Starting phenix.real_space_refine on Wed Mar 5 22:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s4u_19716/03_2025/8s4u_19716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s4u_19716/03_2025/8s4u_19716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s4u_19716/03_2025/8s4u_19716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s4u_19716/03_2025/8s4u_19716.map" model { file = "/net/cci-nas-00/data/ceres_data/8s4u_19716/03_2025/8s4u_19716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s4u_19716/03_2025/8s4u_19716.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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 19 5.16 5 C 2640 2.51 5 N 616 2.21 5 O 705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3980 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "A" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2984 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.58, per 1000 atoms: 0.90 Number of scatterers: 3980 At special positions: 0 Unit cell: (88.81, 67.23, 89.64, 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 19 16.00 O 705 8.00 N 616 7.00 C 2640 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 45 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 494.7 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: 940 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 67.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.556A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.577A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.876A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 100 Processing helix chain 'A' and resid 103 through 119 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.654A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 removed outlier: 3.732A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.841A pdb=" N LEU A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.577A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 311 through 337 removed outlier: 3.816A pdb=" N TYR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.568A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 removed outlier: 3.505A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.134A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.530A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.678A pdb=" N VAL B 93 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 268 hydrogen bonds defined for protein. 777 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: 1.12 Time building geometry restraints manager: 1.24 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: 773 1.33 - 1.45: 1090 1.45 - 1.57: 2194 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4089 Sorted by residual: bond pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 1.523 1.484 0.040 1.34e-02 5.57e+03 8.71e+00 bond pdb=" CA SER A 40 " pdb=" C SER A 40 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.41e-02 5.03e+03 7.22e+00 bond pdb=" CA LYS A 80 " pdb=" C LYS A 80 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.26e-02 6.30e+03 7.15e+00 bond pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 1.532 1.507 0.025 9.60e-03 1.09e+04 7.00e+00 bond pdb=" C LYS A 80 " pdb=" O LYS A 80 " ideal model delta sigma weight residual 1.244 1.219 0.025 9.80e-03 1.04e+04 6.47e+00 ... (remaining 4084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 5507 2.30 - 4.61: 66 4.61 - 6.91: 4 6.91 - 9.22: 0 9.22 - 11.52: 1 Bond angle restraints: 5578 Sorted by residual: angle pdb=" N TYR A 79 " pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 110.80 122.32 -11.52 2.13e+00 2.20e-01 2.93e+01 angle pdb=" C ARG A 78 " pdb=" CA ARG A 78 " pdb=" CB ARG A 78 " ideal model delta sigma weight residual 111.39 116.63 -5.24 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ASN A 53 " pdb=" CA ASN A 53 " pdb=" C ASN A 53 " ideal model delta sigma weight residual 113.41 117.49 -4.08 1.22e+00 6.72e-01 1.12e+01 angle pdb=" N ASP A 427 " pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 110.23 114.94 -4.71 1.45e+00 4.76e-01 1.06e+01 angle pdb=" N ASN A 53 " pdb=" CA ASN A 53 " pdb=" CB ASN A 53 " ideal model delta sigma weight residual 110.47 105.99 4.48 1.46e+00 4.69e-01 9.43e+00 ... (remaining 5573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 2001 14.30 - 28.60: 249 28.60 - 42.90: 69 42.90 - 57.20: 26 57.20 - 71.50: 6 Dihedral angle restraints: 2351 sinusoidal: 876 harmonic: 1475 Sorted by residual: dihedral pdb=" C ARG A 78 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " pdb=" CB ARG A 78 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" CA TYR A 126 " pdb=" C TYR A 126 " pdb=" N ILE A 127 " pdb=" CA ILE A 127 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 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 63.36 29.64 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 2348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 595 0.079 - 