Starting phenix.real_space_refine on Thu Oct 22 22:44:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xgx_66861/10_2026/9xgx_66861_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xgx_66861/10_2026/9xgx_66861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xgx_66861/10_2026/9xgx_66861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xgx_66861/10_2026/9xgx_66861.map" model { file = "/net/cci-nas-00/data/ceres_data/9xgx_66861/10_2026/9xgx_66861_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xgx_66861/10_2026/9xgx_66861_trim.cif" } resolution = 2.8 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= 0.038 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: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 2061 2.51 5 N 547 2.21 5 O 625 1.98 5 H 3105 0.53 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6351 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1752 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "B" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1644 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2941 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 10, 'TRANS': 180} Chain: "E" 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: 0.18 Number of scatterers: 6351 At special positions: 0 Unit cell: (62.1, 66.24, 91.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 O 625 8.00 N 547 7.00 C 2061 6.00 H 3105 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 E 601 " - " ASN E 343 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 154.5 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 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 9 sheets defined 10.8% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.604A pdb=" N THR A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.777A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.516A pdb=" N ASN E 343 " --> pdb=" O GLY E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.053A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.639A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 5.611A pdb=" N GLY A 16 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 70 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 5.084A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 5.084A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.706A pdb=" N VAL B 85 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 24 removed outlier: 3.858A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 67 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.990A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 120 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3105 1.03 - 1.23: 12 1.23 - 1.42: 1469 1.42 - 1.62: 1831 1.62 - 1.81: 14 Bond restraints: 6431 Sorted by residual: bond pdb=" N VAL A 48 " pdb=" CA VAL A 48 " ideal model delta sigma weight residual 1.452 1.493 -0.041 1.18e-02 7.18e+03 1.19e+01 bond pdb=" CA SER A 49 " pdb=" CB SER A 49 " ideal model delta sigma weight residual 1.533 1.473 0.059 1.72e-02 3.38e+03 1.19e+01 bond pdb=" C VAL A 63 " pdb=" O VAL A 63 " ideal model delta sigma weight residual 1.241 1.205 0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N GLN B 37 " pdb=" CA GLN B 37 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.26e+00 bond pdb=" N GLU E 340 " pdb=" CA GLU E 340 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 6.00e+00 ... (remaining 6426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 11402 2.11 - 4.22: 113 4.22 - 6.33: 5 6.33 - 8.44: 0 8.44 - 10.55: 1 Bond angle restraints: 11521 Sorted by residual: angle pdb=" N VAL A 63 " pdb=" CA VAL A 63 " pdb=" CB VAL A 63 " ideal model delta sigma weight residual 111.87 101.32 10.55 2.32e+00 1.86e-01 2.07e+01 angle pdb=" CA VAL E 341 " pdb=" C VAL E 341 " pdb=" O VAL E 341 " ideal model delta sigma weight residual 120.83 116.43 4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" CA GLY E 339 " pdb=" C GLY E 339 " pdb=" O GLY E 339 " ideal model delta sigma weight residual 121.05 117.44 3.61 1.03e+00 9.43e-01 1.23e+01 angle pdb=" N PHE E 338 " pdb=" CA PHE E 338 " pdb=" C PHE E 338 " ideal model delta sigma