Starting phenix.real_space_refine on Wed Jul 1 21:46:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.cif" model { file = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e39_30977/07_2026/7e39_30977.map" } resolution = 3.7 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= 0.000 sd= 0.002 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 15 5.16 5 C 1946 2.51 5 N 525 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3074 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 705 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 97 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 chiralities: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.32 Number of scatterers: 3074 At special positions: 0 Unit cell: (56.16, 103.68, 76.68, 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 15 16.00 O 588 8.00 N 525 7.00 C 1946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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 343 " Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 121.6 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.799A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.173A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.665A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.037A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.613A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 6.210A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.769A pdb=" N MET B 11 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.527A pdb=" N TYR B 49 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.713A pdb=" N VAL C 114 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 225 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: 0.43 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1003 1.34 - 1.46: 799 1.46 - 1.58: 1330 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3150 Sorted by residual: bond pdb=" CG LEU A 387 " pdb=" CD1 LEU A 387 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.26e-01 ... (remaining 3145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4093 1.62 - 3.24: 164 3.24 - 4.86: 29 4.86 - 6.48: 3 6.48 - 8.10: 3 Bond angle restraints: 4292 Sorted by residual: angle pdb=" N GLY C 111 " pdb=" CA GLY C 111 " pdb=" C GLY C 111 " ideal model delta sigma weight residual 113.18 118.81 -5.63 2.37e+00 1.78e-01 5.65e+00 angle pdb=" CA TYR B 94 " pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 113.90 109.63 4.27 1.80e+00 3.09e-01 5.62e+00 angle pdb=" C GLN B 79 " pdb=" CA GLN B 79 " pdb=" CB GLN B 79 " ideal model delta sigma weight residual 109.26 112.71 -3.45 1.47e+00 4.63e-01 5.51e+00 angle pdb=" C GLY B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.87 117.62 4.25 1.83e+00 2.99e-01 5.38e+00 angle pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sigma weight residual 116.30 124.40 -8.10 3.50e+00 8.16e-02 5.36e+00 ... (remaining 4287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 1571 14.32 - 28.63: 182 28.63 - 42.95: 50 42.95 - 57.26: 12 57.26 - 71.58: 7 Dihedral angle restraints: 1822 sinusoidal: 631 harmonic: 1191 Sorted by residual: dihedral pdb=" CA LEU B 78 " pdb=" C LEU B 78 " pdb=" N GLN B 79 " pdb=" CA GLN B 79 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N GLU B 68 " pdb=" CA GLU B 68 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA GLN B 79 " pdb=" C GLN B 79 " pdb=" N PRO B 80 " pdb=" CA PRO B 80 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 310 0.041 - 0.083: 104 0.083 - 0.124: 40 0.124 - 0.166: 11 0.166 - 0.207: 1 Chirality restraints: 466 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL B 43 " pdb=" N VAL B 43 " pdb=" C VAL B 43 " pdb=" CB VAL B 43 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 463 not shown) Planarity restraints: 563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO B 95 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO B 80 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 456 " 0.004 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE A 456 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 456 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 456 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 456 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 456 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 456 " 0.001 2.00e-02 2.50e+03 ... (remaining 560 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 93 2.68 - 3.24: 3074 3.24 - 3.79: 4685 3.79 - 4.35: 6276 4.35 - 4.90: 10301 Nonbonded interactions: 24429 Sorted by model distance: nonbonded pdb=" NZ LYS B 39 " pdb=" O GLU B 81 " model vdw 2.130 3.120 nonbonded pdb=" OG SER B 63 " pdb=" OG1 