Starting phenix.real_space_refine on Mon Feb 10 23:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rr0_24649/02_2025/7rr0_24649.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rr0_24649/02_2025/7rr0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rr0_24649/02_2025/7rr0_24649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rr0_24649/02_2025/7rr0_24649.map" model { file = "/net/cci-nas-00/data/ceres_data/7rr0_24649/02_2025/7rr0_24649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rr0_24649/02_2025/7rr0_24649.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'HIS:plan': 1, 'ASP: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: 2.77, per 1000 atoms: 0.84 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: 0.75 Conformation dependent library (CDL) restraints added in 397.2 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: 0.42 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: 0.95 Time building geometry restraints manager: 0.92 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: 0.270 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- 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 3380 Z= 0.272 Angle : 0.968 11.211 4595 Z= 0.520 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.003 TRP B 50 PHE 0.011 0.001 PHE A 374 TYR 0.011 0.001 TYR B 95 ARG 0.014 0.001 ARG C 78 *********************** 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 : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 PHE cc_start: 0.4991 (m-10) cc_final: 0.4646 (m-10) REVERT: B 73 ASP cc_start: 0.7696 (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: 0.2082 time to fit residues: 28.0283 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 360 ASN B 6 GLN 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 = 0.3841 r_free = 0.3841 target = 0.134940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107401 restraints weight = 5255.238| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.08 r_work: 0.3359 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 3380 Z= 0.419 Angle : 0.717 14.663 4595 Z= 0.380 Chirality : 0.049 0.276 494 Planarity : 0.005 0.032 596 Dihedral : 5.850 57.944 490 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.21 % Allowed : 11.80 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.39), residues: 416 helix: -1.89 (0.95), residues: 26 sheet: 0.83 (0.41), residues: 151 loop : -0.08 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 50 PHE 0.019 0.002 PHE A 377 TYR 0.017 0.002 TYR B 95 ARG 0.007 0.001 ARG A 509 *********************** 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 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6124 (mp0) REVERT: B 12 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8910 (mtpt) REVERT: B 43 GLN cc_start: 0.8901 (mp10) cc_final: 0.8674 (mp10) REVERT: B 73 ASP cc_start: 0.8231 (t70) cc_final: 0.7711 (t70) REVERT: C 24 ARG cc_start: 0.7213 (mmm-85) cc_final: 0.6850 (mmm-85) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.2152 time to fit residues: 23.9270 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 A residue 523 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 12 LYS 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 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.137899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111515 restraints weight = 5077.723| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.95 r_work: 0.3422 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 3380 Z= 0.217 Angle : 0.610 12.020 4595 Z= 0.312 Chirality : 0.043 0.136 494 Planarity : 0.004 0.029 596 Dihedral : 5.353 53.203 490 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.65 % Allowed : 15.17 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.38), residues: 416 helix: -2.29 (0.82), residues: 32 sheet: 0.82 (0.41), residues: 148 loop : -0.03 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 PHE 0.013 0.001 PHE A 347 TYR 0.013 0.001 TYR B 95 ARG 0.005 0.000 ARG C 55 *********************** 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 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6161 (mp0) REVERT: B 12 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8671 (mtpt) REVERT: B 43 GLN cc_start: 0.8830 (mp10) cc_final: 0.8529 (mp10) REVERT: B 73 ASP cc_start: 0.8173 (t70) cc_final: 0.7502 (t70) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.1982 time to fit residues: 22.0885 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 : 0.342 ------------------------------------------------------------------------------- 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 12 LYS 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 12 SER 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 32 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 30 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN B 6 GLN B 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.138151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110878 restraints weight = 5177.293| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.12 r_work: 0.3411 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 3380 Z= 0.209 Angle : 0.600 14.374 4595 Z= 0.309 Chirality : 0.043 0.166 494 Planarity : 0.004 0.032 596 Dihedral : 5.243 53.966 490 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.81 % Allowed : 18.