Starting phenix.real_space_refine on Wed Jul 1 22:11:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.map" model { file = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2026/7v27_31638.cif" } resolution = 4.18 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= 0.000 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 16 5.16 5 C 2065 2.51 5 N 535 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 3252 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" 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: 0.87, per 1000 atoms: 0.27 Number of scatterers: 3252 At special positions: 0 Unit cell: (80.542, 58.576, 99.37, 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 16 16.00 O 636 8.00 N 535 7.00 C 2065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " 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 C 601 " - " ASN C 343 " Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 78.9 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 10 sheets defined 5.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.892A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.642A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'B' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357 removed outlier: 3.604A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 379 through 380 removed outlier: 4.202A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.024A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.680A pdb=" N ARG B 5 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 114 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 36 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU B 52 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP B 38 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 60 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 114 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'A' and resid 19 through 22 removed outlier: 3.639A pdb=" N SER A 67 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.028A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 50 " --> pdb=" O TRP A 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.028A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 50 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 88 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 104 " --> pdb=" O TYR A 88 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 171 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: 0.29 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1026 1.35 - 1.47: 885 1.47 - 1.59: 1403 1.59 - 1.71: 0 1.71 - 1.83: 19 Bond restraints: 3333 Sorted by residual: bond pdb=" C VAL C 382 " pdb=" N SER C 383 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.37e-02 5.33e+03 2.96e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta sigma weight residual 1.455 1.465 -0.010 1.21e-02 6.83e+03 6.90e-01 ... (remaining 3328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 4149 0.83 - 1.67: 303 1.67 - 2.50: 51 2.50 - 3.34: 36 3.34 - 4.17: 5 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N MET A 49 " pdb=" CA MET A 49 " pdb=" C MET A 49 " ideal model delta sigma weight residual 114.04 110.56 3.48 1.24e+00 6.50e-01 7.89e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 107.88 111.39 -3.51 1.41e+00 5.03e-01 6.18e+00 angle pdb=" N SER A 97 " pdb=" CA SER A 97 " pdb=" C SER A 97 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 angle pdb=" CA GLY C 504 " pdb=" C GLY C 504 " pdb=" N TYR C 505 " ideal model delta sigma weight residual 118.95 116.79 2.16 1.06e+00 8.90e-01 4.17e+00 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 121.54 125.16 -3.62 1.91e+00 2.74e-01 3.60e+00 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 1746 15.03 - 30.06: 181 30.06 - 45.10: 28 45.10 - 60.13: 6 60.13 - 75.16: 1 Dihedral angle restraints: 1962 sinusoidal: 744 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 53.66 39.34 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 123.94 -30.94 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -58.76 -27.24 1 1.00e+01 1.00e-02 1.06e+01 ... (remaining 1959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 364 0.038 - 0.075: 103 0.075 - 0.113: 38 0.113 - 0.150: 5 0.150 - 0.188: 1 Chirality restraints: 511 Sorted by residual: chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB THR C 500 " pdb=" CA THR C 500 " pdb=" OG1 THR C 500 " pdb=" CG2 THR C 500 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ILE