Starting phenix.real_space_refine on Wed Sep 17 04:19:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s4u_19716/09_2025/8s4u_19716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s4u_19716/09_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_19716/09_2025/8s4u_19716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s4u_19716/09_2025/8s4u_19716.map" model { file = "/net/cci-nas-00/data/ceres_data/8s4u_19716/09_2025/8s4u_19716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s4u_19716/09_2025/8s4u_19716.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.15, per 1000 atoms: 0.29 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: 0.34 Conformation dependent library (CDL) restraints added in 156.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 0.65 Time building geometry restraints manager: 0.47 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.670 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG A 277 TYR 0.015 0.002 TYR B 94 PHE 0.031 0.002 PHE A 71 TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 4089) covalent geometry : angle 0.64854 ( 5578) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.18675 ( 2) hydrogen bonds : bond 0.22173 ( 262) hydrogen bonds : angle 8.39925 ( 777) link_NAG-ASN : bond 0.02014 ( 1) link_NAG-ASN : angle 3.03854 ( 3) *********************** 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 : 0.108 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: 0.0844 time to fit residues: 7.4702 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 : 0.156 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.143897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131615 restraints weight = 5164.740| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.06 r_work: 0.3363 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4091 Z= 0.153 Angle : 0.576 7.821 5583 Z= 0.303 Chirality : 0.042 0.188 642 Planarity : 0.004 0.028 679 Dihedral : 4.883 42.601 573 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.38), residues: 496 helix: 1.31 (0.30), residues: 299 sheet: -2.19 (0.66), residues: 45 loop : -0.69 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.013 0.001 TYR A 14 PHE 0.020 0.002 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4089) covalent geometry : angle 0.57531 ( 5578) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.19710 ( 2) hydrogen bonds : bond 0.05020 ( 262) hydrogen bonds : angle 4.70852 ( 777) link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 1.16681 ( 3) *********************** 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 89 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.8113 (m-80) cc_final: 0.7664 (m-80) REVERT: A 320 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7378 (mm-30) outliers start: 10 outliers final: 4 residues processed: 84 average time/residue: 0.0653 time to fit residues: 6.9506 Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 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 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 = 0.3667 r_free = 0.3667 target = 0.147732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136315 restraints weight = 4978.268| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 0.96 r_work: 0.3360 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1629 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= 0.192 Angle : 0.601 8.494 5583 Z= 0.312 Chirality : 0.043 0.196 642 Planarity : 0.004 0.033 679 Dihedral : 4.516 18.714 571 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.13 % Allowed : 17.73 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.38), residues: 496 helix: 1.43 (0.30), residues: 299 sheet: -1.74 (0.68), residues: 45 loop : -0.62 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.013 0.002 TYR A 14 PHE 0.024 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 4089) covalent geometry : angle 0.60063 ( 5578) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.91617 ( 2) hydrogen bonds : bond 0.04926 ( 262) hydrogen bonds : angle 4.56222 ( 777) link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 0.98627 ( 3) *********************** 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 77 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.158 Fit side-chains REVERT: B 80 TYR cc_start: 0.8080 (m-80) cc_final: 0.7679 (m-80) REVERT: A 66 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8519 (mm) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.0604 time to fit residues: 5.8905 Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.0070 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 = 0.3619 r_free = 0.3619 target = 0.144509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132096 restraints weight = 5026.438| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.05 r_work: 0.3382 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4091 Z= 0.141 Angle : 0.543 8.678 5583 Z= 0.280 Chirality : 0.041 0.149 642 Planarity : 0.004 0.033 679 Dihedral : 4.324 18.556 571 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.84 % Allowed : 17.