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.39), residues: 416 helix: -2.09 (0.88), residues: 32 sheet: 0.86 (0.42), residues: 147 loop : -0.05 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.011 0.001 PHE A 377 TYR 0.010 0.001 TYR B 95 ARG 0.006 0.000 ARG B 87 *********************** 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 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLN cc_start: 0.8845 (mp10) cc_final: 0.7971 (mp10) REVERT: B 73 ASP cc_start: 0.8175 (t70) cc_final: 0.7595 (t70) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.1989 time to fit residues: 20.8873 Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain B residue 83 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.139254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112254 restraints weight = 5178.498| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.09 r_work: 0.3434 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 3380 Z= 0.199 Angle : 0.613 15.244 4595 Z= 0.312 Chirality : 0.044 0.208 494 Planarity : 0.004 0.033 596 Dihedral : 5.166 53.391 490 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.69 % Allowed : 19.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.39), residues: 416 helix: -1.99 (0.92), residues: 32 sheet: 0.90 (0.42), residues: 152 loop : -0.03 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 PHE 0.011 0.001 PHE A 377 TYR 0.012 0.001 TYR B 95 ARG 0.006 0.000 ARG B 87 *********************** 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 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLN cc_start: 0.8674 (mp10) cc_final: 0.7891 (mp10) REVERT: B 47 TRP cc_start: 0.8653 (t60) cc_final: 0.8427 (t60) REVERT: B 59 ASN cc_start: 0.7723 (t0) cc_final: 0.7399 (t0) REVERT: B 66 GLU cc_start: 0.7979 (pm20) cc_final: 0.7579 (tm-30) REVERT: B 73 ASP cc_start: 0.8173 (t70) cc_final: 0.7570 (t70) REVERT: B 107 TYR cc_start: 0.7900 (t80) cc_final: 0.7568 (t80) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.2156 time to fit residues: 22.4877 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 : 0.390 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain B residue 117 THR 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 39 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.136925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109813 restraints weight = 5290.371| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.09 r_work: 0.3393 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3380 Z= 0.226 Angle : 0.611 15.133 4595 Z= 0.315 Chirality : 0.044 0.198 494 Planarity : 0.004 0.032 596 Dihedral : 5.210 54.334 490 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.53 % Allowed : 19.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.39), residues: 416 helix: -1.94 (0.93), residues: 32 sheet: 0.90 (0.41), residues: 158 loop : 0.02 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR A 380 ARG 0.007 0.000 ARG B 87 *********************** 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 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLN cc_start: 0.8843 (mp10) cc_final: 0.7996 (mp10) REVERT: B 59 ASN cc_start: 0.7752 (t0) cc_final: 0.7364 (t0) REVERT: B 66 GLU cc_start: 0.7983 (pm20) cc_final: 0.7581 (tm-30) REVERT: B 73 ASP cc_start: 0.8128 (t70) cc_final: 0.7459 (t70) REVERT: B 107 TYR cc_start: 0.7952 (t80) cc_final: 0.7552 (t80) REVERT: C 80 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8046 (mm-30) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.2275 time to fit residues: 23.8959 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.135925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108908 restraints weight = 5202.020| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.06 r_work: 0.3377 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3380 Z= 0.250 Angle : 0.634 15.031 4595 Z= 0.323 Chirality : 0.044 0.193 494 Planarity : 0.004 0.030 596 Dihedral : 5.264 54.433 490 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.81 % Allowed : 21.07 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.39), residues: 416 helix: -1.89 (0.93), residues: 32 sheet: 0.84 (0.41), residues: 158 loop : 0.07 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR B 95 ARG 0.007 0.001 ARG B 87 *********************** 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: 10 poor density : 84 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8257 (tppt) cc_final: 0.7990 (tppt) REVERT: B 43 GLN cc_start: 0.8767 (mp10) cc_final: 0.7982 (mp10) REVERT: B 73 ASP cc_start: 0.8094 (t70) cc_final: 0.7423 (t70) REVERT: B 107 TYR cc_start: 0.7956 (t80) cc_final: 0.7528 (t80) REVERT: C 5 THR cc_start: 0.7641 (m) cc_final: 0.7240 (p) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.2362 time to fit residues: 24.7081 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 69 