Starting phenix.real_space_refine on Wed Sep 17 06:11:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dir_46916/09_2025/9dir_46916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dir_46916/09_2025/9dir_46916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dir_46916/09_2025/9dir_46916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dir_46916/09_2025/9dir_46916.map" model { file = "/net/cci-nas-00/data/ceres_data/9dir_46916/09_2025/9dir_46916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dir_46916/09_2025/9dir_46916.cif" } resolution = 2.97 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= 0.072 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 17 5.16 5 C 3669 2.51 5 N 1022 2.21 5 O 1181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5889 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1001 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "B" Number of atoms: 4888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4888 Classifications: {'peptide': 629} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Time building chain proxies: 1.58, per 1000 atoms: 0.27 Number of scatterers: 5889 At special positions: 0 Unit cell: (119, 67.83, 74.97, 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 17 16.00 O 1181 8.00 N 1022 7.00 C 3669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.40 Conformation dependent library (CDL) restraints added in 242.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 5 sheets defined 21.0% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 1 through 76 removed outlier: 3.561A pdb=" N GLY A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 100 Processing helix chain 'A' and resid 101 through 127 Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.254A pdb=" N THR B 42 " --> pdb=" O PRO B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.609A pdb=" N LYS B 603 " --> pdb=" O GLN B 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.605A pdb=" N LEU B 80 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TYR B 130 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 82 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 154 removed outlier: 3.524A pdb=" N ASP B 228 " --> pdb=" O SER B 200 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 344 through 355 current: chain 'B' and resid 364 through 379 removed outlier: 5.411A pdb=" N SER B 379 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 390 current: chain 'B' and resid 404 through 413 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 404 through 413 current: chain 'B' and resid 435 through 440 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 435 through 440 current: chain 'B' and resid 470 through 491 removed outlier: 6.800A pdb=" N LEU B 471 " --> pdb=" O TYR B 516 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR B 516 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE B 473 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR B 514 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA B 475 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 512 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR B 477 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TRP B 510 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP B 479 " --> pdb=" O TRP B 508 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP B 508 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS B 481 " --> pdb=" O LYS B 506 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS B 506 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 483 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B 504 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 530 " --> pdb=" O PRO B 546 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 320 hydrogen bonds defined for protein. 