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.39), residues: 496 helix: 1.64 (0.30), residues: 299 sheet: -0.82 (0.69), residues: 52 loop : -0.40 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 38 TYR 0.013 0.001 TYR A 14 PHE 0.020 0.002 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4089) covalent geometry : angle 0.54291 ( 5578) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.36893 ( 2) hydrogen bonds : bond 0.04298 ( 262) hydrogen bonds : angle 4.29740 ( 777) link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 0.79731 ( 3) *********************** 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 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.190 Fit side-chains REVERT: B 80 TYR cc_start: 0.7975 (m-80) cc_final: 0.7549 (m-80) REVERT: A 66 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8482 (mm) REVERT: A 320 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7151 (mm-30) outliers start: 12 outliers final: 5 residues processed: 79 average time/residue: 0.0698 time to fit residues: 6.9530 Evaluate side-chains 71 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 = 0.3624 r_free = 0.3624 target = 0.144808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132357 restraints weight = 4996.665| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.05 r_work: 0.3371 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4091 Z= 0.143 Angle : 0.541 8.418 5583 Z= 0.279 Chirality : 0.041 0.148 642 Planarity : 0.004 0.033 679 Dihedral : 4.267 18.563 571 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.07 % Allowed : 16.78 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.39), residues: 496 helix: 1.77 (0.30), residues: 299 sheet: -0.52 (0.74), residues: 46 loop : -0.26 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.013 0.001 TYR A 14 PHE 0.021 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4089) covalent geometry : angle 0.54044 ( 5578) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.25477 ( 2) hydrogen bonds : bond 0.04239 ( 262) hydrogen bonds : angle 4.23388 ( 777) link_NAG-ASN : bond 0.00099 ( 1) link_NAG-ASN : angle 0.83170 ( 3) *********************** 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 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.152 Fit side-chains REVERT: B 80 TYR cc_start: 0.7979 (m-80) cc_final: 0.7556 (m-80) REVERT: A 66 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8447 (mm) REVERT: A 320 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7167 (mm-30) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.0635 time to fit residues: 6.2596 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 : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 294 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 = 0.3609 r_free = 0.3609 target = 0.143538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130877 restraints weight = 5133.414| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.08 r_work: 0.3357 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2004 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= 0.159 Angle : 0.555 8.653 5583 Z= 0.286 Chirality : 0.041 0.147 642 Planarity : 0.004 0.033 679 Dihedral : 4.303 19.091 571 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.55 % Allowed : 16.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.39), residues: 496 helix: 1.74 (0.30), residues: 299 sheet: -0.52 (0.74), residues: 46 loop : -0.22 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 38 TYR 0.013 0.002 TYR A 14 PHE 0.022 0.002 PHE A 71 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4089) covalent geometry : angle 0.55507 ( 5578) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.27850 ( 2) hydrogen bonds : bond 0.04348 ( 262) hydrogen bonds : angle 4.26730 ( 777) link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 0.91693 ( 3) *********************** 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7965 (m-80) cc_final: 0.7591 (m-80) REVERT: A 66 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 320 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7144 (mm-30) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.0665 time to fit residues: 6.5765 Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 = 0.142527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129883 restraints weight = 5149.300| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.08 r_work: 0.3346 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4091 Z= 0.174 Angle : 0.572 8.837 5583 Z= 0.295 Chirality : 0.042 0.152 642 Planarity : 0.004 0.033 679 Dihedral : 4.349 19.513 571 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.26 % Allowed : 16.08 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.39), residues: 496 helix: 1.67 (0.30), residues: 299 sheet: -0.57 (0.71), residues: 52 loop : -0.16 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 38 TYR 0.013 0.002 TYR A 14 PHE 0.024 0.002 PHE A 71 TRP 0.017 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 4089) covalent geometry : angle 0.57133 ( 5578) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.31221 ( 2) hydrogen bonds : bond 0.04465 ( 262) hydrogen bonds : angle 4.30820 ( 777) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 1.02842 ( 3) *********************** 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: 18 poor density : 69 time to evaluate : 0.092 Fit side-chains REVERT: B 76 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8148 (mtmm) REVERT: B 80 TYR cc_start: 0.8009 (m-80) cc_final: 0.7562 (m-80) REVERT: A 66 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 320 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7165 (mm-30) outliers start: 18 outliers final: 15 residues processed: 83 average time/residue: 0.0658 time to fit residues: 7.0614 Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 294 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 = 0.3619 r_free = 0.3619 target = 0.144471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131766 restraints weight = 5076.766| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.08 r_work: 0.3370 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4091 Z= 0.147 Angle : 0.549 8.525 5583 Z= 0.282 Chirality : 0.041 0.134 642 Planarity : 0.004 0.033 679 Dihedral : 4.279 19.635 571 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.39), residues: 496 helix: 1.80 (0.30), residues: 299 sheet: -0.32 (0.76), residues: 46 loop : -0.17 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 456 TYR 0.014 0.001 TYR A 336 PHE 0.022 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4089) covalent