THR B 74 " model vdw 2.162 3.040 nonbonded pdb=" NZ LYS B 39 " pdb=" OE2 GLU B 81 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.217 3.120 nonbonded pdb=" O TYR B 49 " pdb=" OG SER B 53 " model vdw 2.225 3.040 ... (remaining 24424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.050 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.005 0.040 3156 Z= 0.215 Angle : 0.776 8.104 4305 Z= 0.421 Chirality : 0.050 0.207 466 Planarity : 0.005 0.057 562 Dihedral : 14.373 71.576 1051 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 are not related in a simple way. whole: -3.52 (0.38), residues: 406 helix: -3.93 (0.60), residues: 33 sheet: -1.59 (0.43), residues: 131 loop : -2.63 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 457 TYR 0.023 0.002 TYR B 94 PHE 0.024 0.002 PHE A 456 TRP 0.012 0.002 TRP C 52 HIS 0.005 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 ( 3150) covalent geometry : angle 0.76795 / 0.42 ( 4292) SS BOND : bond 0.00328 / 0.16 ( 5) SS BOND : angle 2.15827 / 1.25 ( 10) hydrogen bonds : bond 0.18706 / 10.97 ( 94) hydrogen bonds : angle 9.64269 / 6.55 ( 225) link_NAG-ASN : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : angle 2.14049 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.096 Fit side-chains REVERT: A 389 ASP cc_start: 0.7162 (t0) cc_final: 0.6787 (t0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0708 time to fit residues: 3.4381 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061529 restraints weight = 14594.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062871 restraints weight = 7980.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063751 restraints weight = 5254.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064354 restraints weight = 3889.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064751 restraints weight = 3108.903| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3156 Z= 0.224 Angle : 0.722 6.490 4305 Z= 0.378 Chirality : 0.050 0.167 466 Planarity : 0.006 0.058 562 Dihedral : 6.060 24.400 450 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 1.36 % Allowed : 8.84 % Favored : 89.80 % 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 are not related in a simple way. whole: -3.35 (0.38), residues: 406 helix: -3.92 (0.83), residues: 20 sheet: -1.61 (0.42), residues: 134 loop : -2.54 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 98 TYR 0.022 0.002 TYR B 94 PHE 0.023 0.002 PHE A 456 TRP 0.011 0.002 TRP C 52 HIS 0.006 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 ( 3150) covalent geometry : angle 0.71636 / 0.38 ( 4292) SS BOND : bond 0.00342 / 0.19 ( 5) SS BOND : angle 1.77582 / 1.02 ( 10) hydrogen bonds : bond 0.03755 / 2.24 ( 94) hydrogen bonds : angle 7.74976 / 5.29 ( 225) link_NAG-ASN : bond 0.00149 / 0.08 ( 1) link_NAG-ASN : angle 1.84102 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.123 Fit side-chains REVERT: A 365 TYR cc_start: 0.7430 (m-80) cc_final: 0.6692 (m-80) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.0732 time to fit residues: 3.2455 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 14 optimal weight: 0.0470 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.069997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062796 restraints weight = 14208.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064199 restraints weight = 7537.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065102 restraints weight = 4848.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065717 restraints weight = 3535.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066050 restraints weight = 2797.105| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3156 Z= 0.144 Angle : 0.626 8.715 4305 Z= 0.324 Chirality : 0.048 0.165 466 Planarity : 0.005 0.064 562 Dihedral : 5.474 23.603 450 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.72 % Allowed : 13.27 % Favored : 84.01 % 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 are not related in a simple way. whole: -3.12 (0.39), residues: 406 helix: -3.32 (0.89), residues: 21 sheet: -1.46 (0.42), residues: 137 loop : -2.41 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 98 TYR 0.018 0.002 TYR B 94 PHE 0.025 0.002 PHE A 456 TRP 0.009 0.001 TRP C 52 HIS 0.005 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 3150) covalent geometry : angle 0.62241 / 0.32 ( 4292) SS BOND : bond 0.00186 / 0.10 ( 5) SS BOND : angle 1.14579 / 0.65 ( 10) hydrogen bonds : bond 0.03137 / 1.89 ( 94) hydrogen bonds : angle 7.06529 / 4.80 ( 225) link_NAG-ASN : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : angle 1.85967 / 0.