Starting phenix.real_space_refine on Wed Jul 1 22:06:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr0_24649/07_2026/7rr0_24649.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2088 2.51 5 N 561 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3297 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1528 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.05, per 1000 atoms: 0.32 Number of scatterers: 3297 At special positions: 0 Unit cell: (58.3, 68.9, 104.94, 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 18 16.00 O 630 8.00 N 561 7.00 C 2088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 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 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 135.5 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 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: 8 helices and 8 sheets defined 10.9% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.773A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.329A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.060A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.519A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.528A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.033A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TRP B 50 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.033A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.750A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 22 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 19 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 76 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.528A pdb=" N THR C 103 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 252 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: 0.27 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1053 1.34 - 1.46: 887 1.46 - 1.59: 1418 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3380 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" CB PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.53e+00 bond pdb=" CG LEU C 48 " pdb=" CD1 LEU C 48 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CB GLN B 6 " pdb=" CG GLN B 6 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CA THR A 470 " pdb=" C THR A 470 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.35e-02 5.49e+03 1.63e+00 ... (remaining 3375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 4402 2.24 - 4.48: 167 4.48 - 6.73: 18 6.73 - 8.97: 6 8.97 - 11.21: 2 Bond angle restraints: 4595 Sorted by residual: angle pdb=" C GLY C 51 " pdb=" N ALA C 52 " pdb=" CA ALA C 52 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" OG1 THR A 470 " pdb=" CB THR A 470 " pdb=" CG2 THR A 470 " ideal model delta sigma weight residual 109.30 101.40 7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" C ARG A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta sigma weight residual 119.99 123.77 -3.78 1.13e+00 7.83e-01 1.12e+01 angle pdb=" CA ARG A 403 " pdb=" CB ARG A 403 " pdb=" CG ARG A 403 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 ... (remaining 4590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 1788 14.43 - 28.86: 157 28.86 - 43.28: 37 43.28 - 57.71: 10 57.71 - 72.14: 3 Dihedral angle restraints: 1995 sinusoidal: 776 harmonic: 1219 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual -86.00 -112.35 26.35 1 1.00e+01 1.00e-02 9.97e+00 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 118.76 -25.76 1 1.00e+01 1.00e-02 9.54e+00 dihedral pdb=" CA LEU A 461 " pdb=" C LEU A 461 " pdb=" N LYS A 462 " pdb=" CA LYS A 462 " ideal model delta harmonic sigma weight residual 180.00 164.57 15.43 0 5.00e+00 4.00e-02 9.52e+00 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 290 0.040 - 0.080: 125 0.080 - 0.119: 57 0.119 - 0.159: 16 0.159 - 0.199: 6 Chirality restraints: 494 Sorted by residual: chirality pdb=" CB THR A 470 " pdb=" CA THR A 470 " pdb=" OG1 THR A 470 " pdb=" CG2 THR A 470 " both_signs ideal model delta sigma weight residual False 2.55 2.75 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB THR B 91 " pdb=" CA THR B 91 " pdb=" OG1 THR B 91 " pdb=" CG2 THR B 91 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA VAL B 52 " pdb=" N VAL B 52 " pdb=" C VAL B 52 " pdb=" CB VAL B 52 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 491 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 68 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL B 68 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 68 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 69 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 521 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 91 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLN C 91 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN C 91 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR C 92 " 0.012 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1035 2.84 - 3.36: 2598 3.36 - 3.87: 5389 3.87 - 4.39: 5842 4.39 - 4.90: 10738 Nonbonded interactions: 25602 Sorted by model distance: nonbonded pdb=" OD2 ASP B 73 " pdb=" OG1 THR B 76 " model vdw 2.327 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.332 