weight residual 111.71 107.75 3.96 1.15e+00 7.56e-01 1.19e+01 angle pdb=" CA GLN B 37 " pdb=" C GLN B 37 " pdb=" O GLN B 37 " ideal model delta sigma weight residual 120.66 116.83 3.83 1.15e+00 7.56e-01 1.11e+01 ... (remaining 11516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.00: 2650 14.00 - 27.99: 281 27.99 - 41.99: 109 41.99 - 55.98: 56 55.98 - 69.98: 17 Dihedral angle restraints: 3113 sinusoidal: 1653 harmonic: 1460 Sorted by residual: dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -125.05 39.05 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 131.82 -38.82 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CA VAL A 63 " pdb=" CB VAL A 63 " ideal model delta harmonic sigma weight residual 123.40 113.28 10.12 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 3110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 419 0.056 - 0.111: 50 0.111 - 0.167: 18 0.167 - 0.222: 0 0.222 - 0.278: 3 Chirality restraints: 490 Sorted by residual: chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 48 " pdb=" CA VAL A 48 " pdb=" CG1 VAL A 48 " pdb=" CG2 VAL A 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB VAL A 63 " pdb=" CA VAL A 63 " pdb=" CG1 VAL A 63 " pdb=" CG2 VAL A 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 487 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 37 " 0.089 2.00e-02 2.50e+03 9.61e-02 1.38e+02 pdb=" CD GLN B 37 " -0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN B 37 " -0.088 2.00e-02 2.50e+03 pdb=" NE2 GLN B 37 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 37 " -0.141 2.00e-02 2.50e+03 pdb="HE22 GLN B 37 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 38 " 0.048 2.00e-02 2.50e+03 5.60e-02 4.70e+01 pdb=" CD GLN B 38 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 38 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 GLN B 38 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN B 38 " -0.084 2.00e-02 2.50e+03 pdb="HE22 GLN B 38 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 341 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" N PHE E 342 " -0.048 2.00e-02 2.50e+03 pdb=" CA PHE E 342 " 0.012 2.00e-02 2.50e+03 pdb=" H PHE E 342 " 0.021 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 2731 2.39 - 2.94: 14238 2.94 - 3.50: 16155 3.50 - 4.05: 23485 4.05 - 4.60: 32870 Nonbonded interactions: 89479 Sorted by model distance: nonbonded pdb=" H ASN A 73 " pdb="HD22 ASN A 73 " model vdw 1.838 2.100 nonbonded pdb=" HG2 ARG B 18 " pdb="HH11 ARG B 18 " model vdw 1.856 2.270 nonbonded pdb=" HB2 LYS E 378 " pdb=" HZ3 LYS E 378 " model vdw 1.869 2.270 nonbonded pdb=" H VAL A 63 " pdb=" HB VAL A 63 " model vdw 1.883 2.270 nonbonded pdb=" H VAL A 29 " pdb="HD22 ASN A 76 " model vdw 1.884 2.100 ... (remaining 89474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.200 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.004 0.059 3333 Z= 0.218 Angle : 0.635 10.546 4536 Z= 0.373 Chirality : 0.048 0.278 490 Planarity : 0.005 0.059 587 Dihedral : 16.155 69.978 1191 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.29 % Allowed : 23.50 % Favored : 76.22 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 10.53 % 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: -1.84 (0.41), residues: 411 helix: -4.20 (0.73), residues: 20 sheet: -1.03 (0.46), residues: 117 loop : -1.08 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 18 TYR 0.012 0.001 TYR E 369 PHE 0.009 0.001 PHE E 338 TRP 0.009 0.001 TRP E 436 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.22 ( 3326) covalent geometry : angle 0.63421 / 0.37 ( 4521) SS BOND : bond 0.00492 / 0.24 ( 6) SS BOND : angle 0.60781 / 0.29 ( 12) hydrogen bonds : bond 0.19022 / 11.31 ( 103) hydrogen bonds : angle 10.02775 / 6.47 ( 291) link_NAG-ASN : bond 0.00144 / 0.07 ( 1) link_NAG-ASN : angle 1.39848 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6617 (tttt) cc_final: 0.6378 (tptt) REVERT: A 74 SER cc_start: 0.8087 (m) cc_final: 0.7537 (t) REVERT: B 102 GLN cc_start: 0.7604 (mm-40) cc_final: 0.6608 (pm20) REVERT: B 108 ILE cc_start: 0.6587 (tp) cc_final: 0.6267 (mp) REVERT: E 378 LYS cc_start: 