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.127 Fit side-chains REVERT: A 365 TYR cc_start: 0.7514 (m-80) cc_final: 0.6933 (m-80) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.0671 time to fit residues: 3.4418 Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 0.0770 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.068731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061602 restraints weight = 14544.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.062953 restraints weight = 7904.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063863 restraints weight = 5153.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064397 restraints weight = 3780.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064832 restraints weight = 3062.792| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3156 Z= 0.224 Angle : 0.692 7.742 4305 Z= 0.361 Chirality : 0.049 0.169 466 Planarity : 0.006 0.063 562 Dihedral : 5.709 22.473 450 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 3.40 % Allowed : 16.33 % Favored : 80.27 % 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 are not related in a simple way. whole: -3.17 (0.39), residues: 406 helix: -3.09 (1.02), residues: 21 sheet: -1.58 (0.41), residues: 143 loop : -2.41 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 61 TYR 0.020 0.002 TYR B 94 PHE 0.013 0.002 PHE A 377 TRP 0.011 0.002 TRP C 52 HIS 0.005 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 ( 3150) covalent geometry : angle 0.68797 / 0.36 ( 4292) SS BOND : bond 0.00347 / 0.20 ( 5) SS BOND : angle 1.48971 / 0.85 ( 10) hydrogen bonds : bond 0.03619 / 2.28 ( 94) hydrogen bonds : angle 7.25631 / 4.91 ( 225) link_NAG-ASN : bond 0.00025 / 0.01 ( 1) link_NAG-ASN : angle 1.74887 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.126 Fit side-chains REVERT: A 365 TYR cc_start: 0.7501 (m-80) cc_final: 0.6806 (m-80) REVERT: A 493 GLN cc_start: 0.7147 (tm-30) cc_final: 0.6943 (tm-30) outliers start: 10 outliers final: 9 residues processed: 37 average time/residue: 0.0652 time to fit residues: 3.0619 Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.070926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.063848 restraints weight = 14272.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065270 restraints weight = 7457.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066205 restraints weight = 4725.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066778 restraints weight = 3396.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.067248 restraints weight = 2705.681| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3156 Z= 0.100 Angle : 0.588 7.927 4305 Z= 0.303 Chirality : 0.047 0.177 466 Planarity : 0.005 0.066 562 Dihedral : 5.034 23.371 450 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.40 % Allowed : 18.03 % Favored : 78.57 % 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 are not related in a simple way. whole: -2.84 (0.40), residues: 406 helix: -2.86 (1.03), residues: 21 sheet: -1.41 (0.41), residues: 149 loop : -2.16 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.012 0.001 TYR B 94 PHE 0.010 0.001 PHE A 456 TRP 0.009 0.001 TRP C 52 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 3150) covalent geometry : angle 0.58568 / 0.30 ( 4292) SS BOND : bond 0.00082 / 0.04 ( 5) SS BOND : angle 0.81224 / 0.44 ( 10) hydrogen bonds : bond 0.02864 / 1.76 ( 94) hydrogen bonds : angle 6.55458 / 4.43 ( 225) link_NAG-ASN : bond 0.00053 / 0.03 ( 1) link_NAG-ASN : angle 1.81298 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.122 Fit side-chains REVERT: A 365 TYR cc_start: 0.7464 (m-80) cc_final: 0.6747 (m-80) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.0620 time to fit residues: 3.4255 Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.069313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061890 restraints weight = 14337.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063283 restraints weight = 7748.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064202 restraints weight = 5037.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.064842 restraints weight = 3688.