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.340 3.040 nonbonded pdb=" O VAL A 367 " pdb=" OG SER A 371 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU B 46 " pdb=" NH1 ARG B 63 " model vdw 2.352 3.120 ... (remaining 25597 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: 0.540 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.010 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 0.080 3387 Z= 0.211 Angle : 0.970 11.211 4609 Z= 0.521 Chirality : 0.056 0.199 494 Planarity : 0.008 0.065 596 Dihedral : 12.199 72.140 1200 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.12 (0.38), residues: 416 helix: -1.69 (0.96), residues: 25 sheet: 0.90 (0.44), residues: 131 loop : -0.12 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 78 TYR 0.011 0.001 TYR B 95 PHE 0.011 0.001 PHE A 374 TRP 0.030 0.003 TRP B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 ( 3380) covalent geometry : angle 0.96770 / 0.52 ( 4595) SS BOND : bond 0.00479 / 0.25 ( 7) SS BOND : angle 1.49150 / 0.92 ( 14) hydrogen bonds : bond 0.24991 / 15.80 ( 98) hydrogen bonds : angle 10.24079 / 7.17 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 PHE cc_start: 0.4992 (m-10) cc_final: 0.4645 (m-10) REVERT: B 73 ASP cc_start: 0.7695 (t70) cc_final: 0.7373 (t70) REVERT: C 37 TYR cc_start: 0.8370 (m-80) cc_final: 0.8165 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0864 time to fit residues: 11.7732 Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN B 6 GLN B 57 ASN B 59 ASN C 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.142213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115497 restraints weight = 5149.330| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.05 r_work: 0.3477 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 3387 Z= 0.159 Angle : 0.677 16.616 4609 Z= 0.351 Chirality : 0.046 0.269 494 Planarity : 0.005 0.033 596 Dihedral : 4.271 14.483 469 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.09 % Allowed : 11.80 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.26 (0.38), residues: 416 helix: -2.03 (0.82), residues: 32 sheet: 1.28 (0.42), residues: 135 loop : -0.10 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 509 TYR 0.013 0.001 TYR B 95 PHE 0.016 0.002 PHE A 377 TRP 0.010 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 3380) covalent geometry : angle 0.66664 / 0.35 ( 4595) SS BOND : bond 0.00977 / 0.47 ( 7) SS BOND : angle 2.27183 / 2.19 ( 14) hydrogen bonds : bond 0.04048 / 2.59 ( 98) hydrogen bonds : angle 6.67164 / 5.00 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 LEU cc_start: 0.8406 (mt) cc_final: 0.8171 (mp) REVERT: B 63 ARG cc_start: 0.8235 (ptm-80) cc_final: 0.7682 (ptm-80) REVERT: B 73 ASP cc_start: 0.8162 (t70) cc_final: 0.7689 (t70) REVERT: C 24 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6912 (mmm-85) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.0786 time to fit residues: 9.1310 Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112349 restraints weight = 5138.293| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.09 r_work: 0.3438 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 3387 Z= 0.142 Angle : 0.637 14.369 4609 Z= 0.322 Chirality : 0.044 0.168 494 Planarity : 0.004 0.029 596 Dihedral : 4.141 14.953 469 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.37 % Allowed : 15.17 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.38), residues: 416 helix: -2.27 (0.81), residues: 32 sheet: 0.89 (0.42), residues: 147 loop : 0.01 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.013 0.001 TYR B 95 PHE 0.013 0.001 PHE A 377 TRP 0.008 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 3380) covalent geometry : angle 0.62859 / 0.32 ( 4595) SS BOND : bond 0.00875 / 0.42 ( 7) SS BOND : angle 2.01408 / 1.93 ( 14) hydrogen bonds : bond 0.03557 / 2.32 ( 98) hydrogen bonds : angle 6.29346 / 4.71 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: A 517 LEU cc_start: 0.8458 (mt) cc_final: 0.8251 (mt) REVERT: B 73 ASP cc_start: 0.8202 (t70) cc_final: 0.7584 (t70) REVERT: B 107 TYR cc_start: 0.7906 (t80) cc_final: 0.7661 (t80) outliers start: 12 outliers final: 8 residues processed: 100 average time/residue: 0.0922 time to fit residues: 10.7027 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 6 GLN B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.144018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117520 restraints weight = 5087.254| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.11 r_work: 0.3510 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3387 Z= 0.110 Angle : 0.624 15.454 4609 Z= 0.314 Chirality : 0.044 0.217 494 Planarity : 0.004 0.030 596 Dihedral : 3.889 14.223 469 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.69 % Allowed : 17.98 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.21 (0.39), residues: 416 helix: -2.08 (0.88), residues: 32 sheet: 0.94 (0.42), residues: 147 loop : 0.02 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 87 TYR 0.010 0.001 TYR A 451 PHE 0.012 0.001 PHE A 377 TRP 0.008 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 3380) covalent geometry : angle 0.61629 / 