Starting phenix.real_space_refine on Wed Jul 23 18:23:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s4u_19716/07_2025/8s4u_19716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s4u_19716/07_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_19716/07_2025/8s4u_19716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s4u_19716/07_2025/8s4u_19716.map" model { file = "/net/cci-nas-00/data/ceres_data/8s4u_19716/07_2025/8s4u_19716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s4u_19716/07_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-5711/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: 3.75, 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: 0.89 Conformation dependent library (CDL) restraints added in 501.2 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: 0.47 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: 1.21 Time building geometry restraints manager: 1.10 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.180 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- 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 4091 Z= 0.340 Angle : 0.652 11.523 5583 Z= 0.385 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 Details of bonding type rmsd link_NAG-ASN : bond 0.02014 ( 1) link_NAG-ASN : angle 3.03854 ( 3) hydrogen bonds : bond 0.22173 ( 262) hydrogen bonds : angle 8.39925 ( 777) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.18675 ( 2) covalent geometry : bond 0.00589 ( 4089) covalent geometry : angle 0.64854 ( 5578) *********************** 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 : 0.433 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: 0.1895 time to fit residues: 16.8683 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 : 0.475 ------------------------------------------------------------------------------- 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 4091 Z= 0.165 Angle : 0.595 8.263 5583 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 1) link_NAG-ASN : angle 1.95583 ( 3) hydrogen bonds : bond 0.05040 ( 262) hydrogen bonds : angle 4.72341 ( 777) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.25903 ( 2) covalent geometry : bond 0.00382 ( 4089) covalent geometry : angle 0.59365 ( 5578) *********************** 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 : 0.519 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: 0.1796 time to fit residues: 18.8802 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 : 0.466 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.141945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129946 restraints weight = 5051.259| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.02 r_work: 0.3359 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4091 Z= 0.167 Angle : 0.577 8.555 5583 Z= 0.300 Chirality : 0.042 0.180 642 Planarity : 0.004 0.031 679 Dihedral : 4.447 18.651 571 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: 0.82 (0.38), residues: 496 helix: 1.51 (0.30), residues: 299 sheet: -1.67 (0.68), residues: 45 loop : -0.59 (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 0.022 0.002 PHE A 71 TYR 0.013 0.002 TYR A 14 ARG 0.002 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 1) link_NAG-ASN : angle 0.90474 ( 3) hydrogen bonds : bond 0.04700 ( 262) hydrogen bonds : angle 4.47566 ( 777) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.80527 ( 2) covalent geometry : bond 0.00392 ( 4089) covalent geometry : angle 0.57677 ( 5578) *********************** 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 : 0.415 Fit side-chains REVERT: B 80 TYR cc_start: 0.8044 (m-80) cc_final: 0.7656 (m-80) REVERT: A 66 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8532 (mm) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.1504 time to fit residues: 14.8846 Evaluate side-chains 71 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.6980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3582 r_free = 0.3582 target = 0.141393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128759 restraints weight = 5155.900| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.08 r_work: 0.3334 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4091 Z= 0.191 Angle : 0.589 9.177 5583 Z= 0.305 Chirality : 0.043 0.184 642 Planarity : 0.004 0.033 679 Dihedral : 4.495 18.963 571 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.31 % Allowed : 16.08 % 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: 0.96 (0.38), residues: 496 helix: 1.49 (0.30), residues: 299 sheet: -0.84 (0.70), residues: 52 loop : -0.48 (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 135 PHE 0.024 0.002 PHE A 71 TYR 0.013 0.002 TYR A 14 ARG 0.001 0.000 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 0.96394 ( 3) hydrogen bonds : bond 0.04735 ( 262) hydrogen bonds : angle 4.46112 ( 777) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.30602 ( 2) covalent geometry : bond 0.00459 ( 4089) covalent geometry : angle 0.58879 ( 5578) *********************** 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.448 Fit side-chains REVERT: B 80 TYR cc_start: 0.8030 (m-80) cc_final: 0.7599 (m-80) REVERT: A 66 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 320 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7193 (mm-30) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.1514 time to fit residues: 15.1900 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128834 restraints weight = 5214.118| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.09 r_work: 0.3331 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4091 Z= 0.190 Angle : 0.590 9.159 5583 Z= 0.304 Chirality : 0.043 0.176 642 Planarity : 0.004 0.034 679 Dihedral : 4.493 19.645 571 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.55 % Allowed : 16.08 % 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: 1.00 (0.38), residues: 496 helix: 1.49 (0.29), residues: 299 sheet: -0.71 (0.71), residues: 52 loop : -0.43 (0.55), residues: 145 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 0.013 0.002 TYR A 14 ARG 0.002 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 0.99782 ( 3) hydrogen bonds : bond 0.04666 ( 262) hydrogen bonds : angle 4.42541 ( 777) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.31958 ( 2) covalent geometry : bond 0.00455 ( 4089) covalent geometry : angle 0.59025 ( 5578) *********************** 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 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.746 Fit side-chains REVERT: B 80 TYR cc_start: 0.8041 (m-80) cc_final: 0.7632 (m-80) REVERT: A 66 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 320 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7172 (mm-30) outliers start: 15 outliers final: 13 residues processed: 79 average time/residue: 0.1440 time to fit residues: 14.5606 Evaluate side-chains 77 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.146203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134086 restraints weight = 4965.479| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.01 r_work: 0.3389 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4091 Z= 0.130 Angle : 0.533 8.965 5583 Z= 0.274 Chirality : 0.040 0.131 642 Planarity : 0.004 0.033 679 Dihedral : 4.247 19.410 571 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.60 % Allowed : 17.49 % 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: 1.43 (0.39), residues: 496 helix: 1.79 (0.30), residues: 299 sheet: -0.50 (0.71), residues: 52 loop : -0.17 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.020 0.002 PHE A 71 TYR 0.014 0.001 TYR A 79 ARG 0.001 0.000 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 0.83318 ( 3) hydrogen bonds : bond 0.04071 ( 262) hydrogen bonds : angle 4.19789 ( 777) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.32418 ( 2) covalent geometry : bond 0.00295 ( 4089) covalent geometry : angle 0.53288 ( 5578) *********************** 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 77 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7912 (m-80) cc_final: 0.7543 (m-80) REVERT: A 66 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 320 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7163 (mm-30) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.1636 time to fit residues: 15.4641 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 : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.143414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131028 restraints weight = 5081.943| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.05 r_work: 0.3348 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4091 Z= 0.171 Angle : 0.572 9.214 5583 Z= 0.294 Chirality : 0.042 0.152 642 Planarity : 0.004 0.033 679 Dihedral : 4.343 19.153 571 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.90 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: 1.36 (0.39), residues: 496 helix: 1.70 (0.30), residues: 298 sheet: -0.49 (0.71), residues: 52 loop : -0.10 (0.56), residues: 146 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 0.001 0.000 ARG B 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 0.98682 ( 3) hydrogen bonds : bond 0.04410 ( 262) hydrogen bonds : angle 4.30976 ( 777) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.28185 ( 2) covalent geometry : bond 0.00408 ( 4089) covalent geometry : angle 0.57139 ( 5578) *********************** 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 87 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7951 (m-80) cc_final: 0.7575 (m-80) REVERT: A 66 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8502 (mm) REVERT: A 320 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7154 (mm-30) outliers start: 17 outliers final: 15 residues processed: 84 average time/residue: 0.1584 time to fit residues: 17.0576 Evaluate side-chains 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.144039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131564 restraints weight = 5031.887| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.05 r_work: 0.3368 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 0.043 4091 Z= 0.152 Angle : 0.560 9.066 5583 Z= 0.287 Chirality : 0.041 0.134 642 Planarity : 0.004 0.033 679 Dihedral : 4.315 19.562 571 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.55 % Allowed : 17.73 % 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: 1.47 (0.39), residues: 496 helix: 1.78 (0.30), residues: 299 sheet: -0.39 (0.71), residues: 52 loop : -0.09 (0.56), residues: 145 