Starting phenix.real_space_refine on Mon Jan 13 20:38:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s4u_19716/01_2025/8s4u_19716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s4u_19716/01_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_19716/01_2025/8s4u_19716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s4u_19716/01_2025/8s4u_19716.map" model { file = "/net/cci-nas-00/data/ceres_data/8s4u_19716/01_2025/8s4u_19716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s4u_19716/01_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-5571/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: 3.74, per 1000 atoms: 0.94 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: 1.00 Conformation dependent library (CDL) restraints added in 499.2 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: 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: 0.42 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: 1.10 Time building geometry restraints manager: 1.16 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.410 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- 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 : 0.457 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: 0.2029 time to fit residues: 18.0844 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 : 0.411 ------------------------------------------------------------------------------- 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: 0.3359 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- 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 : 0.413 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.8139 (m-80) cc_final: 0.7698 (m-80) REVERT: A 320 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7219 (mm-30) outliers start: 10 outliers final: 4 residues processed: 82 average time/residue: 0.1485 time to fit residues: 15.5360 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 : 0.438 ------------------------------------------------------------------------------- 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: 0.0020 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.142844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130527 restraints weight = 5037.411| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.05 r_work: 0.3356 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4089 Z= 0.230 Angle : 0.562 8.489 5578 Z= 0.292 Chirality : 0.042 0.168 642 Planarity : 0.004 0.030 679 Dihedral : 4.387 18.397 571 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.36 % Allowed : 17.26 % 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: 0.90 (0.38), residues: 496 helix: 1.57 (0.30), residues: 299 sheet: -1.65 (0.68), residues: 45 loop : -0.54 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.013 0.002 TYR A 14 ARG 0.001 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: 10 poor density : 70 time to evaluate : 0.480 Fit side-chains REVERT: B 80 TYR cc_start: 0.8013 (m-80) cc_final: 0.7637 (m-80) REVERT: A 66 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8535 (mm) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.1645 time to fit residues: 16.1730 Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 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 = 0.3599 r_free = 0.3599 target = 0.142781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130180 restraints weight = 5134.033| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.08 r_work: 0.3348 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1826 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= 0.263 Angle : 0.570 8.970 5578 Z= 0.294 Chirality : 0.042 0.172 642 Planarity : 0.004 0.032 679 Dihedral : 4.406 18.797 571 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 1.10 (0.39), residues: 496 helix: 1.59 (0.30), residues: 299 sheet: -0.77 (0.71), residues: 52 loop : -0.39 (0.56), 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 14 ARG 0.002 0.000 ARG B 38 *********************** 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 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.8027 (m-80) cc_final: 0.7590 (m-80) REVERT: A 66 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 320 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7150 (mm-30) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.1506 time to fit residues: 14.7132 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 : 0.429 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain A residue 312 SER 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: 0.6980 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: 0.4980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.0040 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130965 restraints weight = 5185.161| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.09 r_work: 0.3365 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1977 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= 0.231 Angle : 0.551 8.811 5578 Z= 0.284 Chirality : 0.041 0.151 642 Planarity : 0.004 0.032 679 Dihedral : 4.326 19.156 571 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.07 % Allowed : 16.31 % 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: 1.31 (0.39), residues: 496 helix: 1.70 (0.30), residues: 299 sheet: -0.43 (0.76), residues: 46 loop : -0.29 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.013 0.002 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 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7995 (m-80) cc_final: 0.7596 (m-80) REVERT: A 66 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8470 (mm) REVERT: A 320 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7153 (mm-30) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.1511 time to fit residues: 14.9237 Evaluate side-chains 75 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain A residue 312 SER 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: 0.9980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.141556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128702 restraints weight = 5052.929| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.09 r_work: 0.3334 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4089 Z= 0.299 Angle : 0.589 9.032 5578 Z= 0.303 Chirality : 0.043 0.169 642 Planarity : 0.004 0.033 679 Dihedral : 4.436 19.646 571 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.78 % Allowed : 16.31 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.38), residues: 496 helix: 1.55 (0.30), residues: 299 sheet: -0.53 (0.72), residues: 52 loop : -0.24 (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 0.025 0.002 PHE A 71 TYR 0.013 0.002 TYR A 14 ARG 0.001 0.000 ARG B 112 *********************** 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 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.8018 (m-80) cc_final: 0.7625 (m-80) REVERT: A 66 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 320 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7108 (mm-30) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.1528 time to fit residues: 14.9376 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 : 0.460 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.141442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128614 restraints weight = 5105.230| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.08 r_work: 0.3331 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4089 Z= 0.333 Angle : 0.613 9.444 5578 Z= 0.315 Chirality : 0.044 0.174 642 Planarity : 0.004 0.033 679 Dihedral : 4.531 20.284 571 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.02 % Allowed : 17.26 % Favored : 78.72 % 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: 1.00 (0.38), residues: 496 helix: 1.42 (0.29), residues: 299 sheet: -0.55 (0.71), residues: 52 loop : -0.30 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.001 0.000 HIS A 135 PHE 0.027 0.002 PHE A 71 TYR 0.015 0.002 TYR A 336 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 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.495 Fit side-chains REVERT: B 80 TYR cc_start: 0.8056 (m-80) cc_final: 0.7642 (m-80) REVERT: A 66 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8508 (mm) REVERT: A 320 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7123 (mm-30) outliers start: 17 outliers final: 16 residues processed: 79 average time/residue: 0.1555 time to fit residues: 15.5091 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 : 0.422 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 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 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129032 restraints weight = 5068.199| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.08 r_work: 0.3341 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4089 Z= 0.284 Angle : 0.588 9.039 5578 Z= 0.302 Chirality : 0.042 0.146 642 Planarity : 0.004 0.034 679 Dihedral : 4.462 20.305 571 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.78 % Allowed : 17.49 % Favored : 78.72 % 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: 1.17 (0.38), residues: 496 helix: 1.56 (0.30), residues: 298 sheet: -0.46 (0.72), residues: 52 loop : -0.25 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.024 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 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.8026 (m-80) cc_final: 0.7640 (m-80) REVERT: A 66 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8523 (mm) REVERT: A 320 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7134 (mm-30) outliers start: 16 outliers final: 15 residues processed: 76 average time/residue: 0.1467 time to fit residues: 14.3048 Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.142709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130485 restraints weight = 5119.466| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.02 r_work: 0.3357 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4089 Z= 0.252 Angle : 0.571 9.033 5578 Z= 0.294 Chirality : 0.042 0.135 642 Planarity : 0.004 0.033 679 Dihedral : 4.371 20.275 571 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.26 % Allowed : 17.02 % Favored : 78.72 % 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: 1.31 (0.39), residues: 496 helix: 1.65 (0.30), residues: 298 sheet: -0.36 (0.73), residues: 52 loop : -0.18 (0.56), residues: 146 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 0.023 0.002 PHE A 71 TYR 0.014 0.002 TYR A 445 ARG 0.001 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 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7957 (m-80) cc_final: 0.7593 (m-80) REVERT: A 66 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8503 (mm) REVERT: A 271 GLU cc_start: 0.4398 (pm20) cc_final: 0.3619 (pt0) REVERT: A 320 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7157 (mm-30) outliers start: 18 outliers final: 17 residues processed: 78 average time/residue: 0.1531 time to fit residues: 15.1319 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 : 0.443 ------------------------------------------------------------------------------- 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 157 LEU 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 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: 0.5980 chunk 41 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.143228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130500 restraints weight = 5076.870| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.07 r_work: 0.3356 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4089 Z= 0.255 Angle : 0.572 8.539 5578 Z= 0.296 Chirality : 0.042 0.136 642 Planarity : 0.004 0.034 679 Dihedral : 4.377 20.175 571 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.02 % Allowed : 17.26 % Favored : 78.72 % 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: 1.31 (0.38), residues: 496 helix: 1.67 (0.30), residues: 298 sheet: -0.36 (0.72), residues: 52 loop : -0.22 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.023 0.002 PHE A 71 TYR 0.014 0.002 TYR A 445 ARG 0.001 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: 17 poor density : 63 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7949 (m-80) cc_final: 0.7584 (m-80) REVERT: A 66 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8502 (mm) REVERT: A 271 GLU cc_start: 0.4377 (pm20) cc_final: 0.3590 (pt0) REVERT: A 320 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 452 ILE cc_start: 0.8057 (mt) cc_final: 0.7854 (mt) outliers start: 17 outliers final: 15 residues processed: 76 average time/residue: 0.1570 time to fit residues: 15.2075 Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 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 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129250 restraints weight = 5064.088| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.08 r_work: 0.3344 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2049 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= 0.276 Angle : 0.580 8.773 5578 Z= 0.299 Chirality : 0.042 0.144 642 Planarity : 0.004 0.033 679 Dihedral : 4.418 19.988 571 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.02 % Allowed : 17.02 % Favored : 78.96 % 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: 1.25 (0.38), residues: 496 helix: 1.61 (0.30), residues: 298 sheet: -0.38 (0.73), residues: 52 loop : -0.21 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.024 0.002 PHE A 71 TYR 0.014 0.002 TYR A 445 ARG 0.001 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.63 seconds wall clock time: 43 minutes 35.30 seconds (2615.30 seconds total)