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065177 restraints weight = 2922.231| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3156 Z= 0.195 Angle : 0.653 8.447 4305 Z= 0.338 Chirality : 0.048 0.162 466 Planarity : 0.005 0.064 562 Dihedral : 5.265 22.109 450 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.74 % Allowed : 19.73 % Favored : 76.53 % 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 are not related in a simple way. whole: -2.88 (0.40), residues: 406 helix: -3.03 (0.99), residues: 21 sheet: -1.32 (0.41), residues: 146 loop : -2.26 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 466 TYR 0.019 0.002 TYR B 94 PHE 0.015 0.002 PHE A 456 TRP 0.009 0.001 TRP C 52 HIS 0.004 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 3150) covalent geometry : angle 0.64912 / 0.34 ( 4292) SS BOND : bond 0.00233 / 0.13 ( 5) SS BOND : angle 1.30285 / 0.74 ( 10) hydrogen bonds : bond 0.03261 / 2.03 ( 94) hydrogen bonds : angle 6.73054 / 4.58 ( 225) link_NAG-ASN : bond 0.00036 / 0.02 ( 1) link_NAG-ASN : angle 1.72225 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.073 Fit side-chains REVERT: A 365 TYR cc_start: 0.7559 (m-80) cc_final: 0.6972 (m-80) REVERT: A 493 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6906 (tm-30) outliers start: 11 outliers final: 7 residues processed: 40 average time/residue: 0.0610 time to fit residues: 3.0390 Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.0170 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063277 restraints weight = 14351.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064725 restraints weight = 7630.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065684 restraints weight = 4843.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.066299 restraints weight = 3492.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.066673 restraints weight = 2731.062| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3156 Z= 0.117 Angle : 0.618 8.765 4305 Z= 0.318 Chirality : 0.047 0.172 466 Planarity : 0.005 0.065 562 Dihedral : 5.016 23.212 450 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.06 % Allowed : 19.73 % Favored : 77.21 % 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 are not related in a simple way. whole: -2.81 (0.40), residues: 406 helix: -2.87 (1.01), residues: 21 sheet: -1.53 (0.39), residues: 163 loop : -2.01 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.016 0.001 TYR B 94 PHE 0.013 0.001 PHE A 456 TRP 0.009 0.001 TRP C 52 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 3150) covalent geometry : angle 0.61520 / 0.32 ( 4292) SS BOND : bond 0.00098 / 0.05 ( 5) SS BOND : angle 0.92917 / 0.52 ( 10) hydrogen bonds : bond 0.02899 / 1.77 ( 94) hydrogen bonds : angle 6.37044 / 4.32 ( 225) link_NAG-ASN : bond 0.00113 / 0.06 ( 1) link_NAG-ASN : angle 1.75961 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.111 Fit side-chains REVERT: A 365 TYR cc_start: 0.7480 (m-80) cc_final: 0.6876 (m-80) REVERT: A 493 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6873 (tm-30) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.0517 time to fit residues: 2.6214 Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062660 restraints weight = 14666.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064122 restraints weight = 7872.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.065007 restraints weight = 5046.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065659 restraints weight = 3714.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066000 restraints weight = 2918.920| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3156 Z= 0.152 Angle : 0.625 8.301 4305 Z= 0.324 Chirality : 0.047 0.157 466 Planarity : 0.005 0.064 562 Dihedral : 5.056 24.114 450 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.08 % Allowed : 19.05 % Favored : 76.87 % 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 are not related in a simple way. whole: -2.76 (0.40), residues: 406 helix: -2.77 (1.03), residues: 21 sheet: -1.41 (0.40), residues: 160 loop : -2.07 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.019 0.001 TYR B 94 PHE 0.011 0.001 PHE A 456 TRP 0.008 0.001 TRP C 52 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3150) covalent geometry : angle 0.62269 / 0.32 ( 4292) SS BOND : bond 0.00174 / 0.10 ( 5) SS BOND : angle 1.06399 / 0.60 ( 10) hydrogen bonds : bond 0.03057 / 1.88 ( 94) hydrogen bonds : angle 6.34645 / 4.30 ( 225) link_NAG-ASN : bond 0.00109 / 0.06 ( 1) link_NAG-ASN : angle 1.58681 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.071 Fit side-chains REVERT: A 365 TYR cc_start: 0.7520 (m-80) cc_final: 0.6886 (m-80) REVERT: A 493 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6918 (tm-30) outliers start: 12 outliers final: 9 residues processed: 37 average time/residue: 0.0410 time to fit residues: 1.9548 Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.069924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.062809 restraints weight = 14506.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064191 restraints weight = 7852.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065047 restraints weight = 5075.