903 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: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1988 1.34 - 1.46: 1160 1.46 - 1.57: 2821 1.57 - 1.69: 0 1.69 - 1.80: 34 Bond restraints: 6003 Sorted by residual: bond pdb=" CG GLU A 29 " pdb=" CD GLU A 29 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.68e-01 bond pdb=" CG GLU A 106 " pdb=" CD GLU A 106 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.68e-01 bond pdb=" CA GLU A 29 " pdb=" CB GLU A 29 " ideal model delta sigma weight residual 1.528 1.543 -0.014 1.66e-02 3.63e+03 7.27e-01 bond pdb=" CD GLU A 29 " pdb=" OE1 GLU A 29 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.04e-01 bond pdb=" CG LEU B 100 " pdb=" CD2 LEU B 100 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.98e-01 ... (remaining 5998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 7954 1.69 - 3.37: 141 3.37 - 5.06: 14 5.06 - 6.74: 6 6.74 - 8.43: 1 Bond angle restraints: 8116 Sorted by residual: angle pdb=" N GLU A 29 " pdb=" CA GLU A 29 " pdb=" CB GLU A 29 " ideal model delta sigma weight residual 110.28 115.91 -5.63 1.55e+00 4.16e-01 1.32e+01 angle pdb=" C LEU A 105 " pdb=" N GLU A 106 " pdb=" CA GLU A 106 " ideal model delta sigma weight residual 120.28 116.14 4.14 1.34e+00 5.57e-01 9.57e+00 angle pdb=" CA GLU A 29 " pdb=" CB GLU A 29 " pdb=" CG GLU A 29 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.42e+00 angle pdb=" C LEU A 28 " pdb=" N GLU A 29 " pdb=" CA GLU A 29 " ideal model delta sigma weight residual 120.31 116.07 4.24 1.52e+00 4.33e-01 7.77e+00 angle pdb=" N GLU A 106 " pdb=" CA GLU A 106 " pdb=" CB GLU A 106 " ideal model delta sigma weight residual 110.12 113.87 -3.75 1.47e+00 4.63e-01 6.50e+00 ... (remaining 8111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3346 17.91 - 35.81: 200 35.81 - 53.72: 36 53.72 - 71.63: 8 71.63 - 89.53: 5 Dihedral angle restraints: 3595 sinusoidal: 1434 harmonic: 2161 Sorted by residual: dihedral pdb=" CA MET B 422 " pdb=" C MET B 422 " pdb=" N TYR B 423 " pdb=" CA TYR B 423 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP B 534 " pdb=" C ASP B 534 " pdb=" N THR B 535 " pdb=" CA THR B 535 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASP B 347 " pdb=" CB ASP B 347 " pdb=" CG ASP B 347 " pdb=" OD1 ASP B 347 " ideal model delta sinusoidal sigma weight residual -30.00 -87.22 57.22 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 559 0.033 - 0.066: 222 0.066 - 0.099: 54 0.099 - 0.132: 36 0.132 - 0.166: 2 Chirality restraints: 873 Sorted by residual: chirality pdb=" CA GLU A 29 " pdb=" N GLU A 29 " pdb=" C GLU A 29 " pdb=" CB GLU A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA LEU A 105 " pdb=" N LEU A 105 " pdb=" C LEU A 105 " pdb=" CB LEU A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA LYS A 121 " pdb=" N LYS A 121 " pdb=" C LYS A 121 " pdb=" CB LYS A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 870 not shown) Planarity restraints: 1068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 100 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 101 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 25 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.68e+00 pdb=" C ARG A 25 " -0.022 2.00e-02 2.50e+03 pdb=" O ARG A 25 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU A 26 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 26 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 27 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " 0.017 5.00e-02 4.00e+02 ... (remaining 1065 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 134 2.68 - 3.23: 5662 3.23 - 3.79: 9650 3.79 - 4.34: 12836 4.34 - 4.90: 22354 Nonbonded interactions: 50636 Sorted by model distance: nonbonded pdb=" NH1 ARG B 107 " pdb=" OE2 GLU B 109 " model vdw 2.124 3.120 nonbonded pdb=" OD1 ASP B 511 " pdb=" ND2 ASN B 528 " model vdw 2.190 3.120 nonbonded pdb=" NH2 ARG A 9 " pdb=" OD2 ASP B 491 " model vdw 2.190 3.120 nonbonded pdb=" NH2 ARG B 223 " pdb=" OD2 ASP B 256 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASP B 572 " pdb=" N ARG B 573 " model vdw 2.226 3.120 ... (remaining 50631 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: 0.760 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.620 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5281 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 0.028 6003 Z= 0.175 Angle : 0.575 8.428 8116 Z= 0.307 Chirality : 0.042 0.166 873 Planarity : 0.004 0.066 1068 Dihedral : 12.368 89.532 2219 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.32), residues: 750 helix: 1.13 (0.43), residues: 131 sheet: -0.13 (0.28), residues: 363 loop : 0.39 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.017 0.001 TYR B 119 PHE 0.011 0.001 PHE B 414 TRP 0.004 0.001 TRP B 439 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6003) covalent geometry : angle 0.57522 ( 8116) hydrogen bonds : bond 0.18364 ( 320) hydrogen bonds : angle 8.64246 ( 903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6217 (pttp) cc_final: 0.5677 (ptmm) REVERT: A 84 LYS cc_start: 0.6841 (ttpp) cc_final: 0.6552 (ttpt) REVERT: A 107 GLU cc_start: 0.6562 (tm-30) cc_final: 0.6147 (tm-30) REVERT: B 45 SER cc_start: 0.7460 (m) cc_final: 0.6986 (t) REVERT: B 209 THR cc_start: 0.7217 (m) cc_final: 0.6957 (p) REVERT: B 449 THR cc_start: 0.7080 (p) cc_final: 0.6689 (t) REVERT: B 513 MET cc_start: 0.7272 (mpp) cc_final: 0.6923 (mpp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4749 time to fit residues: 73.7310 Evaluate side-chains 94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.169228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139442 restraints weight = 5352.156| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.64 r_work: 0.3482 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6003 Z= 0.195 Angle : 0.657 7.540 8116 Z= 0.351 Chirality : 0.046 0.152 873 Planarity : 0.005 0.062 1068 Dihedral : 4.724 32.267 827 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.73 % Allowed : 9.95 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.31), residues: 750 helix: 1.38 (0.41), residues: 134 sheet: -0.19 (0.27), residues: 359 loop : 0.20 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 102 TYR 0.016 0.002 TYR B 485 PHE 0.020 0.002 PHE B 457 TRP 0.012 0.002 TRP B 439 HIS 0.002 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6003) covalent geometry : angle 0.65704 ( 8116) hydrogen bonds : bond 0.04077 ( 320) hydrogen bonds : angle 6.03934 ( 903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.231 Fit side-chains REVERT: A 5 LYS cc_start: 0.5937 (pttp) cc_final: 0.5373 (ptmm) REVERT: A 8 LYS cc_start: 0.5661 (ttpp) cc_final: 0.5193 (ttpp) REVERT: A 19 GLU cc_start: 0.6152 (tm-30) cc_final: 0.5868 (tm-30) REVERT: A 45 LYS cc_start: 0.6187 (mmtt) cc_final: 0.5869 (tttm) REVERT: A 84 LYS cc_start: 0.6975 (ttpp) cc_final: 0.6570 (ttpt) REVERT: A 111 MET cc_start: 0.7221 (ptm) cc_final: 0.7012 (ppp) REVERT: B 45 SER cc_start: 0.8164 (m) cc_final: 0.7785 (t) REVERT: B 68 ASP cc_start: 0.7054 (m-30) cc_final: 0.6732 (m-30) REVERT: B 92 THR cc_start: 0.7478 (p) cc_final: 0.7148 (t) REVERT: B 94 HIS cc_start: 0.7209 (m90) cc_final: 0.6807 (m170) REVERT: B 139 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7210 (mt) REVERT: B 140 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6904 (mm-40) REVERT: B 233 LYS cc_start: 0.6560 (ttmm) cc_final: 0.5996 (tptt) REVERT: B 236 GLN cc_start: 0.6887 (mt0) cc_final: 0.6653 (mt0) REVERT: B 277 ILE cc_start: 0.8307 (mt) cc_final: 0.7708 (pt) REVERT: B 287 GLN cc_start: 0.5703 (mm-40) cc_final: 0.5195 (pm20) REVERT: B 376 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.6671 (mpp-170) REVERT: B 423 TYR cc_start: 0.7053 (m-80) cc_final: 0.6361 (m-80) REVERT: B 451 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6256 (pt0) REVERT: B 605 MET cc_start: 0.8144 (tmt) cc_final: 0.7941 (tmt) REVERT: B 609 LEU