B 39 " pdb=" N ILE B 39 " pdb=" C ILE B 39 " pdb=" CB ILE B 39 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 508 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.46e-01 pdb=" N PRO C 521 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 45 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO A 46 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 31 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO B 32 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.012 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 546 2.76 - 3.30: 3043 3.30 - 3.83: 5332 3.83 - 4.37: 5987 4.37 - 4.90: 10409 Nonbonded interactions: 25317 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.252 3.040 nonbonded pdb=" O ILE B 106 " pdb=" OH TYR A 38 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 9 " pdb=" O LYS A 105 " model vdw 2.309 3.040 nonbonded pdb=" O ARG C 408 " pdb=" NE2 GLN C 414 " model vdw 2.313 3.120 ... (remaining 25312 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.690 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.002 0.027 3340 Z= 0.124 Angle : 0.537 4.173 4559 Z= 0.306 Chirality : 0.040 0.188 511 Planarity : 0.003 0.024 580 Dihedral : 11.658 75.160 1170 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -4.40 (0.34), residues: 415 helix: -3.86 (0.99), residues: 13 sheet: -2.42 (0.44), residues: 126 loop : -3.32 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 408 TYR 0.007 0.001 TYR B 96 PHE 0.008 0.001 PHE C 338 TRP 0.005 0.001 TRP B 55 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 ( 3333) covalent geometry : angle 0.53502 / 0.31 ( 4544) SS BOND : bond 0.00420 / 0.21 ( 6) SS BOND : angle 0.90340 / 0.71 ( 12) hydrogen bonds : bond 0.31656 / 21.56 ( 58) hydrogen bonds : angle 11.20114 / 7.79 ( 171) link_NAG-ASN : bond 0.00202 / 0.11 ( 1) link_NAG-ASN : angle 1.03656 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 358 ILE cc_start: 0.9209 (mm) cc_final: 0.8992 (mt) REVERT: C 365 TYR cc_start: 0.8446 (m-80) cc_final: 0.8241 (m-80) REVERT: C 405 ASP cc_start: 0.9094 (m-30) cc_final: 0.8536 (m-30) REVERT: C 449 TYR cc_start: 0.8758 (m-80) cc_final: 0.8523 (m-10) REVERT: B 13 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7520 (tmtt) REVERT: B 49 TRP cc_start: 0.8957 (t60) cc_final: 0.8682 (t60) REVERT: B 56 ASP cc_start: 0.8641 (m-30) cc_final: 0.8431 (m-30) REVERT: B 104 ASP cc_start: 0.8474 (t0) cc_final: 0.8229 (t0) REVERT: A 64 PHE cc_start: 0.8558 (m-80) cc_final: 0.8290 (m-10) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0969 time to fit residues: 12.4446 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 ASN C 448 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 62 ASN A 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069871 restraints weight = 11809.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072641 restraints weight = 6841.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074667 restraints weight = 4642.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076076 restraints weight = 3464.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077119 restraints weight = 2764.334| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3340 Z= 0.187 Angle : 0.634 6.543 4559 Z= 0.326 Chirality : 0.045 0.218 511 Planarity : 0.004 0.032 580 Dihedral : 3.952 14.906 459 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % 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: -3.78 (0.36), residues: 415 helix: -3.68 (0.87), residues: 13 sheet: -2.02 (0.46), residues: 123 loop : -2.85 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 408 TYR 0.014 0.002 TYR C 421 PHE 0.010 0.001 PHE C 392 TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 3333) covalent geometry : angle 0.62845 / 0.32 ( 4544) SS BOND : bond 0.00656 / 0.31 ( 6) SS BOND : angle 1.61329 / 1.39 ( 12) hydrogen bonds : bond 0.04777 / 3.04 ( 58) hydrogen bonds : angle 7.63685 / 5.23 ( 171) link_NAG-ASN : bond 0.00238 / 0.13 ( 1) link_NAG-ASN : angle 1.32707 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8018 (p0) cc_final: 0.7711 (p0) REVERT: C 398 ASP cc_start: 0.9151 (m-30) cc_final: 0.8672 (m-30) REVERT: C 405 ASP cc_start: 0.8979 (m-30) cc_final: 0.8563 (p0) REVERT: C 458 LYS cc_start: 0.8702 (pptt) cc_final: 0.8299 (pttm) REVERT: C 461 LEU cc_start: 0.7147 (tp) cc_final: 0.6884 (tp) REVERT: B 13 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7637 (tmtt) REVERT: B 45 LYS cc_start: 0.9276 (tptp) cc_final: 0.9062 (tptp) REVERT: B 49 TRP cc_start: 0.8844 (t60) cc_final: 0.8441 (t60) REVERT: B 57 ASP cc_start: 0.8637 (t0) cc_final: 0.8406 (t0) REVERT: A 64 PHE cc_start: 0.8113 (m-80) cc_final: 0.7374 (m-10) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0907 time to fit residues: 8.8701 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 360 ASN ** A 39 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 = 0.3443 r_free = 0.3443 target = 0.083856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068657 restraints weight = 11546.