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065691 restraints weight = 3762.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.065943 restraints weight = 2953.205| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3156 Z= 0.164 Angle : 0.638 8.178 4305 Z= 0.331 Chirality : 0.047 0.156 466 Planarity : 0.005 0.065 562 Dihedral : 5.110 24.695 450 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.40 % Allowed : 20.07 % Favored : 76.53 % 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 are not related in a simple way. whole: -2.76 (0.40), residues: 406 helix: -2.71 (1.04), residues: 21 sheet: -1.42 (0.39), residues: 160 loop : -2.06 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 24 TYR 0.018 0.001 TYR B 94 PHE 0.012 0.002 PHE A 456 TRP 0.009 0.001 TRP C 52 HIS 0.004 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 3150) covalent geometry : angle 0.63554 / 0.33 ( 4292) SS BOND : bond 0.00211 / 0.12 ( 5) SS BOND : angle 1.11888 / 0.64 ( 10) hydrogen bonds : bond 0.03127 / 1.91 ( 94) hydrogen bonds : angle 6.41269 / 4.34 ( 225) link_NAG-ASN : bond 0.00111 / 0.06 ( 1) link_NAG-ASN : angle 1.62746 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.112 Fit side-chains REVERT: A 365 TYR cc_start: 0.7464 (m-80) cc_final: 0.6834 (m-80) outliers start: 10 outliers final: 9 residues processed: 35 average time/residue: 0.0528 time to fit residues: 2.3880 Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.069218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062113 restraints weight = 14161.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063463 restraints weight = 7740.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064315 restraints weight = 5014.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064909 restraints weight = 3724.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065202 restraints weight = 2969.383| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3156 Z= 0.217 Angle : 0.706 8.012 4305 Z= 0.367 Chirality : 0.048 0.166 466 Planarity : 0.005 0.064 562 Dihedral : 5.439 26.975 450 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 3.40 % Allowed : 20.07 % Favored : 76.53 % 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 are not related in a simple way. whole: -2.91 (0.40), residues: 406 helix: -3.18 (0.79), residues: 27 sheet: -1.45 (0.39), residues: 159 loop : -2.13 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 466 TYR 0.023 0.002 TYR B 94 PHE 0.012 0.002 PHE A 456 TRP 0.010 0.002 TRP C 52 HIS 0.004 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 3150) covalent geometry : angle 0.70256 / 0.37 ( 4292) SS BOND : bond 0.00314 / 0.18 ( 5) SS BOND : angle 1.35599 / 0.78 ( 10) hydrogen bonds : bond 0.03429 / 2.08 ( 94) hydrogen bonds : angle 6.72558 / 4.56 ( 225) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.65336 / 0.78 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.160 Fit side-chains REVERT: A 365 TYR cc_start: 0.7545 (m-80) cc_final: 0.6977 (m-80) outliers start: 10 outliers final: 7 residues processed: 34 average time/residue: 0.0456 time to fit residues: 2.0053 Evaluate side-chains 37 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064208 restraints weight = 14283.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065661 restraints weight = 7543.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.066621 restraints weight = 4773.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.067250 restraints weight = 3408.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.067572 restraints weight = 2648.594| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3156 Z= 0.106 Angle : 0.615 9.037 4305 Z= 0.318 Chirality : 0.046 0.184 466 Planarity : 0.004 0.066 562 Dihedral : 4.895 27.247 450 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.70 % Allowed : 21.77 % Favored : 76.53 % 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 are not related in a simple way. whole: -2.69 (0.40), residues: 406 helix: -2.84 (0.86), residues: 27 sheet: -1.44 (0.39), residues: 164 loop : -1.89 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.010 0.001 TYR A 365 PHE 0.008 0.001 PHE B 83 TRP 0.006 0.001 TRP C 52 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 3150) covalent geometry : angle 0.61356 / 0.32 ( 4292) SS BOND : bond 0.00051 / 0.03 ( 5) SS BOND : angle 0.78962 / 0.43 ( 10) hydrogen bonds : bond 0.02807 / 1.70 ( 94) hydrogen bonds : angle 6.09687 / 4.12 ( 225) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 1.64610 / 0.76 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 687.62 seconds wall clock time: 12 minutes 33.21 seconds (753.21 seconds total)