints weight = 3590.327| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4103 Z= 0.327 Angle : 0.606 8.499 5595 Z= 0.312 Chirality : 0.042 0.169 630 Planarity : 0.004 0.058 682 Dihedral : 5.910 69.545 556 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.28 % Allowed : 19.95 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.39), residues: 496 helix: 0.31 (0.33), residues: 282 sheet: -0.80 (0.93), residues: 35 loop : -1.32 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 439 TYR 0.017 0.001 TYR A 336 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.400 Fit side-chains REVERT: A 18 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7953 (mm) REVERT: A 198 PHE cc_start: 0.8007 (m-80) cc_final: 0.6622 (t80) REVERT: A 384 MET cc_start: 0.8532 (tpp) cc_final: 0.8288 (mmt) outliers start: 18 outliers final: 16 residues processed: 61 average time/residue: 0.1314 time to fit residues: 10.5743 Evaluate side-chains 64 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 44 optimal weight: 0.0770 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.139076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.129111 restraints weight = 4547.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129915 restraints weight = 3813.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.129998 restraints weight = 3367.327| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4103 Z= 0.196 Angle : 0.529 7.345 5595 Z= 0.275 Chirality : 0.040 0.165 630 Planarity : 0.004 0.056 682 Dihedral : 5.707 71.111 556 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.75 % Allowed : 20.43 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.39), residues: 496 helix: 0.52 (0.33), residues: 282 sheet: -0.63 (0.94), residues: 35 loop : -1.19 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.010 0.001 PHE A 439 TYR 0.018 0.001 TYR A 336 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.426 Fit side-chains REVERT: A 18 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7913 (mm) REVERT: A 198 PHE cc_start: 0.8073 (m-80) cc_final: 0.6657 (t80) REVERT: A 421 MET cc_start: 0.8394 (ttp) cc_final: 0.8169 (ptt) outliers start: 20 outliers final: 14 residues processed: 59 average time/residue: 0.1577 time to fit residues: 11.9935 Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.139185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.129184 restraints weight = 4629.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130078 restraints weight = 3860.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.130379 restraints weight = 3372.164| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4103 Z= 0.208 Angle : 0.530 6.820 5595 Z= 0.273 Chirality : 0.040 0.163 630 Planarity : 0.004 0.055 682 Dihedral : 5.641 70.326 556 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.04 % Allowed : 21.62 % 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: -0.32 (0.39), residues: 496 helix: 0.58 (0.33), residues: 283 sheet: -0.90 (0.82), residues: 45 loop : -1.27 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.001 PHE A 439 TYR 0.017 0.001 TYR A 336 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.425 Fit side-chains REVERT: A 18 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7837 (mm) REVERT: A 198 PHE cc_start: 0.8067 (m-80) cc_final: 0.6652 (t80) outliers start: 17 outliers final: 14 residues processed: 58 average time/residue: 0.1580 time to fit residues: 11.8805 Evaluate side-chains 58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.129786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.119554 restraints weight = 4708.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.120132 restraints weight = 4081.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.120978 restraints weight = 3660.186| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4103 Z= 0.338 Angle : 0.613 7.306 5595 Z= 0.314 Chirality : 0.043 0.165 630 Planarity : 0.004 0.056 682 Dihedral : 5.960 69.479 556 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.75 % Allowed : 20.90 % 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: -0.49 (0.38), residues: 496 helix: 0.42 (0.32), residues: 282 sheet: -0.98 (0.84), residues: 42 loop : -1.27 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.004 0.002 HIS A 364 PHE 0.015 0.001 PHE A 439 TYR 0.019 0.001 TYR A 336 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.418 Fit side-chains REVERT: A 18 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7987 (mm) REVERT: A 198 PHE cc_start: 0.8090 (m-80) cc_final: 0.6666 (t80) REVERT: A 385 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8909 (tt) outliers start: 20 outliers final: 16 residues processed: 57 average time/residue: 0.1400 time to fit residues: 10.6160 Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 385 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.135565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.125834 restraints weight = 4667.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.126465 restraints weight = 4028.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.127191 restraints weight = 3620.637| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4103 Z= 0.218 Angle : 0.541 6.511 5595 Z= 0.279 Chirality : 0.040 0.163 630 Planarity : 0.004 0.055 682 Dihedral : 5.744 70.740 556 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.28 % Allowed : 21.14 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.39), residues: 496 helix: 0.55 (0.33), residues: 283 sheet: -0.72 (0.83), residues: 43 loop : -1.31 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.001 PHE A 439 TYR 0.011 0.001 TYR A 14 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.434 Fit side-chains REVERT: A 18 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7846 (mm) REVERT: A 198 PHE cc_start: 0.8121 (m-80) cc_final: 0.6706 (t80) outliers start: 18 outliers final: 15 residues processed: 57 average time/residue: 0.1541 time to fit residues: 11.3925 Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 28 optimal weight: 0.0980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.141689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131289 restraints weight = 4613.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131863 restraints weight = 3887.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131863 restraints weight = 3513.176| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.004 0.036 4103 Z= 0.221 Angle : 0.542 6.451 5595 Z= 0.279 Chirality : 0.040 0.161 630 Planarity : 0.004 0.055 682 Dihedral : 5.694 69.703 556 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.04 % Allowed : 21.85 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.39), residues: 496 helix: 0.58 (0.33), residues: 283 sheet: -0.60 (0.84), residues: 43 loop : -1.31 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.011 0.001 TYR A 336 ARG 0.001 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.405 Fit side-chains REVERT: B 83 MET cc_start: 0.8019 (mtm) cc_final: 0.7814 (ptp) REVERT: A 18 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7876 (mm) REVERT: A 198 PHE cc_start: 0.8127 (m-80) cc_final: 0.6792 (t80) outliers start: 17 outliers final: 16 residues processed: 56 average time/residue: 0.1429 time to fit residues: 10.6646 Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.0000 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.0010 chunk 7 optimal weight: 0.0270 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.1848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130097 restraints weight = 4630.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131092 restraints weight = 3784.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.131998 restraints weight = 3261.050| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4103 Z= 0.142 Angle : 0.494 5.653 5595 Z= 0.255 Chirality : 0.039 0.157 630 Planarity : 0.004 0.053 682 Dihedral : 5.431 69.968 556 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.56 % Allowed : 22.09 % 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: -0.05 (0.39), residues: 496 helix: 0.77 (0.33), residues: 284 sheet: -0.54 (0.83), residues: 45 loop : -1.18 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.001 0.000 HIS A 135 PHE 0.009 0.001 PHE A 198 TYR 0.014 0.001 TYR A 14 ARG 0.001 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.12 seconds wall clock time: 28 minutes 43.36 seconds (1723.36 seconds total)