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.135301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108519 restraints weight = 5184.032| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.05 r_work: 0.3377 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3380 Z= 0.249 Angle : 0.648 14.912 4595 Z= 0.331 Chirality : 0.044 0.187 494 Planarity : 0.004 0.030 596 Dihedral : 5.294 54.252 490 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 20.51 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.40), residues: 416 helix: -1.83 (0.96), residues: 32 sheet: 0.75 (0.41), residues: 158 loop : 0.06 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR B 95 ARG 0.008 0.001 ARG B 87 *********************** 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 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLN cc_start: 0.8760 (mp10) cc_final: 0.8019 (mp10) REVERT: B 65 GLN cc_start: 0.8357 (tt0) cc_final: 0.7846 (mt0) REVERT: B 66 GLU cc_start: 0.8144 (pm20) cc_final: 0.7733 (tm-30) REVERT: B 73 ASP cc_start: 0.8086 (t70) cc_final: 0.7362 (t70) REVERT: B 107 TYR cc_start: 0.7953 (t80) cc_final: 0.7495 (t80) REVERT: C 24 ARG cc_start: 0.7419 (mmm-85) cc_final: 0.6828 (mmm160) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.2174 time to fit residues: 23.3183 Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 69 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.137351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110616 restraints weight = 5217.918| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.01 r_work: 0.3413 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3380 Z= 0.217 Angle : 0.644 14.763 4595 Z= 0.329 Chirality : 0.044 0.179 494 Planarity : 0.004 0.033 596 Dihedral : 5.216 53.532 490 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.53 % Allowed : 22.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.40), residues: 416 helix: -1.80 (0.97), residues: 32 sheet: 0.78 (0.41), residues: 158 loop : 0.07 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 47 PHE 0.010 0.001 PHE A 377 TYR 0.013 0.001 TYR A 380 ARG 0.008 0.001 ARG C 55 *********************** 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 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8269 (tppt) cc_final: 0.8021 (tppt) REVERT: A 471 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: B 43 GLN cc_start: 0.8762 (mp10) cc_final: 0.8086 (mp10) REVERT: B 65 GLN cc_start: 0.8313 (tt0) cc_final: 0.7832 (mt0) REVERT: B 66 GLU cc_start: 0.8127 (pm20) cc_final: 0.7714 (tm-30) REVERT: B 73 ASP cc_start: 0.8152 (t70) cc_final: 0.7454 (t70) REVERT: B 107 TYR cc_start: 0.7933 (t80) cc_final: 0.7490 (t80) REVERT: C 24 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.7100 (mmm160) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.1973 time to fit residues: 19.7147 Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 69 THR 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 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106677 restraints weight = 5110.624| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.11 r_work: 0.3342 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3380 Z= 0.291 Angle : 0.688 14.921 4595 Z= 0.353 Chirality : 0.045 0.188 494 Planarity : 0.005 0.032 596 Dihedral : 5.410 54.799 490 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.25 % Allowed : 23.88 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.40), residues: 416 helix: -1.88 (0.96), residues: 32 sheet: 0.69 (0.41), residues: 158 loop : 0.02 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 47 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.001 TYR A 380 ARG 0.008 0.001 ARG C 55 ********************** 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 87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 GLN cc_start: 0.8707 (mp10) cc_final: 0.7946 (mp10) REVERT: B 73 ASP cc_start: 0.8042 (t70) cc_final: 0.7276 (t70) REVERT: B 107 TYR cc_start: 0.8023 (t80) cc_final: 0.7530 (t80) REVERT: C 80 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8145 (mp0) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.2300 time to fit residues: 22.5173 Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 117 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 5 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.0060 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110512 restraints weight = 5150.662| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.10 r_work: 0.3398 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3380 Z= 0.224 Angle : 0.686 14.632 4595 Z= 0.348 Chirality : 0.044 0.174 494 Planarity : 0.004 0.032 596 Dihedral : 5.183 53.069 490 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.25 % Allowed : 23.88 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.40), residues: 416 helix: -1.98 (0.94), residues: 32 sheet: 0.78 (0.42), residues: 158 loop : 0.10 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 47 PHE 0.011 0.001 PHE A 377 TYR 0.013 0.001 TYR A 380 ARG 0.008 0.001 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2053.05 seconds wall clock time: 37 minutes 13.24 seconds (2233.24 seconds total)