Starting phenix.real_space_refine on Tue Mar 3 11:31:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rr0_24649/03_2026/7rr0_24649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr0_24649/03_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_24649/03_2026/7rr0_24649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr0_24649/03_2026/7rr0_24649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rr0_24649/03_2026/7rr0_24649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr0_24649/03_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-5986/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.30 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: 0.17 Conformation dependent library (CDL) restraints added in 123.9 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: 0.13 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: 0.47 Time building geometry restraints manager: 0.28 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: 1807 14.43 - 28.86: 157 28.86 - 43.28: 37 43.28 - 57.71: 12 57.71 - 72.14: 3 Dihedral angle restraints: 2016 sinusoidal: 797 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 2013 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: 0.200 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.400 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 12.282 72.140 1221 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 covalent geometry : bond 0.00449 ( 3380) covalent geometry : angle 0.96770 ( 4595) SS BOND : bond 0.00479 ( 7) SS BOND : angle 1.49150 ( 14) hydrogen bonds : bond 0.24991 ( 98) hydrogen bonds : angle 10.24079 ( 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 : 0.128 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: 0.0893 time to fit residues: 12.0118 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... Flipped N/Q/H residues before XYZ refinement: A 343 ASN B 6 GLN B 57 ASN B 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.142160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115200 restraints weight = 5159.425| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.07 r_work: 0.3478 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2658 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= 0.158 Angle : 0.678 16.565 4609 Z= 0.352 Chirality : 0.046 0.267 494 Planarity : 0.005 0.033 596 Dihedral : 5.485 55.865 490 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.09 % Allowed : 12.08 % Favored : 84.83 % 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: -2.05 (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 0.017 0.002 PHE A 377 TRP 0.010 0.001 TRP A 436 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3380) covalent geometry : angle 0.66773 ( 4595) SS BOND : bond 0.00972 ( 7) SS BOND : angle 2.25349 ( 14) hydrogen bonds : bond 0.04018 ( 98) hydrogen bonds : angle 6.64253 ( 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 : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.8232 (ptm-80) cc_final: 0.7680 (ptm-80) REVERT: B 73 ASP cc_start: 0.8174 (t70) cc_final: 0.7704 (t70) REVERT: C 24 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.6947 (mmm-85) outliers start: 11 outliers final: 7 residues processed: 100 average time/residue: 0.0842 time to fit residues: 9.8081 Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3882 r_free = 0.3882 target = 0.138087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.110887 restraints weight = 5153.438| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.07 r_work: 0.3415 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3387 Z= 0.157 Angle : 0.644 13.640 4609 Z= 0.326 Chirality : 0.044 0.153 494 Planarity : 0.004 0.029 596 Dihedral : 5.397 54.741 490 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.81 % Allowed : 15.73 % 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: 0.18 (0.39), residues: 416 helix: -2.33 (0.81), residues: 32 sheet: 0.90 (0.41), residues: 150 loop : 0.05 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 87 TYR 0.015 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 covalent geometry : bond 0.00379 ( 3380) covalent geometry : angle 0.63493 ( 4595) SS BOND : bond 0.00866 ( 7) SS BOND : angle 2.03392 ( 14) hydrogen bonds : bond 0.03591 ( 98) hydrogen bonds : angle 6.31173 ( 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 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: B 73 ASP cc_start: 0.8228 (t70) cc_final: 0.7602 (t70) REVERT: B 107 TYR cc_start: 0.7927 (t80) cc_final: 0.7668 (t80) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.1016 time to fit residues: 10.9066 Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 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: 0.0030 chunk 35 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.116899 restraints weight = 5095.474| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.08 r_work: 0.3497 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 3387 Z= 0.112 Angle : 0.621 15.353 4609 Z= 0.313 Chirality : 0.044 0.204 494 Planarity : 0.004 0.029 596 Dihedral : 5.104 52.935 490 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.97 % Allowed : 17.42 % Favored : 80.62 % 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: -2.11 (0.88), residues: 32 sheet: 0.92 (0.42), residues: 147 loop : 0.04 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 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 covalent geometry : bond 0.00271 ( 3380) covalent geometry : angle 0.61341 ( 4595) SS BOND : bond 0.00762 ( 7) SS BOND : angle 1.85895 ( 14) hydrogen bonds : bond 0.03169 ( 98) hydrogen bonds : angle 5.91523 ( 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 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: B 73 ASP cc_start: 0.8199 (t70) cc_final: 0.7542 (t70) REVERT: B 107 TYR cc_start: 0.7891 (t80) cc_final: 0.7519 (t80) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.1013 time to fit residues: 10.9237 Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.141297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114383 restraints weight = 5061.449| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.05 r_work: 0.3469 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 3387 Z= 0.135 Angle : 0.635 14.816 4609 Z= 0.321 Chirality : 0.043 0.183 494 Planarity : 0.004 0.030 596 Dihedral : 5.210 54.135 490 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.37 % Allowed : 17.70 % Favored : 78.93 % 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: -1.94 (0.94), residues: 32 sheet: 1.07 (0.43), residues: 145 loop : 0.05 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.013 0.001 TYR B 95 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3380) covalent geometry : angle 0.62724 ( 4595) SS BOND : bond 0.00861 ( 7) SS BOND : angle 1.89463 ( 14) hydrogen bonds : bond 0.03169 ( 98) hydrogen bonds : angle 5.96241 ( 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 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8855 (ptm-80) cc_final: 0.8624 (ttp80) REVERT: A 471 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: B 66 GLU cc_start: 0.8019 (pm20) cc_final: 0.7630 (tm-30) REVERT: B 73 ASP cc_start: 0.8184 (t70) cc_final: 0.7451 (t70) REVERT: B 82 GLU cc_start: 0.7781 (tt0) cc_final: 0.7289 (mt-10) REVERT: B 107 TYR cc_start: 0.7894 (t80) cc_final: 0.7416 (t80) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 0.0811 time to fit residues: 8.9244 Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112199 restraints weight = 5128.625| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.10 r_work: 0.3432 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3387 Z= 0.150 Angle : 0.643 15.357 4609 Z= 0.326 Chirality : 0.044 0.219 494 Planarity : 0.004 0.029 596 Dihedral : 5.268 54.309 490 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.37 % Allowed : 18.26 % 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: 0.23 (0.39), residues: 416 helix: -1.97 (0.94), residues: 32 sheet: 1.04 (0.43), residues: 145 loop : -0.04 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 87 TYR 0.014 0.001 TYR B 95 PHE 0.012 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3380) covalent geometry : angle 0.63552 ( 4595) SS BOND : bond 0.00754 ( 7) SS BOND : angle 1.83747 ( 14) hydrogen bonds : bond 0.03211 ( 98) hydrogen bonds : angle 5.97378 ( 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 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8822 (ptm-80) cc_final: 0.8605 (ttp80) REVERT: A 471 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: B 66 GLU cc_start: 0.7967 (pm20) cc_final: 0.7632 (tm-30) REVERT: B 73 ASP cc_start: 0.8197 (t70) cc_final: 0.7469 (t70) REVERT: B 107 TYR cc_start: 0.7894 (t80) cc_final: 0.7382 (t80) REVERT: C 46 ARG cc_start: 0.8554 (ttp-170) cc_final: 0.8322 (tmm160) REVERT: C 59 ILE cc_start: 0.8135 (mp) cc_final: 0.7769 (tp) outliers start: 12 outliers final: 11 residues processed: 91 average time/residue: 0.0841 time to fit residues: 8.9482 Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3900 r_free = 0.3900 target = 0.139607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.112496 restraints weight = 5207.642| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.11 r_work: 0.3435 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3903 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= 0.134 Angle : 0.638 15.088 4609 Z= 0.325 Chirality : 0.044 0.211 494 Planarity : 0.004 0.027 596 Dihedral : 5.200 53.727 490 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.09 % Allowed : 18.54 % 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: 0.19 (0.39), residues: 416 helix: -1.97 (0.94), residues: 32 sheet: 0.93 (0.43), residues: 147 loop : -0.02 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 87 TYR 0.011 0.001 TYR B 95 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3380) covalent geometry : angle 0.63111 ( 4595) SS BOND : bond 0.00925 ( 7) SS BOND : angle 1.84212 ( 14) hydrogen bonds : bond 0.03125 ( 98) hydrogen bonds : angle 5.85233 ( 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 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8830 (ptm-80) cc_final: 0.8614 (ttp80) REVERT: A 444 LYS cc_start: 0.8268 (tppt) cc_final: 0.8005 (tppt) REVERT: B 66 GLU cc_start: 0.7973 (pm20) cc_final: 0.7634 (tm-30) REVERT: B 73 ASP cc_start: 0.8137 (t70) cc_final: 0.7415 (t70) REVERT: B 107 TYR cc_start: 0.7871 (t80) cc_final: 0.7321 (t80) REVERT: C 59 ILE cc_start: 0.8069 (mp) cc_final: 0.7815 (tp) REVERT: C 80 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7931 (mm-30) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.0911 time to fit residues: 9.5804 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 : 0.112 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3876 r_free = 0.3876 target = 0.137745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110542 restraints weight = 5232.064| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.10 r_work: 0.3414 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3387 Z= 0.164 Angle : 0.661 15.080 4609 Z= 0.336 Chirality : 0.045 0.212 494 Planarity : 0.004 0.027 596 Dihedral : 5.346 54.427 490 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.09 % Allowed : 19.66 % Favored : 77.25 % 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: -2.01 (0.94), residues: 32 sheet: 0.75 (0.41), residues: 156 loop : 0.10 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 