0.6507 (mtmm) cc_final: 0.6042 (pttt) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 1.1118 time to fit residues: 78.8916 Evaluate side-chains 45 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142439 restraints weight = 9740.667| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.86 r_work: 0.3601 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3333 Z= 0.116 Angle : 0.524 5.366 4536 Z= 0.272 Chirality : 0.043 0.148 490 Planarity : 0.004 0.043 587 Dihedral : 5.246 57.914 484 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.72 % Allowed : 25.21 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.75 (0.41), residues: 411 helix: -4.52 (0.50), residues: 20 sheet: -1.13 (0.43), residues: 131 loop : -0.85 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.011 0.001 TYR A 33 PHE 0.014 0.001 PHE E 486 TRP 0.007 0.001 TRP E 436 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 3326) covalent geometry : angle 0.52263 / 0.27 ( 4521) SS BOND : bond 0.00265 / 0.13 ( 6) SS BOND : angle 0.63061 / 0.32 ( 12) hydrogen bonds : bond 0.03448 / 2.18 ( 103) hydrogen bonds : angle 7.05476 / 4.65 ( 291) link_NAG-ASN : bond 0.00201 / 0.10 ( 1) link_NAG-ASN : angle 1.12566 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6751 (tttt) cc_final: 0.6339 (tptt) REVERT: B 18 ARG cc_start: 0.7394 (mmm160) cc_final: 0.7079 (tpp80) REVERT: B 102 GLN cc_start: 0.7547 (mm-40) cc_final: 0.6596 (pm20) REVERT: E 378 LYS cc_start: 0.6568 (mtmm) cc_final: 0.6174 (pttt) REVERT: E 383 SER cc_start: 0.4759 (OUTLIER) cc_final: 0.4549 (m) outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.9145 time to fit residues: 40.8471 Evaluate side-chains 41 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [24, 9, 31, 36, 8, 3, 19, 37, 30, 29, 38] chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133875 restraints weight = 9832.279| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.84 r_work: 0.3529 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3333 Z= 0.190 Angle : 0.581 5.681 4536 Z= 0.301 Chirality : 0.044 0.147 490 Planarity : 0.004 0.033 587 Dihedral : 5.634 54.742 484 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.01 % Allowed : 22.64 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.77 (0.41), residues: 411 helix: -4.43 (0.57), residues: 20 sheet: -1.00 (0.46), residues: 119 loop : -0.99 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 466 TYR 0.014 0.002 TYR E 473 PHE 0.011 0.002 PHE E 497 TRP 0.008 0.001 TRP A 36 HIS 0.001 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 3326) covalent geometry : angle 0.57907 / 0.30 ( 4521) SS BOND : bond 0.00410 / 0.20 ( 6) SS BOND : angle 0.84389 / 0.45 ( 12) hydrogen bonds : bond 0.03863 / 2.51 ( 103) hydrogen bonds : angle 6.75200 / 4.45 ( 291) link_NAG-ASN : bond 0.00212 / 0.10 ( 1) link_NAG-ASN : angle 1.22741 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7427 (mmm160) REVERT: B 102 GLN cc_start: 0.7674 (mm-40) cc_final: 0.6729 (pm20) REVERT: E 383 SER cc_start: 0.4805 (OUTLIER) cc_final: 0.4565 (m) outliers start: 14 outliers final: 10 residues processed: 44 average time/residue: 0.6274 time to fit residues: 29.0207 Evaluate side-chains 45 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [5, 27, 35, 16, 12, 8, 9, 23, 31, 22, 29] chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.0040 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 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 = 0.3953 r_free = 0.3953 target = 0.167135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136609 restraints weight = 9885.145| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.84 r_work: 0.3594 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3333 Z= 0.122 Angle : 0.511 5.414 4536 Z= 0.266 Chirality : 0.042 0.141 490 Planarity : 0.004 0.027 587 Dihedral : 5.353 52.527 484 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.01 % Allowed : 21.49 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.71 (0.41), residues: 411 helix: -4.35 (0.63), residues: 20 sheet: -1.08 (0.44), residues: 126 loop : -0.86 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 