0.157: 44 0.157 - 0.236: 1 0.236 - 0.314: 1 0.314 - 0.393: 1 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA ARG A 78 " pdb=" N ARG A 78 " pdb=" C ARG A 78 " pdb=" CB ARG A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA TYR A 79 " pdb=" N TYR A 79 " pdb=" C TYR A 79 " pdb=" CB TYR A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN A 45 " pdb=" N ASN A 45 " pdb=" C ASN A 45 " pdb=" CB ASN A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 639 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.323 2.00e-02 2.50e+03 2.77e-01 9.58e+02 pdb=" C7 NAG A 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 75 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ASP A 75 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP A 75 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 76 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 71 " -0.013 2.00e-02 2.50e+03 1.32e-02 3.04e+00 pdb=" CG PHE A 71 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 71 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 71 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 71 " -0.001 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1143 2.80 - 3.32: 3886 3.32 - 3.85: 6611 3.85 - 4.37: 8178 4.37 - 4.90: 13988 Nonbonded interactions: 33806 Sorted by model distance: nonbonded pdb=" O GLN A 428 " pdb=" OE1 GLN A 428 " model vdw 2.272 3.040 nonbonded pdb=" O LEU A 349 " pdb=" OG SER A 353 " model vdw 2.312 3.040 nonbonded pdb=" O ARG A 144 " pdb=" OG1 THR A 147 " model vdw 2.354 3.040 nonbonded pdb=" O TRP A 285 " pdb=" OG1 THR A 289 " model vdw 2.359 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OD1 ASP A 311 " model vdw 2.361 3.040 ... (remaining 33801 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.130 Find NCS groups from input model: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 0.040 4089 Z= 0.376 Angle : 0.649 11.523 5578 Z= 0.384 Chirality : 0.047 0.393 642 Planarity : 0.011 0.277 679 Dihedral : 14.848 71.500 1408 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.24 % Allowed : 19.15 % Favored : 80.61 % Cbeta Deviations : 0.21 % 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: -0.73 (0.37), residues: 496 helix: 0.27 (0.30), residues: 284 sheet: -2.99 (0.76), residues: 33 loop : -1.05 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 PHE 0.031 0.002 PHE A 71 TYR 0.015 0.002 TYR B 94 ARG 0.003 0.001 ARG A 277 *********************** 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 73 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.630 Fit side-chains REVERT: B 80 TYR cc_start: 0.7940 (m-80) cc_final: 0.7425 (m-80) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.2239 time to fit residues: 20.0013 Evaluate side-chains 67 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 397 ASN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130850 restraints weight = 5124.135| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.01 r_work: 0.3361 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4089 Z= 0.248 Angle : 0.594 8.263 5578 Z= 0.312 Chirality : 0.043 0.203 642 Planarity : 0.004 0.029 679 Dihedral : 4.978 42.208 573 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.36 % Allowed : 16.31 % Favored : 81.32 % 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 (0.38), residues: 496 helix: 1.26 (0.30), residues: 298 sheet: -2.16 (0.66), residues: 45 loop : -0.74 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.014 0.002 TYR A 14 ARG 0.002 0.000 ARG B 38 *********************** 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 86 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.8145 (m-80) cc_final: 0.7702 (m-80) REVERT: A 320 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7211 (mm-30) outliers start: 10 outliers final: 4 residues processed: 82 average time/residue: 0.1438 time to fit residues: 15.0154 Evaluate side-chains 71 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 300 GLN A 316 ASN A 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129509 restraints weight = 5049.250| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.00 r_work: 0.3348 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4089 Z= 0.279 Angle : 0.590 8.746 5578 Z= 0.306 Chirality : 0.043 0.190 642 Planarity : 0.004 0.031 679 Dihedral : 4.497 18.939 571 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.60 % Allowed : 17.26 % Favored : 80.14 % 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: 0.75 (0.38), residues: 496 helix: 1.46 (0.30), residues: 299 sheet: -1.67 (0.68), residues: 45 loop : -0.63 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.023 0.002 PHE A 71 TYR 0.013 0.002 TYR A 14 ARG 0.002 0.000 ARG B 38 *********************** 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 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.481 Fit side-chains REVERT: B 80 TYR cc_start: 0.8074 (m-80) cc_final: 0.7680 (m-80) REVERT: A 66 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8551 (mm) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.1478 time to fit residues: 14.7829 Evaluate side-chains 73 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131919 restraints weight = 5107.359| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.04 r_work: 0.3387 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4089 Z= 0.219 Angle : 0.547 8.562 5578 Z= 0.283 Chirality : 0.041 0.152 642 Planarity : 0.004 0.033 679 Dihedral : 4.339 18.835 571 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.84 % Allowed : 16.55 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.38), residues: 496 helix: 1.66 (0.30), residues: 299 sheet: -0.72 (0.73), residues: 46 loop : -0.46 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.013 0.001 TYR A 14 ARG 0.001 0.000 ARG B 67 *********************** 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 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.372 Fit side-chains REVERT: B 80 TYR cc_start: 0.8011 (m-80) cc_final: 0.7587 (m-80) REVERT: A 66 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 320 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7176 (mm-30) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1611 time to fit residues: 15.7946 Evaluate side-chains 74 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129915 restraints weight = 5204.777| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.09 r_work: 0.3347 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4089 Z= 0.263 Angle : 0.570 8.600 5578 Z= 0.294 Chirality : 0.042 0.162 642 Planarity : 0.004 0.033 679 Dihedral : 4.385 19.320 571 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.55 % Allowed : 15.84 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.39), residues: 496 helix: 1.64 (0.30), residues: 299 sheet: -0.57 (0.72), residues: 52 loop : -0.32 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.023 0.002 PHE A 71 TYR 0.013 0.002 TYR A 14 ARG 0.002 0.000 ARG B 38 *********************** 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.420 Fit side-chains REVERT: B 80 TYR cc_start: 0.8001 (m-80) cc_final: 0.7583 (m-80) REVERT: A 66 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 320 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7183 (mm-30) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1536 time to fit residues: 15.3899 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.0060 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131846 restraints weight = 5004.900| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.02 r_work: 0.3351 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4089 Z= 0.261 Angle : 0.568 8.738 5578 Z= 0.292 Chirality : 0.042 0.152 642 Planarity : 0.004 0.033 679 Dihedral : 4.367 19.511 571 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.78 % Allowed : 15.84 % Favored : 80.38 % 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: 1.24 (0.39), residues: 496 helix: 1.62 (0.30), residues: 299 sheet: -0.50 (0.72), residues: 52 loop : -0.24 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.023 0.002 PHE A 71 TYR 0.013 0.002 TYR A 336 ARG 0.002 0.000 ARG B 38 *********************** 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 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.476 Fit side-chains REVERT: B 76 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8132 (mtmm) REVERT: B 80 TYR cc_start: 0.8006 (m-80) cc_final: 0.7563 (m-80) REVERT: A 66 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8486 (mm) REVERT: A 320 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7152 (mm-30) outliers start: 16 outliers final: 15 residues processed: 79 average time/residue: 0.1516 time to fit residues: 15.2695 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 316 ASN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128796 restraints weight = 5099.767| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.08 r_work: 0.3327 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4089 Z= 0.314 Angle : 0.600 8.778 5578 Z= 0.309 Chirality : 0.043 0.166 642 Planarity : 0.004 0.033 679 Dihedral : 4.467 20.017 571 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.26 % Allowed : 16.31 % Favored : 79.43 % 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: 1.10 (0.38), residues: 496 helix: 1.51 (0.30), residues: 299 sheet: -0.54 (0.71), residues: 52 loop : -0.29 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.026 0.002 PHE A 71 TYR 0.014 0.002 TYR B 94 ARG 0.002 0.000 ARG B 38 *********************** 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 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.413 Fit side-chains REVERT: B 76 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8148 (mtmm) REVERT: B 80 TYR cc_start: 0.8035 (m-80) cc_final: 0.7584 (m-80) REVERT: A 66 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 