0.31 ( 4595) SS BOND : bond 0.00620 / 0.30 ( 7) SS BOND : angle 1.84557 / 1.76 ( 14) hydrogen bonds : bond 0.03165 / 2.06 ( 98) hydrogen bonds : angle 5.88865 / 4.41 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8264 (t70) cc_final: 0.7634 (t70) REVERT: B 107 TYR cc_start: 0.7894 (t80) cc_final: 0.7524 (t80) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.0722 time to fit residues: 8.2742 Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 0.0040 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.143018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116263 restraints weight = 5061.670| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.07 r_work: 0.3487 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3387 Z= 0.121 Angle : 0.642 14.907 4609 Z= 0.320 Chirality : 0.043 0.199 494 Planarity : 0.004 0.030 596 Dihedral : 3.938 16.279 469 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.53 % Allowed : 19.10 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.39), residues: 416 helix: -1.92 (0.94), residues: 32 sheet: 1.10 (0.43), residues: 145 loop : 0.01 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.011 0.001 TYR A 380 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 3380) covalent geometry : angle 0.63457 / 0.32 ( 4595) SS BOND : bond 0.00854 / 0.41 ( 7) SS BOND : angle 1.83251 / 1.75 ( 14) hydrogen bonds : bond 0.03164 / 2.09 ( 98) hydrogen bonds : angle 5.89372 / 4.40 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8847 (ptm-80) cc_final: 0.8612 (ttp80) REVERT: A 471 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: B 66 GLU cc_start: 0.7981 (pm20) cc_final: 0.7633 (tm-30) REVERT: B 73 ASP cc_start: 0.8243 (t70) cc_final: 0.7590 (t70) REVERT: B 82 GLU cc_start: 0.7724 (tt0) cc_final: 0.7249 (mt-10) REVERT: B 107 TYR cc_start: 0.7879 (t80) cc_final: 0.7395 (t80) outliers start: 9 outliers final: 8 residues processed: 92 average time/residue: 0.0861 time to fit residues: 9.2009 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112348 restraints weight = 5108.295| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.07 r_work: 0.3436 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3387 Z= 0.162 Angle : 0.653 14.975 4609 Z= 0.331 Chirality : 0.044 0.196 494 Planarity : 0.004 0.029 596 Dihedral : 4.065 17.499 469 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.37 % Allowed : 19.66 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.26 (0.39), residues: 416 helix: -2.01 (0.92), residues: 32 sheet: 1.09 (0.43), residues: 145 loop : -0.02 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 87 TYR 0.015 0.001 TYR B 95 PHE 0.011 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 3380) covalent geometry : angle 0.64527 / 0.33 ( 4595) SS BOND : bond 0.00938 / 0.45 ( 7) SS BOND : angle 1.92496 / 1.82 ( 14) hydrogen bonds : bond 0.03244 / 2.16 ( 98) hydrogen bonds : angle 5.96504 / 4.44 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8820 (ptm-80) cc_final: 0.8592 (ttp80) REVERT: B 66 GLU cc_start: 0.8011 (pm20) cc_final: 0.7641 (tm-30) REVERT: B 73 ASP cc_start: 0.8173 (t70) cc_final: 0.7425 (t70) REVERT: B 107 TYR cc_start: 0.7899 (t80) cc_final: 0.7374 (t80) REVERT: C 59 ILE cc_start: 0.8140 (mp) cc_final: 0.7770 (tp) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.0857 time to fit residues: 9.4519 Evaluate side-chains 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113496 restraints weight = 5207.954| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.14 r_work: 0.3445 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3387 Z= 0.130 Angle : 0.647 14.814 4609 Z= 0.325 Chirality : 0.043 0.181 494 Planarity : 0.004 0.027 596 Dihedral : 3.969 16.710 469 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 19.66 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.28 (0.39), residues: 416 helix: -1.94 (0.94), residues: 32 sheet: 1.10 (0.43), residues: 145 loop : -0.03 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 87 TYR 0.012 0.001 TYR B 95 PHE 0.010 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 3380) covalent geometry : angle 0.63906 / 0.32 ( 4595) SS BOND : bond 0.00904 / 0.43 ( 7) SS BOND : angle 1.90420 / 1.82 ( 14) hydrogen bonds : bond 0.03149 / 2.10 ( 98) hydrogen bonds : angle 5.91119 / 4.41 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8819 (ptm-80) cc_final: 0.8592 (ttp80) REVERT: A 444 LYS cc_start: 0.8265 (tppt) cc_final: 0.7998 (tppt) REVERT: B 66 GLU cc_start: 0.7980 (pm20) cc_final: 0.7631 (tm-30) REVERT: B 73 ASP cc_start: 0.8176 (t70) cc_final: 0.7436 (t70) REVERT: B 107 TYR cc_start: 0.7871 (t80) cc_final: 0.7311 (t80) outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.0742 time to fit residues: 8.4134 Evaluate side-chains 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111277 restraints weight = 5228.102| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.11 r_work: 0.3421 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3387 Z= 0.162 Angle : 0.663 14.827 4609 Z= 0.335 Chirality : 0.044 0.183 494 Planarity : 0.004 0.028 596 Dihedral : 4.097 17.991 469 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.65 % Allowed : 19.38 