466 TYR 0.011 0.001 TYR A 33 PHE 0.007 0.001 PHE E 429 TRP 0.006 0.001 TRP E 436 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3326) covalent geometry : angle 0.50979 / 0.27 ( 4521) SS BOND : bond 0.00300 / 0.14 ( 6) SS BOND : angle 0.60886 / 0.30 ( 12) hydrogen bonds : bond 0.03278 / 2.12 ( 103) hydrogen bonds : angle 6.36761 / 4.20 ( 291) link_NAG-ASN : bond 0.00166 / 0.08 ( 1) link_NAG-ASN : angle 1.16911 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7412 (pt) REVERT: B 18 ARG cc_start: 0.7675 (mmm160) cc_final: 0.7452 (mmm160) REVERT: B 102 GLN cc_start: 0.7676 (mm-40) cc_final: 0.6753 (pm20) REVERT: E 383 SER cc_start: 0.4867 (OUTLIER) cc_final: 0.4615 (m) outliers start: 14 outliers final: 10 residues processed: 46 average time/residue: 0.7176 time to fit residues: 34.6431 Evaluate side-chains 49 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [3, 35, 28, 23, 37, 26, 13, 15, 19, 20, 9] chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135164 restraints weight = 9974.278| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.86 r_work: 0.3545 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3333 Z= 0.115 Angle : 0.495 5.441 4536 Z= 0.257 Chirality : 0.042 0.138 490 Planarity : 0.003 0.026 587 Dihedral : 5.188 50.518 484 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.44 % Allowed : 22.35 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.66 (0.41), residues: 411 helix: -4.48 (0.50), residues: 27 sheet: -0.91 (0.44), residues: 129 loop : -0.76 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 466 TYR 0.011 0.001 TYR A 33 PHE 0.008 0.001 PHE E 486 TRP 0.006 0.001 TRP E 436 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 3326) covalent geometry : angle 0.49403 / 0.26 ( 4521) SS BOND : bond 0.00298 / 0.14 ( 6) SS BOND : angle 0.60567 / 0.31 ( 12) hydrogen bonds : bond 0.03154 / 2.04 ( 103) hydrogen bonds : angle 6.16058 / 4.06 ( 291) link_NAG-ASN : bond 0.00161 / 0.08 ( 1) link_NAG-ASN : angle 1.17305 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7681 (mt0) cc_final: 0.7209 (mm-40) REVERT: A 18 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7379 (pt) REVERT: B 102 GLN cc_start: 0.7715 (mm-40) cc_final: 0.6689 (pm20) REVERT: E 336 CYS cc_start: 0.3953 (OUTLIER) cc_final: 0.3110 (m) REVERT: E 383 SER cc_start: 0.4860 (OUTLIER) cc_final: 0.4607 (m) outliers start: 12 outliers final: 7 residues processed: 42 average time/residue: 0.6177 time to fit residues: 27.3903 Evaluate side-chains 46 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [27, 28, 25, 21, 17, 35, 31, 12, 11, 15, 7] chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.168525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137624 restraints weight = 9857.052| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.88 r_work: 0.3558 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3333 Z= 0.103 Angle : 0.482 5.444 4536 Z= 0.250 Chirality : 0.042 0.136 490 Planarity : 0.003 0.025 587 Dihedral : 5.066 49.253 484 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.44 % Allowed : 22.06 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.56 (0.41), residues: 411 helix: -4.44 (0.51), residues: 27 sheet: -0.80 (0.43), residues: 129 loop : -0.71 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.010 0.001 TYR A 33 PHE 0.007 0.001 PHE E 429 TRP 0.006 0.001 TRP E 436 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 3326) covalent geometry : angle 0.48127 / 0.25 ( 4521) SS BOND : bond 0.00279 / 0.13 ( 6) SS BOND : angle 0.58599 / 0.29 ( 12) hydrogen bonds : bond 0.03022 / 1.95 ( 103) hydrogen bonds : angle 6.04198 / 3.97 ( 291) link_NAG-ASN : bond 0.00167 / 0.08 ( 1) link_NAG-ASN : angle 1.13804 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7660 (mt0) cc_final: 0.7295 (mm-40) REVERT: A 18 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7418 (pt) REVERT: B 102 GLN cc_start: 0.7722 (mm-40) cc_final: 0.6707 (pm20) REVERT: E 336 CYS cc_start: 0.3961 (OUTLIER) cc_final: 0.2890 (m) REVERT: E 383 SER cc_start: 0.4867 (OUTLIER) cc_final: 0.4614 (m) outliers start: 12 outliers final: 6 residues processed: 41 