320 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7165 (mm-30) outliers start: 18 outliers final: 16 residues processed: 80 average time/residue: 0.1499 time to fit residues: 15.3434 Evaluate side-chains 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128864 restraints weight = 5064.818| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.06 r_work: 0.3337 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4089 Z= 0.315 Angle : 0.604 9.155 5578 Z= 0.311 Chirality : 0.043 0.156 642 Planarity : 0.004 0.033 679 Dihedral : 4.505 20.190 571 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.26 % Allowed : 16.31 % Favored : 79.43 % 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: 1.10 (0.38), residues: 496 helix: 1.50 (0.30), residues: 298 sheet: -0.48 (0.72), residues: 52 loop : -0.28 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.026 0.002 PHE A 71 TYR 0.015 0.002 TYR A 445 ARG 0.002 0.000 ARG B 38 *********************** 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.451 Fit side-chains REVERT: B 76 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8131 (mtmm) REVERT: B 80 TYR cc_start: 0.8027 (m-80) cc_final: 0.7579 (m-80) REVERT: A 66 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8535 (mm) REVERT: A 320 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7171 (mm-30) outliers start: 18 outliers final: 17 residues processed: 78 average time/residue: 0.1580 time to fit residues: 15.6360 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.145183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132544 restraints weight = 5082.030| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.06 r_work: 0.3373 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4089 Z= 0.204 Angle : 0.545 8.439 5578 Z= 0.280 Chirality : 0.040 0.132 642 Planarity : 0.004 0.033 679 Dihedral : 4.254 20.387 571 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.31 % Allowed : 17.49 % Favored : 79.20 % 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: 1.51 (0.39), residues: 496 helix: 1.83 (0.30), residues: 298 sheet: -0.21 (0.77), residues: 46 loop : -0.18 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.014 0.001 TYR A 79 ARG 0.002 0.000 ARG B 38 *********************** 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 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7914 (m-80) cc_final: 0.7561 (m-80) REVERT: A 66 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8506 (mm) REVERT: A 271 GLU cc_start: 0.4493 (pm20) cc_final: 0.3725 (pt0) REVERT: A 320 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7205 (mm-30) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.1473 time to fit residues: 15.0706 Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129923 restraints weight = 5085.014| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.08 r_work: 0.3356 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4089 Z= 0.282 Angle : 0.591 9.082 5578 Z= 0.306 Chirality : 0.042 0.139 642 Planarity : 0.004 0.033 679 Dihedral : 4.389 17.735 571 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.55 % Allowed : 18.20 % Favored : 78.25 % 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: 1.29 (0.38), residues: 496 helix: 1.66 (0.30), residues: 298 sheet: -0.30 (0.72), residues: 52 loop : -0.26 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.024 0.002 PHE A 71 TYR 0.014 0.002 TYR A 445 ARG 0.002 0.000 ARG B 38 ********************** 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 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.485 Fit side-chains REVERT: B 76 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8120 (mtmm) REVERT: B 80 TYR cc_start: 0.7999 (m-80) cc_final: 0.7577 (m-80) REVERT: A 66 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8499 (mm) REVERT: A 271 GLU cc_start: 0.4392 (pm20) cc_final: 0.3612 (pt0) REVERT: A 320 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7203 (mm-30) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.1653 time to fit residues: 16.0500 Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.144181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131568 restraints weight = 5035.668| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.07 r_work: 0.3382 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4089 Z= 0.217 Angle : 0.546 8.479 5578 Z= 0.283 Chirality : 0.041 0.133 642 Planarity : 0.004 0.034 679 Dihedral : 4.260 17.287 571 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.78 % Allowed : 17.97 % Favored : 78.25 % 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: 1.52 (0.39), residues: 496 helix: 1.81 (0.30), residues: 298 sheet: -0.08 (0.77), residues: 46 loop : -0.15 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.014 0.002 TYR A 79 ARG 0.002 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.34 seconds wall clock time: 46 minutes 9.93 seconds (2769.93 seconds total)