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 0.022 0.002 PHE A 71 TYR 0.014 0.001 TYR A 79 ARG 0.001 0.000 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 0.94686 ( 3) hydrogen bonds : bond 0.04252 ( 262) hydrogen bonds : angle 4.26750 ( 777) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.25591 ( 2) covalent geometry : bond 0.00358 ( 4089) covalent geometry : angle 0.55966 ( 5578) *********************** 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 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7894 (m-80) cc_final: 0.7526 (m-80) REVERT: A 66 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 271 GLU cc_start: 0.4476 (pm20) cc_final: 0.3716 (pt0) REVERT: A 320 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7176 (mm-30) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.1450 time to fit residues: 14.2556 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 : 0.415 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.142445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129600 restraints weight = 5136.173| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.09 r_work: 0.3339 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4091 Z= 0.178 Angle : 0.582 9.292 5583 Z= 0.299 Chirality : 0.042 0.140 642 Planarity : 0.004 0.033 679 Dihedral : 4.395 19.664 571 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.55 % Allowed : 17.73 % 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: 1.33 (0.38), residues: 496 helix: 1.69 (0.30), residues: 298 sheet: -0.44 (0.71), residues: 52 loop : -0.17 (0.55), residues: 146 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 0.024 0.002 PHE A 71 TYR 0.013 0.002 TYR A 79 ARG 0.002 0.000 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00018 ( 1) link_NAG-ASN : angle 1.02041 ( 3) hydrogen bonds : bond 0.04472 ( 262) hydrogen bonds : angle 4.33735 ( 777) SS BOND : bond 0.00266 ( 1) SS BOND : angle 0.36885 ( 2) covalent geometry : bond 0.00427 ( 4089) covalent geometry : angle 0.58132 ( 5578) *********************** 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.421 Fit side-chains REVERT: B 80 TYR cc_start: 0.7970 (m-80) cc_final: 0.7597 (m-80) REVERT: A 66 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 271 GLU cc_start: 0.4456 (pm20) cc_final: 0.3662 (pt0) REVERT: A 320 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 452 ILE cc_start: 0.8097 (mt) cc_final: 0.7893 (mt) outliers start: 15 outliers final: 14 residues processed: 78 average time/residue: 0.1399 time to fit residues: 14.1482 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 : 0.411 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.142673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129969 restraints weight = 5096.465| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.08 r_work: 0.3352 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4091 Z= 0.172 Angle : 0.579 9.170 5583 Z= 0.298 Chirality : 0.042 0.140 642 Planarity : 0.004 0.033 679 Dihedral : 4.387 19.598 571 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: 1.35 (0.38), residues: 496 helix: 1.71 (0.30), residues: 298 sheet: -0.41 (0.71), residues: 52 loop : -0.19 (0.54), 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 0.023 0.002 PHE A 71 TYR 0.015 0.002 TYR A 445 ARG 0.002 0.000 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 1.00758 ( 3) hydrogen bonds : bond 0.04405 ( 262) hydrogen bonds : angle 4.32226 ( 777) SS BOND : bond 0.00226 ( 1) SS BOND : angle 0.35374 ( 2) covalent geometry : bond 0.00410 ( 4089) covalent geometry : angle 0.57883 ( 5578) ********************** 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 : 0.422 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7976 (m-80) cc_final: 0.7607 (m-80) REVERT: A 66 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8493 (mm) REVERT: A 271 GLU cc_start: 0.4450 (pm20) cc_final: 0.3680 (pt0) REVERT: A 320 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7170 (mm-30) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.1399 time to fit residues: 13.8932 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 : 0.412 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129584 restraints weight = 5057.737| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.06 r_work: 0.3346 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4091 Z= 0.197 Angle : 0.598 9.476 5583 Z= 0.308 Chirality : 0.043 0.154 642 Planarity : 0.004 0.033 679 Dihedral : 4.484 19.397 571 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.78 % Allowed : 17.73 % Favored : 78.49 % 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 (0.38), residues: 496 helix: 1.60 (0.30), residues: 297 sheet: -0.48 (0.71), residues: 52 loop : -0.22 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 PHE 0.025 0.002 PHE A 71 TYR 0.015 0.002 TYR A 445 ARG 0.002 0.000 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 1.08822 ( 3) hydrogen bonds : bond 0.04629 ( 262) hydrogen bonds : angle 4.42145 ( 777) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.36926 ( 2) covalent geometry : bond 0.00475 ( 4089) covalent geometry : angle 0.59812 ( 5578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2752.42 seconds wall clock time: 48 minutes 10.76 seconds (2890.76 seconds total)