average time/residue: 0.6248 time to fit residues: 27.0139 Evaluate side-chains 44 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [19, 15, 10, 3, 17, 24, 35, 30, 18, 21, 13] chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.166138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135006 restraints weight = 9896.123| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.87 r_work: 0.3575 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3333 Z= 0.142 Angle : 0.510 5.451 4536 Z= 0.265 Chirality : 0.043 0.136 490 Planarity : 0.004 0.027 587 Dihedral : 5.217 49.389 484 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.44 % Allowed : 22.64 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.57 (0.41), residues: 411 helix: -4.44 (0.53), residues: 26 sheet: -0.86 (0.44), residues: 126 loop : -0.71 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.012 0.001 TYR A 33 PHE 0.018 0.001 PHE E 338 TRP 0.005 0.001 TRP A 36 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3326) covalent geometry : angle 0.50883 / 0.27 ( 4521) SS BOND : bond 0.00347 / 0.17 ( 6) SS BOND : angle 0.74820 / 0.38 ( 12) hydrogen bonds : bond 0.03274 / 2.13 ( 103) hydrogen bonds : angle 6.16905 / 4.05 ( 291) link_NAG-ASN : bond 0.00199 / 0.09 ( 1) link_NAG-ASN : angle 1.02938 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7640 (mt0) cc_final: 0.7199 (mm-40) REVERT: A 18 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7414 (pt) REVERT: A 102 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8564 (mmt-90) REVERT: B 102 GLN cc_start: 0.7721 (mm-40) cc_final: 0.6832 (pm20) REVERT: E 336 CYS cc_start: 0.4158 (OUTLIER) cc_final: 0.3141 (m) REVERT: E 383 SER cc_start: 0.4805 (OUTLIER) cc_final: 0.4544 (m) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.6908 time to fit residues: 31.9161 Evaluate side-chains 49 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [3, 12, 1, 10, 33, 35, 4, 26, 19, 8, 30] chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.164927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134167 restraints weight = 9802.457| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.84 r_work: 0.3516 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3333 Z= 0.166 Angle : 0.537 5.618 4536 Z= 0.279 Chirality : 0.043 0.138 490 Planarity : 0.004 0.027 587 Dihedral : 5.437 50.264 484 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.72 % Allowed : 22.92 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.61 (0.41), residues: 411 helix: -4.42 (0.52), residues: 26 sheet: -0.93 (0.44), residues: 126 loop : -0.71 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.013 0.001 TYR A 33 PHE 0.011 0.001 PHE E 338 TRP 0.007 0.001 TRP E 353 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 3326) covalent geometry : angle 0.53516 / 0.28 ( 4521) SS BOND : bond 0.00391 / 0.19 ( 6) SS BOND : angle 0.86462 / 0.43 ( 12) hydrogen bonds : bond 0.03416 / 2.24 ( 103) hydrogen bonds : angle 6.26817 / 4.11 ( 291) link_NAG-ASN : bond 0.00165 / 0.08 ( 1) link_NAG-ASN : angle 1.11027 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7590 (mt0) cc_final: 0.7304 (mm-40) REVERT: A 102 ARG cc_start: 0.8764 (tpp-160) cc_final: 0.8517 (mmt-90) REVERT: B 102 GLN cc_start: 0.7756 (mm-40) cc_final: 0.6817 (pm20) REVERT: E 336 CYS cc_start: 0.4277 (OUTLIER) cc_final: 0.3252 (m) REVERT: E 383 SER cc_start: 0.4639 (OUTLIER) cc_final: 0.4390 (m) outliers start: 13 outliers final: 8 residues processed: 43 average time/residue: 0.7179 time to fit residues: 32.3216 Evaluate side-chains 46 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 515 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [36, 2, 12, 14, 35, 34, 21, 10, 38, 29, 18] chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.166973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136154 restraints weight = 9887.770| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.86 r_work: 0.3531 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3333 Z= 0.130 Angle : 0.510 5.540 4536 Z= 0.266 Chirality : 0.042 0.133 490 Planarity : 0.004 0.027 587 Dihedral : 5.346 50.077 484 