cc_start: 0.8034 (mt) cc_final: 0.7789 (mt) REVERT: B 613 ASN cc_start: 0.8552 (t0) cc_final: 0.8295 (t0) REVERT: B 633 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7925 (mtmm) outliers start: 17 outliers final: 8 residues processed: 143 average time/residue: 0.5762 time to fit residues: 86.3105 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 285 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150675 restraints weight = 5383.102| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.59 r_work: 0.3457 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6003 Z= 0.164 Angle : 0.552 6.641 8116 Z= 0.291 Chirality : 0.043 0.139 873 Planarity : 0.005 0.069 1068 Dihedral : 4.260 28.204 827 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.33 % Allowed : 14.93 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.31), residues: 750 helix: 1.73 (0.41), residues: 135 sheet: -0.43 (0.27), residues: 344 loop : 0.08 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 25 TYR 0.013 0.002 TYR B 295 PHE 0.014 0.002 PHE B 457 TRP 0.009 0.001 TRP B 270 HIS 0.002 0.001 HIS B 428 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6003) covalent geometry : angle 0.55198 ( 8116) hydrogen bonds : bond 0.03926 ( 320) hydrogen bonds : angle 5.71004 ( 903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.227 Fit side-chains REVERT: A 5 LYS cc_start: 0.6516 (pttp) cc_final: 0.5959 (ptmm) REVERT: A 84 LYS cc_start: 0.7338 (ttpp) cc_final: 0.6882 (ttpt) REVERT: A 86 MET cc_start: 0.7076 (mmm) cc_final: 0.6820 (mmm) REVERT: A 111 MET cc_start: 0.7737 (ptm) cc_final: 0.7212 (ptt) REVERT: B 45 SER cc_start: 0.8365 (m) cc_final: 0.7877 (t) REVERT: B 51 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6247 (mtt90) REVERT: B 233 LYS cc_start: 0.6985 (ttmm) cc_final: 0.6549 (tptt) REVERT: B 287 GLN cc_start: 0.5932 (mm-40) cc_final: 0.5350 (pm20) REVERT: B 328 TYR cc_start: 0.8773 (p90) cc_final: 0.8308 (p90) REVERT: B 343 GLN cc_start: 0.8250 (tt0) cc_final: 0.7254 (tm130) REVERT: B 376 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7240 (mpp-170) REVERT: B 451 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: B 513 MET cc_start: 0.8742 (mpp) cc_final: 0.8388 (mtp) REVERT: B 603 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7267 (mmmt) outliers start: 27 outliers final: 15 residues processed: 119 average time/residue: 0.5510 time to fit residues: 68.8507 Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 625 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN B 88 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150584 restraints weight = 5428.550| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.55 r_work: 0.3441 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6003 Z= 0.154 Angle : 0.522 6.841 8116 Z= 0.275 Chirality : 0.042 0.135 873 Planarity : 0.004 0.068 1068 Dihedral : 4.239 31.803 827 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.65 % Allowed : 16.05 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.31), residues: 750 helix: 1.87 (0.40), residues: 135 sheet: -0.53 (0.27), residues: 346 loop : 0.06 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 25 TYR 0.012 0.002 TYR B 328 PHE 0.012 0.002 PHE B 457 TRP 0.009 0.001 TRP B 270 HIS 0.001 0.000 HIS B 428 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6003) covalent geometry : angle 0.52212 ( 8116) hydrogen bonds : bond 0.03413 ( 320) hydrogen bonds : angle 5.55305 ( 903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.297 Fit side-chains REVERT: A 84 LYS cc_start: 0.7576 (ttpp) cc_final: 0.7158 (ttpt) REVERT: A 111 MET cc_start: 0.7790 (ptm) cc_final: 0.7279 (ptt) REVERT: B 45 SER cc_start: 0.8354 (m) cc_final: 0.7891 (t) REVERT: B 67 GLN cc_start: 0.8406 (tt0) cc_final: 0.7777 (tt0) REVERT: B 86 ILE cc_start: 0.8172 (mt) cc_final: 0.7752 (mt) REVERT: B 200 SER cc_start: 0.8069 (t) cc_final: 0.7749 (m) REVERT: B 