87 TYR 0.016 0.001 TYR B 95 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3380) covalent geometry : angle 0.65320 ( 4595) SS BOND : bond 0.00956 ( 7) SS BOND : angle 1.89927 ( 14) hydrogen bonds : bond 0.03270 ( 98) hydrogen bonds : angle 6.03429 ( 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 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 ASP cc_start: 0.8083 (t70) cc_final: 0.7355 (t70) REVERT: B 107 TYR cc_start: 0.7901 (t80) cc_final: 0.7334 (t80) REVERT: C 5 THR cc_start: 0.7571 (m) cc_final: 0.7170 (p) REVERT: C 59 ILE cc_start: 0.8067 (mp) cc_final: 0.7815 (tp) outliers start: 11 outliers final: 11 residues processed: 92 average time/residue: 0.1037 time to fit residues: 10.8738 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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: 0.0870 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.139356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.112595 restraints weight = 5143.209| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.06 r_work: 0.3436 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4155 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= 0.134 Angle : 0.674 14.983 4609 Z= 0.340 Chirality : 0.044 0.205 494 Planarity : 0.004 0.036 596 Dihedral : 5.216 53.258 490 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.09 % Allowed : 19.66 % Favored : 77.25 % 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: 0.24 (0.39), residues: 416 helix: -2.01 (0.94), residues: 32 sheet: 0.82 (0.40), residues: 155 loop : 0.12 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 55 TYR 0.013 0.001 TYR A 380 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP B 47 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3380) covalent geometry : angle 0.66647 ( 4595) SS BOND : bond 0.00932 ( 7) SS BOND : angle 1.88997 ( 14) hydrogen bonds : bond 0.03132 ( 98) hydrogen bonds : angle 5.82657 ( 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 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8333 (tppt) cc_final: 0.8041 (tppt) REVERT: B 63 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7473 (ptm160) REVERT: B 66 GLU cc_start: 0.8076 (pm20) cc_final: 0.7723 (tm-30) REVERT: B 73 ASP cc_start: 0.8090 (t70) cc_final: 0.7336 (t70) REVERT: B 107 TYR cc_start: 0.7873 (t80) cc_final: 0.7305 (t80) REVERT: C 5 THR cc_start: 0.7529 (m) cc_final: 0.7104 (p) REVERT: C 46 ARG cc_start: 0.8558 (ttp-170) cc_final: 0.8334 (ttp-170) REVERT: C 80 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8168 (mp0) outliers start: 11 outliers final: 10 residues processed: 92 average time/residue: 0.0819 time to fit residues: 8.7817 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.139782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.112734 restraints weight = 5164.306| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.09 r_work: 0.3445 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4243 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= 0.132 Angle : 0.672 14.834 4609 Z= 0.340 Chirality : 0.044 0.203 494 Planarity : 0.004 0.034 596 Dihedral : 5.231 53.395 490 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.81 % Allowed : 20.79 % Favored : 76.40 % 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: 0.27 (0.40), residues: 416 helix: -2.09 (0.92), residues: 32 sheet: 0.73 (0.41), residues: 156 loop : 0.25 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 55 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 covalent geometry : bond 0.00326 ( 3380) covalent geometry : angle 0.66557 ( 4595) SS BOND : bond 0.00923 ( 7) SS BOND : angle 1.86508 ( 14) hydrogen bonds : bond 0.03060 ( 98) hydrogen bonds : angle 5.90134 ( 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 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8333 (tppt) cc_final: 0.8016 (tppt) REVERT: A 498 GLN cc_start: 0.8504 (mm110) cc_final: 0.8022 (mm-40) REVERT: B 65 GLN cc_start: 0.8383 (tt0) cc_final: 0.7885 (mt0) REVERT: B 66 GLU cc_start: 0.8169 (pm20) cc_final: 0.7756 (tm-30) REVERT: B 73 ASP cc_start: 0.8083 (t70) cc_final: 0.7327 (t70) REVERT: B 107 TYR cc_start: 0.7872 (t80) cc_final: 0.7311 (t80) REVERT: C 5 THR cc_start: 0.7585 (m) cc_final: 0.7144 (p) REVERT: C 46 ARG cc_start: 0.8499 (ttp-170) cc_final: 0.8204 (ttp-170) REVERT: C 80 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8298 (mp0) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.0917 time to fit residues: 9.4336 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN C 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113155 restraints weight = 5174.778| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.08 r_work: 0.3446 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4320 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= 0.135 Angle : 0.677 14.764 4609 Z= 0.343 Chirality : 0.044 0.202 494 Planarity : 0.004 0.032 596 Dihedral : 5.210 53.542 490 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.37 % Allowed : 20.79 % Favored : 75.84 % 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: 0.22 (0.40), residues: 416 helix: -2.14 (0.91), residues: 32 sheet: 0.67 (0.42), residues: 158 loop : 0.23 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 55 TYR 0.013 0.001 TYR A 380 PHE 0.010 0.001 PHE A 377 TRP 0.009 0.001 TRP B 47 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3380) covalent geometry : angle 0.67011 ( 4595) SS BOND : bond 0.00926 ( 7) SS BOND : angle 1.87344 ( 14) hydrogen bonds : bond 0.03047 ( 98) hydrogen bonds : angle 5.75284 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1072.01 seconds wall clock time: 18 minutes 58.16 seconds (1138.16 seconds total)