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.18 (0.39), residues: 416 helix: -1.94 (0.94), residues: 32 sheet: 0.87 (0.41), residues: 151 loop : 0.00 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 87 TYR 0.012 0.001 TYR B 95 PHE 0.011 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 ( 3380) covalent geometry : angle 0.65575 / 0.33 ( 4595) SS BOND : bond 0.00940 / 0.45 ( 7) SS BOND : angle 1.94700 / 1.84 ( 14) hydrogen bonds : bond 0.03219 / 2.14 ( 98) hydrogen bonds : angle 5.91244 / 4.41 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8161 (t70) cc_final: 0.7432 (t70) REVERT: B 107 TYR cc_start: 0.7890 (t80) cc_final: 0.7321 (t80) REVERT: C 5 THR cc_start: 0.7565 (m) cc_final: 0.7169 (p) outliers start: 13 outliers final: 11 residues processed: 95 average time/residue: 0.0935 time to fit residues: 10.3175 Evaluate side-chains 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113400 restraints weight = 5158.002| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.11 r_work: 0.3451 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 3387 Z= 0.133 Angle : 0.686 15.200 4609 Z= 0.345 Chirality : 0.044 0.213 494 Planarity : 0.004 0.032 596 Dihedral : 4.046 15.881 469 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 20.79 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.21 (0.39), residues: 416 helix: -1.96 (0.94), residues: 32 sheet: 0.79 (0.40), residues: 156 loop : 0.10 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 87 TYR 0.013 0.001 TYR A 380 PHE 0.011 0.001 PHE A 377 TRP 0.008 0.001 TRP B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 3380) covalent geometry : angle 0.67956 / 0.34 ( 4595) SS BOND : bond 0.00723 / 0.35 ( 7) SS BOND : angle 1.81178 / 1.72 ( 14) hydrogen bonds : bond 0.03230 / 2.13 ( 98) hydrogen bonds : angle 5.86282 / 4.40 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8272 (tppt) cc_final: 0.7966 (tppt) REVERT: B 12 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8530 (mtpt) REVERT: B 63 ARG cc_start: 0.7844 (ptm-80) cc_final: 0.7486 (ptm160) REVERT: B 66 GLU cc_start: 0.8064 (pm20) cc_final: 0.7697 (tm-30) REVERT: B 73 ASP cc_start: 0.8083 (t70) cc_final: 0.7375 (t70) REVERT: B 107 TYR cc_start: 0.7880 (t80) cc_final: 0.7304 (t80) REVERT: C 5 THR cc_start: 0.7648 (m) cc_final: 0.7220 (p) REVERT: C 80 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8177 (mp0) outliers start: 8 outliers final: 7 residues processed: 97 average time/residue: 0.0826 time to fit residues: 9.3086 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.111378 restraints weight = 5169.711| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.08 r_work: 0.3427 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3387 Z= 0.159 Angle : 0.718 15.097 4609 Z= 0.362 Chirality : 0.045 0.217 494 Planarity : 0.004 0.031 596 Dihedral : 4.137 17.037 469 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.37 % Allowed : 21.63 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.17 (0.39), residues: 416 helix: -2.03 (0.93), residues: 32 sheet: 0.64 (0.40), residues: 151 loop : 0.18 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 87 TYR 0.014 0.001 TYR A 380 PHE 0.011 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 3380) covalent geometry : angle 0.71152 / 0.36 ( 4595) SS BOND : bond 0.00994 / 0.48 ( 7) SS BOND : angle 1.86121 / 1.72 ( 14) hydrogen bonds : bond 0.03249 / 2.16 ( 98) hydrogen bonds : angle 5.81136 / 4.40 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8347 (tppt) cc_final: 0.8072 (tppt) REVERT: A 471 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: A 498 GLN cc_start: 0.8546 (mm110) cc_final: 0.8058 (mm-40) REVERT: B 65 GLN cc_start: 0.8457 (tt0) cc_final: 0.7957 (mt0) REVERT: B 66 GLU cc_start: 0.8145 (pm20) cc_final: 0.7715 (tm-30) REVERT: B 73 ASP cc_start: 0.8053 (t70) cc_final: 0.7305 (t70) REVERT: B 107 TYR cc_start: 0.7898 (t80) cc_final: 0.7315 (t80) REVERT: C 80 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8170 (mp0) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.0876 time to fit residues: 9.9554 Evaluate side-chains 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111445 restraints weight = 5158.652| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.06 r_work: 0.3424 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3387 Z= 0.160 Angle : 0.708 15.086 4609 Z= 0.358 Chirality : 0.045 0.217 494 Planarity : 0.004 0.026 596 Dihedral : 4.181 16.793 469 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.09 % Allowed : 21.91 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.08 (0.40), residues: 416 helix: -2.07 (0.93), residues: 32 sheet: 0.54 (0.41), residues: 156 loop : 0.14 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 87 TYR 0.013 0.001 TYR A 380 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 3380) covalent geometry : angle 0.70157 / 0.35 ( 4595) SS BOND : bond 0.00963 / 0.46 ( 7) SS BOND : angle 1.88003 / 1.75 ( 14) hydrogen bonds : bond 0.03314 / 2.21 ( 98) hydrogen bonds : angle 5.83468 / 4.41 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1011.03 seconds wall clock time: 17 minutes 58.24 seconds (1078.24 seconds total)