270 TRP cc_start: 0.7802 (p-90) cc_final: 0.7500 (p90) REVERT: B 343 GLN cc_start: 0.8268 (tt0) cc_final: 0.7323 (tm130) REVERT: B 376 ARG cc_start: 0.7934 (mtp-110) cc_final: 0.7372 (mpp-170) REVERT: B 426 SER cc_start: 0.8778 (p) cc_final: 0.8199 (m) REVERT: B 451 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6646 (pt0) REVERT: B 498 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8078 (ptp) REVERT: B 603 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7602 (tptp) outliers start: 29 outliers final: 14 residues processed: 105 average time/residue: 0.5032 time to fit residues: 55.7890 Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 94 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146630 restraints weight = 5487.671| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.55 r_work: 0.3392 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6003 Z= 0.184 Angle : 0.545 7.183 8116 Z= 0.286 Chirality : 0.043 0.131 873 Planarity : 0.004 0.070 1068 Dihedral : 4.368 34.567 827 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.98 % Allowed : 16.21 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.31), residues: 750 helix: 1.84 (0.41), residues: 134 sheet: -0.67 (0.27), residues: 346 loop : 0.04 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 25 TYR 0.013 0.002 TYR B 423 PHE 0.013 0.002 PHE B 615 TRP 0.007 0.001 TRP B 270 HIS 0.002 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6003) covalent geometry : angle 0.54549 ( 8116) hydrogen bonds : bond 0.03472 ( 320) hydrogen bonds : angle 5.67611 ( 903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.207 Fit side-chains REVERT: A 86 MET cc_start: 0.7581 (mmm) cc_final: 0.7177 (mmm) REVERT: A 111 MET cc_start: 0.7813 (ptm) cc_final: 0.7329 (ptt) REVERT: B 45 SER cc_start: 0.8343 (m) cc_final: 0.7745 (t) REVERT: B 67 GLN cc_start: 0.8325 (tt0) cc_final: 0.7859 (tt0) REVERT: B 86 ILE cc_start: 0.8185 (mt) cc_final: 0.7788 (mt) REVERT: B 200 SER cc_start: 0.8264 (t) cc_final: 0.7932 (m) REVERT: B 270 TRP cc_start: 0.7787 (p-90) cc_final: 0.7489 (p90) REVERT: B 343 GLN cc_start: 0.8317 (tt0) cc_final: 0.7363 (tm130) REVERT: B 376 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7377 (mpp-170) REVERT: B 426 SER cc_start: 0.8809 (p) cc_final: 0.8273 (m) REVERT: B 444 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7776 (p0) REVERT: B 451 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: B 481 LYS cc_start: 0.7818 (ttmt) cc_final: 0.6792 (mtmt) REVERT: B 498 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8181 (ptp) REVERT: B 539 GLU cc_start: 0.7785 (tp30) cc_final: 0.7585 (mm-30) REVERT: B 583 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6454 (tmmt) REVERT: B 603 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7694 (tptp) outliers start: 31 outliers final: 19 residues processed: 107 average time/residue: 0.5316 time to fit residues: 59.7276 Evaluate side-chains 106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 chunk 52 optimal weight: 3.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.157312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125329 restraints weight = 5391.527| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.73 r_work: 0.3310 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.7635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6003 Z= 0.198 Angle : 0.557 6.488 8116 Z= 0.294 Chirality : 0.043 0.130 873 Planarity : 0.004 0.070 1068 Dihedral : 4.424 36.569 827 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.82 % Allowed : 16.69 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.31), residues: 750 helix: 1.66 (0.41), residues: 135 sheet: -0.80 (0.28), residues: 346 loop : 0.02 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 25 TYR 0.012 0.002 TYR B 423 PHE 0.014 0.002 PHE B 615 TRP 0.007 0.001 TRP B 270 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6003) covalent