geometry : angle 0.54847 ( 5578) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.26734 ( 2) hydrogen bonds : bond 0.04188 ( 262) hydrogen bonds : angle 4.22765 ( 777) link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 0.93776 ( 3) *********************** 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 84 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7928 (m-80) cc_final: 0.7584 (m-80) REVERT: A 66 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8497 (mm) REVERT: A 271 GLU cc_start: 0.4544 (pm20) cc_final: 0.3755 (pt0) REVERT: A 320 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7182 (mm-30) outliers start: 17 outliers final: 16 residues processed: 80 average time/residue: 0.0689 time to fit residues: 6.9877 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 : 0.122 ------------------------------------------------------------------------------- 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 294 GLN 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 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 = 0.3590 r_free = 0.3590 target = 0.142223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129386 restraints weight = 5191.639| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.09 r_work: 0.3362 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2044 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= 0.193 Angle : 0.588 9.053 5583 Z= 0.303 Chirality : 0.043 0.151 642 Planarity : 0.004 0.034 679 Dihedral : 4.390 19.638 571 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.02 % Allowed : 17.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.38), residues: 496 helix: 1.63 (0.30), residues: 298 sheet: -0.47 (0.72), residues: 52 loop : -0.25 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.013 0.002 TYR A 14 PHE 0.025 0.002 PHE A 71 TRP 0.016 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 4089) covalent geometry : angle 0.58817 ( 5578) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.27451 ( 2) hydrogen bonds : bond 0.04563 ( 262) hydrogen bonds : angle 4.34892 ( 777) link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 1.04195 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.148 Fit side-chains REVERT: B 76 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8132 (mtmm) REVERT: B 80 TYR cc_start: 0.7994 (m-80) cc_final: 0.7574 (m-80) REVERT: A 66 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8513 (mm) REVERT: A 271 GLU cc_start: 0.4501 (pm20) cc_final: 0.3706 (pt0) REVERT: A 320 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7180 (mm-30) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.0659 time to fit residues: 6.7188 Evaluate side-chains 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 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 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133166 restraints weight = 5028.266| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.02 r_work: 0.3427 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2085 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= 0.164 Angle : 0.569 9.415 5583 Z= 0.292 Chirality : 0.042 0.138 642 Planarity : 0.004 0.032 679 Dihedral : 4.327 19.588 571 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.02 % Allowed : 17.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.38), residues: 496 helix: 1.74 (0.30), residues: 298 sheet: -0.31 (0.77), residues: 46 loop : -0.28 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.012 0.002 TYR A 14 PHE 0.023 0.002 PHE A 71 TRP 0.018 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4089) covalent geometry : angle 0.56850 ( 5578) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.29009 ( 2) hydrogen bonds : bond 0.04347 ( 262) hydrogen bonds : angle 4.27775 ( 777) link_NAG-ASN : bond 0.00027 ( 1) link_NAG-ASN : angle 0.97219 ( 3) ********************** 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 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7951 (m-80) cc_final: 0.7602 (m-80) REVERT: A 66 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8528 (mm) REVERT: A 271 GLU cc_start: 0.4423 (pm20) cc_final: 0.3646 (pt0) REVERT: A 320 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 452 ILE cc_start: 0.8087 (mt) cc_final: 0.7887 (mt) outliers start: 17 outliers final: 16 residues processed: 78 average time/residue: 0.0673 time to fit residues: 6.7602 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 : 0.138 ------------------------------------------------------------------------------- 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 294 GLN 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 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.0370 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135178 restraints weight = 5095.878| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.03 r_work: 0.3389 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4091 Z= 0.142 Angle : 0.541 8.908 5583 Z= 0.279 Chirality : 0.041 0.134 642 Planarity : 0.004 0.032 679 Dihedral : 4.279 19.384 571 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.78 % Allowed : 17.97 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.39), residues: 496 helix: 1.82 (0.30), residues: 298 sheet: -0.26 (0.78), residues: 46 loop : -0.13 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.013 0.001 TYR A 79 PHE 0.021 0.002 PHE A 71 TRP 0.019 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4089) covalent geometry : angle 0.54068 ( 5578) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.31872 ( 2) hydrogen bonds : bond 0.04178 ( 262) hydrogen bonds : angle 4.23101 ( 777) link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 0.95598 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.76 seconds wall clock time: 23 minutes 14.29 seconds (1394.29 seconds total)