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071332 restraints weight = 6683.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073234 restraints weight = 4555.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074619 restraints weight = 3417.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075606 restraints weight = 2742.838| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3340 Z= 0.177 Angle : 0.626 8.179 4559 Z= 0.318 Chirality : 0.045 0.195 511 Planarity : 0.004 0.029 580 Dihedral : 4.234 13.829 459 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -3.42 (0.37), residues: 415 helix: -3.13 (1.10), residues: 13 sheet: -1.85 (0.47), residues: 119 loop : -2.58 (0.32), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 408 TYR 0.019 0.002 TYR C 495 PHE 0.010 0.001 PHE C 392 TRP 0.010 0.001 TRP B 55 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 3333) covalent geometry : angle 0.62117 / 0.32 ( 4544) SS BOND : bond 0.00652 / 0.32 ( 6) SS BOND : angle 1.60901 / 1.31 ( 12) hydrogen bonds : bond 0.03523 / 2.27 ( 58) hydrogen bonds : angle 6.46809 / 4.41 ( 171) link_NAG-ASN : bond 0.00140 / 0.07 ( 1) link_NAG-ASN : angle 1.19399 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.7858 (p0) cc_final: 0.7535 (p0) REVERT: C 390 LEU cc_start: 0.8701 (tp) cc_final: 0.8388 (tp) REVERT: C 394 ASN cc_start: 0.7674 (t0) cc_final: 0.6856 (t0) REVERT: C 398 ASP cc_start: 0.9123 (m-30) cc_final: 0.8601 (m-30) REVERT: B 49 TRP cc_start: 0.8949 (t60) cc_final: 0.8608 (t60) REVERT: A 49 MET cc_start: 0.7736 (ttm) cc_final: 0.7393 (ttm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0772 time to fit residues: 7.8849 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.0020 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068160 restraints weight = 11501.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.070970 restraints weight = 6555.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072908 restraints weight = 4379.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074266 restraints weight = 3254.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075258 restraints weight = 2600.569| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3340 Z= 0.172 Angle : 0.649 8.765 4559 Z= 0.327 Chirality : 0.045 0.209 511 Planarity : 0.004 0.037 580 Dihedral : 4.453 19.130 459 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -3.21 (0.38), residues: 415 helix: -3.00 (1.08), residues: 13 sheet: -1.63 (0.48), residues: 125 loop : -2.46 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.021 0.002 TYR C 495 PHE 0.022 0.002 PHE A 64 TRP 0.010 0.001 TRP B 55 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 3333) covalent geometry : angle 0.64213 / 0.32 ( 4544) SS BOND : bond 0.00742 / 0.36 ( 6) SS BOND : angle 1.93989 / 1.80 ( 12) hydrogen bonds : bond 0.03297 / 2.09 ( 58) hydrogen bonds : angle 6.20046 / 4.17 ( 171) link_NAG-ASN : bond 0.00151 / 0.08 ( 1) link_NAG-ASN : angle 1.15167 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 390 LEU cc_start: 0.8745 (tp) cc_final: 0.8469 (tp) REVERT: C 394 ASN cc_start: 0.7284 (t0) cc_final: 0.6424 (t0) REVERT: C 398 ASP cc_start: 0.9063 (m-30) cc_final: 0.8554 (m-30) REVERT: C 405 ASP cc_start: 0.9056 (m-30) cc_final: 0.8648 (p0) REVERT: B 49 TRP cc_start: 0.8876 (t60) cc_final: 0.8446 (t60) REVERT: A 49 MET cc_start: 0.8094 (ttm) cc_final: 0.7870 (ttm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0658 time to fit residues: 6.4138 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN A 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068471 restraints weight = 11614.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071174 restraints weight = 6840.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073075 restraints weight = 4657.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074398 restraints weight = 3507.