geometry : angle 0.55716 ( 8116) hydrogen bonds : bond 0.03450 ( 320) hydrogen bonds : angle 5.76037 ( 903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.178 Fit side-chains REVERT: A 84 LYS cc_start: 0.7124 (ttpp) cc_final: 0.6921 (ttpp) REVERT: A 86 MET cc_start: 0.7025 (mmm) cc_final: 0.6518 (mmm) REVERT: A 91 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6308 (mm-30) REVERT: A 111 MET cc_start: 0.7391 (ptm) cc_final: 0.6975 (ptt) REVERT: B 45 SER cc_start: 0.8138 (m) cc_final: 0.7490 (t) REVERT: B 51 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.5848 (mtt90) REVERT: B 67 GLN cc_start: 0.8089 (tt0) cc_final: 0.7442 (tt0) REVERT: B 69 VAL cc_start: 0.8348 (t) cc_final: 0.8136 (p) REVERT: B 86 ILE cc_start: 0.7633 (mt) cc_final: 0.7333 (mt) REVERT: B 200 SER cc_start: 0.7908 (t) cc_final: 0.7479 (m) REVERT: B 237 THR cc_start: 0.7333 (t) cc_final: 0.7094 (p) REVERT: B 270 TRP cc_start: 0.7601 (p-90) cc_final: 0.7268 (p90) REVERT: B 277 ILE cc_start: 0.8520 (mt) cc_final: 0.7920 (mp) REVERT: B 281 GLU cc_start: 0.8285 (tt0) cc_final: 0.7821 (tt0) REVERT: B 343 GLN cc_start: 0.8214 (tt0) cc_final: 0.6943 (tm130) REVERT: B 376 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.6931 (mpp-170) REVERT: B 426 SER cc_start: 0.8520 (p) cc_final: 0.7997 (m) REVERT: B 444 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7391 (p0) REVERT: B 451 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6526 (pt0) REVERT: B 452 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8103 (m) REVERT: B 481 LYS cc_start: 0.7536 (ttmt) cc_final: 0.6459 (mtmm) REVERT: B 498 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7825 (ptp) REVERT: B 583 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.5964 (tmmt) REVERT: B 603 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7474 (tptp) outliers start: 30 outliers final: 17 residues processed: 113 average time/residue: 0.4749 time to fit residues: 56.5231 Evaluate side-chains 118 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 88 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130570 restraints weight = 5375.651| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.61 r_work: 0.3373 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6003 Z= 0.142 Angle : 0.515 6.556 8116 Z= 0.272 Chirality : 0.041 0.128 873 Planarity : 0.004 0.067 1068 Dihedral : 4.223 32.932 827 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.65 % Allowed : 18.78 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.31), residues: 750 helix: 1.65 (0.41), residues: 134 sheet: -0.78 (0.28), residues: 343 loop : 0.02 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 460 TYR 0.010 0.001 TYR B 423 PHE 0.011 0.001 PHE B 407 TRP 0.007 0.001 TRP B 352 HIS 0.001 0.000 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6003) covalent geometry : angle 0.51463 ( 8116) hydrogen bonds : bond 0.03233 ( 320) hydrogen bonds : angle 5.57894 ( 903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.234 Fit side-chains REVERT: A 22 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.4942 (ttpp) REVERT: A 86 MET cc_start: 0.7385 (mmm) cc_final: 0.6906 (mmm) REVERT: A 111 MET cc_start: 0.7644 (ptm) cc_final: 0.7210 (ptt) REVERT: A 120 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 45 SER cc_start: 0.8235 (m) cc_final: 0.7631 (t) REVERT: B 51 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.5955 (mtt90) REVERT: B 67 GLN cc_start: 0.8199 (tt0) cc_final: 0.7578 (tt0) REVERT: B 69 VAL cc_start: 0.8419 (t) cc_final: 0.8212 (p) REVERT: B 107 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7185 (ttt90) REVERT: B 200 SER cc_start: 0.8099 (t) cc_final: 0.7726 (m) REVERT: B 233 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7340 (mmmm) REVERT: B 252 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8238 (t) REVERT: B 270 TRP cc_start: 0.7743 (p-90) cc_final: 