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.87 % Allowed : 23.78 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.52 (0.41), residues: 411 helix: -4.42 (0.53), residues: 26 sheet: -0.91 (0.44), residues: 126 loop : -0.63 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.011 0.001 TYR A 33 PHE 0.014 0.001 PHE E 338 TRP 0.005 0.001 TRP E 436 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3326) covalent geometry : angle 0.50909 / 0.27 ( 4521) SS BOND : bond 0.00321 / 0.15 ( 6) SS BOND : angle 0.71738 / 0.35 ( 12) hydrogen bonds : bond 0.03191 / 2.08 ( 103) hydrogen bonds : angle 6.12674 / 4.01 ( 291) link_NAG-ASN : bond 0.00183 / 0.09 ( 1) link_NAG-ASN : angle 0.92178 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 GLU cc_start: 0.6948 (tt0) cc_final: 0.6746 (tt0) REVERT: A 3 GLN cc_start: 0.7638 (mt0) cc_final: 0.7213 (mm-40) REVERT: B 102 GLN cc_start: 0.7773 (mm-40) cc_final: 0.6794 (pm20) REVERT: E 336 CYS cc_start: 0.4361 (OUTLIER) cc_final: 0.3254 (m) outliers start: 10 outliers final: 8 residues processed: 41 average time/residue: 0.7296 time to fit residues: 31.3090 Evaluate side-chains 43 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [12, 7, 11, 15, 20, 3, 38, 9, 18, 8, 32] chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.168424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137692 restraints weight = 9739.428| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.85 r_work: 0.3536 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3333 Z= 0.116 Angle : 0.501 5.579 4536 Z= 0.261 Chirality : 0.042 0.134 490 Planarity : 0.004 0.026 587 Dihedral : 5.251 49.250 484 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.58 % Allowed : 23.78 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.40 (0.41), residues: 411 helix: -4.40 (0.54), residues: 26 sheet: -0.81 (0.44), residues: 129 loop : -0.54 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.011 0.001 TYR A 33 PHE 0.011 0.001 PHE E 338 TRP 0.005 0.001 TRP A 107 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3326) covalent geometry : angle 0.49983 / 0.26 ( 4521) SS BOND : bond 0.00296 / 0.14 ( 6) SS BOND : angle 0.67640 / 0.33 ( 12) hydrogen bonds : bond 0.03096 / 2.02 ( 103) hydrogen bonds : angle 6.03949 / 3.95 ( 291) link_NAG-ASN : bond 0.00186 / 0.09 ( 1) link_NAG-ASN : angle 0.99834 / 0.58 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7635 (mt0) cc_final: 0.7192 (mm-40) REVERT: A 102 ARG cc_start: 0.8738 (tpp-160) cc_final: 0.8533 (mmt-90) REVERT: B 102 GLN cc_start: 0.7760 (mm-40) cc_final: 0.6800 (pm20) REVERT: E 336 CYS cc_start: 0.4391 (OUTLIER) cc_final: 0.3286 (m) outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.8035 time to fit residues: 35.2095 Evaluate side-chains 43 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [24, 10, 31, 1, 30, 23, 14, 7, 15, 11, 27] chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.166822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136572 restraints weight = 9860.401| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.82 r_work: 0.3538 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3333 Z= 0.127 Angle : 0.506 5.563 4536 Z= 0.264 Chirality : 0.043 0.134 490 Planarity : 0.004 0.027 587 Dihedral : 5.269 48.886 484 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.29 % Allowed : 24.36 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.40 (0.41), residues: 411 helix: -4.34 (0.57), residues: 26 sheet: -0.77 (0.44), residues: 126 loop : -0.57 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.012 0.001 TYR A 33 PHE 0.011 0.001 PHE E 338 TRP 0.004 0.001 TRP A 107 HIS 0.000 0.000 HIS E 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 3326) covalent geometry : angle 0.50515 / 0.26 ( 4521) SS BOND : bond 0.00313 / 0.15 ( 6) SS BOND : angle 0.69972 / 0.34 ( 12) hydrogen bonds : bond 0.03177 / 2.08 ( 103) hydrogen bonds : angle 6.06581 / 3.97 ( 291) link_NAG-ASN : bond 0.00201 / 0.10 ( 1) link_NAG-ASN : angle 0.96327 / 0.56 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.37 seconds wall clock time: 45 minutes 12.38 seconds (2712.38 seconds total)