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075353 restraints weight = 2835.760| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3340 Z= 0.140 Angle : 0.634 7.345 4559 Z= 0.322 Chirality : 0.045 0.226 511 Planarity : 0.004 0.036 580 Dihedral : 4.324 15.100 459 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -3.04 (0.38), residues: 415 helix: -3.17 (0.90), residues: 13 sheet: -1.56 (0.50), residues: 121 loop : -2.31 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.010 0.002 TYR C 453 PHE 0.017 0.001 PHE A 64 TRP 0.038 0.002 TRP A 37 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3333) covalent geometry : angle 0.63042 / 0.32 ( 4544) SS BOND : bond 0.00675 / 0.34 ( 6) SS BOND : angle 1.45765 / 1.33 ( 12) hydrogen bonds : bond 0.03405 / 2.16 ( 58) hydrogen bonds : angle 5.95112 / 4.00 ( 171) link_NAG-ASN : bond 0.00049 / 0.03 ( 1) link_NAG-ASN : angle 0.86032 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8092 (p0) cc_final: 0.7746 (p0) REVERT: C 390 LEU cc_start: 0.8641 (tp) cc_final: 0.8391 (tp) REVERT: C 394 ASN cc_start: 0.7548 (t0) cc_final: 0.6723 (t0) REVERT: C 398 ASP cc_start: 0.9074 (m-30) cc_final: 0.8551 (m-30) REVERT: C 405 ASP cc_start: 0.9018 (m-30) cc_final: 0.8673 (p0) REVERT: B 49 TRP cc_start: 0.8837 (t60) cc_final: 0.8043 (t60) REVERT: A 49 MET cc_start: 0.8249 (ttm) cc_final: 0.8005 (ttm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0757 time to fit residues: 7.1544 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066365 restraints weight = 11868.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068891 restraints weight = 7082.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.070702 restraints weight = 4899.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.071962 restraints weight = 3748.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072874 restraints weight = 3051.647| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3340 Z= 0.191 Angle : 0.685 6.528 4559 Z= 0.350 Chirality : 0.046 0.247 511 Planarity : 0.004 0.039 580 Dihedral : 4.693 20.325 459 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 (0.38), residues: 415 helix: -2.59 (1.01), residues: 13 sheet: -1.54 (0.48), residues: 124 loop : -2.16 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 408 TYR 0.014 0.002 TYR C 453 PHE 0.018 0.002 PHE A 64 TRP 0.022 0.002 TRP A 37 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 3333) covalent geometry : angle 0.67832 / 0.35 ( 4544) SS BOND : bond 0.00862 / 0.44 ( 6) SS BOND : angle 1.82296 / 1.56 ( 12) hydrogen bonds : bond 0.03355 / 2.11 ( 58) hydrogen bonds : angle 6.06028 / 4.09 ( 171) link_NAG-ASN : bond 0.00289 / 0.15 ( 1) link_NAG-ASN : angle 1.39574 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 390 LEU cc_start: 0.8691 (tp) cc_final: 0.8393 (tp) REVERT: C 398 ASP cc_start: 0.9057 (m-30) cc_final: 0.8554 (m-30) REVERT: C 405 ASP cc_start: 0.9009 (m-30) cc_final: 0.8533 (p0) REVERT: B 59 LYS cc_start: 0.9019 (mptt) cc_final: 0.8415 (mptt) REVERT: B 71 ILE cc_start: 0.9419 (tp) cc_final: 0.8960 (tp) REVERT: A 49 MET cc_start: 0.8457 (ttm) cc_final: 0.8184 (ttt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0701 time to fit residues: 6.1865 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 11 optimal weight: 0.0980 chunk 6 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.084058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068341 restraints weight = 11831.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.070911 restraints weight = 7029.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072706 restraints weight = 4885.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073960 restraints weight = 3741.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074872 restraints weight = 3070.866| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3340 Z= 0.142 Angle : 0.657 6.579 4559 Z= 0.335 Chirality : 0.046 0.251 511 Planarity : 0.004 0.039 580 Dihedral : 4.526 16.787 459 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.77 (0.39), residues: 415 helix: -2.57 (0.96), residues: 13 sheet: -1.49 (0.47), residues: 127 loop : -2.07 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 40 TYR 0.016 0.002 TYR C 495 PHE 0.019 0.001 PHE A 64 TRP 0.018 0.002 TRP A 37 HIS 0.000 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 3333) covalent geometry : angle 0.65192 / 0.33 ( 4544) SS BOND : bond 0.00717 / 0.36 ( 6) SS BOND : angle 1.68594 / 1.50 ( 12) hydrogen bonds : bond 0.03147 / 2.00 ( 58) hydrogen bonds : angle 5.91486 / 3.99 ( 171) link_NAG-ASN : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : angle 0.93374 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8280 (p0) cc_final: 0.7924 (p0) REVERT: C 394 ASN cc_start: 0.7366 (t0) cc_final: 0.6398 (t0) REVERT: C 398 ASP cc_start: 0.8937 (m-30) cc_final: 0.8440 (m-30) REVERT: C 405 ASP cc_start: 0.8984 (m-30) cc_final: 0.8519 (p0) REVERT: B 49 TRP cc_start: 0.8923 (t60) cc_final: 0.8331 (t60) REVERT: A 49 MET cc_start: 0.8482 (ttm) cc_final: 0.7954 (ttt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0823 time to fit residues: 7.5032 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.0370 chunk 29 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070025 restraints weight = 11946.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072555 restraints weight = 6980.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074344 restraints weight = 4812.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.075626 restraints weight = 3659.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076378 restraints weight = 2972.685| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3340 Z= 0.127 Angle : 0.662 6.869 4559 Z= 0.336 Chirality : 0.046 0.263 511 Planarity : 0.004 0.039 580 Dihedral : 4.473 16.584 459 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -2.63 (0.39), residues: 415 helix: -1.90 (1.15), residues: 13 sheet: -1.47 (0.46), residues: 127 loop : -1.96 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 408 TYR 0.012 0.001 TYR C 453 PHE 0.019 0.001 PHE A 64 TRP 0.018 0.002 TRP A 37 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3333) covalent geometry : angle 0.65798 / 0.33 ( 4544) SS BOND : bond 0.00656 / 0.33 ( 6) SS BOND : angle 1.55530 / 1.44 ( 12) hydrogen bonds : bond 0.02904 / 1.82 ( 58) hydrogen bonds : angle 5.89963 / 3.95 ( 171) link_NAG-ASN : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : angle 0.93177 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 377 PHE cc_start: 0.9190 (t80) cc_final: 0.8835 (t80) REVERT: C 394 ASN cc_start: 0.7627 (t0) cc_final: 0.6788 (t0) REVERT: C 398 ASP cc_start: 0.8827 (m-30) cc_final: 0.8253 (m-30) REVERT: C 405 ASP cc_start: 0.8989 (m-30) cc_final: 0.8439 (m-30) REVERT: C 408 ARG cc_start: 0.8792 (pmt170) cc_final: 0.7962 (pmt170) REVERT: C 458 LYS cc_start: 0.8625 (pptt) cc_final: 0.7969 (mmtp) REVERT: C 493 GLN cc_start: 0.9048 (tp40) cc_final: 0.8661 (tm-30) REVERT: B 45 LYS cc_start: 0.9055 (tptp) cc_final: 0.8729 (tptp) REVERT: B 49 TRP cc_start: 0.8816 (t60) cc_final: 0.8076 (t60) REVERT: B 100 LEU cc_start: 0.8795 (tp) cc_final: 0.8546 (tp) REVERT: A 49 MET cc_start: 0.8356 (ttm) cc_final: 0.7834 (ttt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0792 time to fit residues: 7.1537 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 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 = 0.3397 r_free = 0.3397 target = 0.081117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066058 restraints weight = 11678.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068635 restraints weight = 6732.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.070373 restraints weight = 4545.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071645 restraints weight = 3429.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072573 restraints weight = 2778.521| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3340 Z= 0.221 Angle : 0.736 9.358 4559 Z= 0.373 Chirality : 0.047 0.281 511 Planarity : 0.005 0.048 580 Dihedral : 4.859 19.241 459 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -2.58 (0.39), residues: 415 helix: -1.14 (1.31), residues: 13 sheet: -1.39 (0.46), residues: 123 loop : -1.99 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 408 TYR 0.016 0.002 TYR C 495 PHE 0.024 0.002 PHE A 64 TRP 0.015 0.002 TRP A 37 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 ( 3333) covalent geometry : angle 0.73071 / 0.37 ( 4544) SS BOND : bond 0.00810 / 0.41 ( 6) SS BOND : angle 1.81068 / 1.56 ( 12) hydrogen bonds : bond 0.03481 / 2.20 ( 58) hydrogen bonds : angle 6.08108 / 4.11 ( 171) link_NAG-ASN : bond 0.00330 / 0.17 ( 1) link_NAG-ASN : angle 1.43344 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8788 (pttt) cc_final: 0.8561 (pttm) REVERT: C 394 ASN cc_start: 0.7479 (t0) cc_final: 0.6478 (t0) REVERT: C 398 ASP cc_start: 0.9049 (m-30) cc_final: 0.8465 (m-30) REVERT: C 405 ASP cc_start: 0.9056 (m-30) cc_final: 0.8451 (m-30) REVERT: C 408 ARG cc_start: 0.8864 (pmt170) cc_final: 0.8042 (pmt170) REVERT: B 87 MET cc_start: 0.7634 (ttm) cc_final: 0.7219 (ttp) REVERT: B 100 LEU cc_start: 0.8999 (tp) cc_final: 0.8784 (tp) REVERT: A 49 MET cc_start: 0.8432 (ttm) cc_final: 0.7931 (ttm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0836 time to fit residues: 7.6163 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.0040 chunk 29 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 overall best weight: 0.2428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068456 restraints weight = 11502.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071070 restraints weight = 6560.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072945 restraints weight = 4462.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074239 restraints weight = 3396.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075197 restraints weight = 2766.877| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3340 Z= 0.134 Angle : 0.703 6.852 4559 Z= 0.355 Chirality : 0.046 0.273 511 Planarity : 0.004 0.044 580 Dihedral : 4.532 16.599 459 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.51 (0.39), residues: 415 helix: -1.16 (1.30), residues: 13 sheet: -1.51 (0.46), residues: 121 loop : -1.84 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 408 TYR 0.012 0.001 TYR A 38 PHE 0.039 0.002 PHE C 497 TRP 0.017 0.002 TRP A 37 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 3333) covalent geometry : angle 0.69944 / 0.35 ( 4544) SS BOND : bond 0.00742 / 0.37 ( 6) SS BOND : angle 1.56968 / 1.43 ( 12) hydrogen bonds : bond 0.02804 / 1.82 ( 58) hydrogen bonds : angle 5.73934 / 3.85 ( 171) link_NAG-ASN : bond 0.00152 / 0.08 ( 1) link_NAG-ASN : angle 0.75051 / 0.44 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 PHE cc_start: 0.9155 (t80) cc_final: 0.8847 (t80) REVERT: C 378 LYS cc_start: 0.8697 (pttt) cc_final: 0.8475 (pttm) REVERT: C 394 ASN cc_start: 0.7663 (t0) cc_final: 0.6760 (t0) REVERT: C 398 ASP cc_start: 0.8896 (m-30) cc_final: 0.8349 (m-30) REVERT: C 405 ASP cc_start: 0.9094 (m-30) cc_final: 0.8508 (p0) REVERT: C 493 GLN cc_start: 0.8967 (tp40) cc_final: 0.8761 (tm-30) REVERT: B 1 GLN cc_start: 0.9066 (pp30) cc_final: 0.8855 (pp30) REVERT: B 45 LYS cc_start: 0.9045 (tptp) cc_final: 0.8793 (tptp) REVERT: B 49 TRP cc_start: 0.8880 (t60) cc_final: 0.8176 (t60) REVERT: B 87 MET cc_start: 0.7513 (ttm) cc_final: 0.7198 (ttp) REVERT: B 100 LEU cc_start: 0.8834 (tp) cc_final: 0.8576 (tp) REVERT: A 49 MET cc_start: 0.8380 (ttm) cc_final: 0.8006 (ttm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0569 time to fit residues: 5.1641 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 29 optimal weight: 0.0060 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 450 ASN C 460 ASN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.083602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068122 restraints weight = 11780.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070734 restraints weight = 6844.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072538 restraints weight = 4663.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073846 restraints weight = 3547.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074794 restraints weight = 2885.355| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3340 Z= 0.161 Angle : 0.701 6.767 4559 Z= 0.361 Chirality : 0.047 0.279 511 Planarity : 0.005 0.045 580 Dihedral : 4.750 18.414 459 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 0.28 % Allowed : 1.11 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.48 (0.39), residues: 415 helix: -1.13 (1.33), residues: 13 sheet: -1.46 (0.46), residues: 121 loop : -1.85 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.013 0.002 TYR A 38 PHE 0.032 0.002 PHE C 497 TRP 0.012 0.002 TRP A 37 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 3333) covalent geometry : angle 0.69657 / 0.36 ( 4544) SS BOND : bond 0.00711 / 0.35 ( 6) SS BOND : angle 1.60221 / 1.42 ( 12) hydrogen bonds : bond 0.03136 / 2.00 ( 58) hydrogen bonds : angle 5.83264 / 3.93 ( 171) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 1.10977 / 0.65 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 890.18 seconds wall clock time: 16 minutes 5.91 seconds (965.91 seconds total)