0.7429 (p90) REVERT: B 277 ILE cc_start: 0.8682 (mt) cc_final: 0.8116 (mp) REVERT: B 281 GLU cc_start: 0.8352 (tt0) cc_final: 0.7961 (tt0) REVERT: B 343 GLN cc_start: 0.8219 (tt0) cc_final: 0.7079 (tm130) REVERT: B 376 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7193 (mpp-170) REVERT: B 426 SER cc_start: 0.8464 (p) cc_final: 0.8042 (m) REVERT: B 451 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6665 (pt0) REVERT: B 481 LYS cc_start: 0.7767 (ttmt) cc_final: 0.6585 (mtmt) REVERT: B 498 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7968 (ptp) REVERT: B 583 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6052 (tmmt) outliers start: 29 outliers final: 15 residues processed: 113 average time/residue: 0.4991 time to fit residues: 59.1868 Evaluate side-chains 113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132930 restraints weight = 5304.554| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.84 r_work: 0.3275 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.7950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6003 Z= 0.211 Angle : 0.559 7.150 8116 Z= 0.295 Chirality : 0.043 0.130 873 Planarity : 0.004 0.073 1068 Dihedral : 4.431 37.452 827 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.82 % Allowed : 19.90 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.31), residues: 750 helix: 1.50 (0.41), residues: 134 sheet: -0.93 (0.28), residues: 346 loop : -0.02 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 460 TYR 0.011 0.002 TYR B 423 PHE 0.014 0.002 PHE B 615 TRP 0.007 0.001 TRP B 439 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6003) covalent geometry : angle 0.55885 ( 8116) hydrogen bonds : bond 0.03451 ( 320) hydrogen bonds : angle 5.78996 ( 903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.238 Fit side-chains REVERT: A 22 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.4742 (ttpp) REVERT: A 86 MET cc_start: 0.7137 (mmm) cc_final: 0.6683 (mmm) REVERT: A 91 GLU cc_start: 0.6264 (mm-30) cc_final: 0.6009 (mm-30) REVERT: A 106 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5612 (mm-30) REVERT: A 111 MET cc_start: 0.7409 (ptm) cc_final: 0.7036 (ptt) REVERT: A 120 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 45 SER cc_start: 0.8068 (m) cc_final: 0.7417 (t) REVERT: B 51 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.5846 (mtt90) REVERT: B 67 GLN cc_start: 0.8059 (tt0) cc_final: 0.7400 (tt0) REVERT: B 69 VAL cc_start: 0.8401 (t) cc_final: 0.8188 (p) REVERT: B 77 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7373 (mtp85) REVERT: B 94 HIS cc_start: 0.7873 (m170) cc_final: 0.7278 (m170) REVERT: B 200 SER cc_start: 0.7885 (t) cc_final: 0.7425 (m) REVERT: B 207 LYS cc_start: 0.7609 (tttt) cc_final: 0.7251 (mtpp) REVERT: B 233 LYS cc_start: 0.7369 (mtpt) cc_final: 0.7057 (mmmm) REVERT: B 270 TRP cc_start: 0.7578 (p-90) cc_final: 0.7247 (p90) REVERT: B 277 ILE cc_start: 0.8540 (mt) cc_final: 0.7949 (mp) REVERT: B 281 GLU cc_start: 0.8311 (tt0) cc_final: 0.7824 (tt0) REVERT: B 343 GLN cc_start: 0.8295 (tt0) cc_final: 0.6997 (tm-30) REVERT: B 376 ARG cc_start: 0.7878 (mtp-110) cc_final: 0.6951 (mpp-170) REVERT: B 419 MET cc_start: 0.8159 (mtm) cc_final: 0.7238 (mtm) REVERT: B 421 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 426 SER cc_start: 0.8462 (p) cc_final: 0.8004 (m) REVERT: B 444 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 451 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6778 (pt0) REVERT: B 481 LYS cc_start: 0.7629 (ttmt) cc_final: 0.6471 (mtmm) REVERT: B 498 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7934 (ptp) REVERT: B 583 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6177 (tmmt) outliers start: 30 outliers final: 16 residues processed: 113 average time/residue: 0.5200 time to fit residues: 61.6331 Evaluate side-chains 116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.159800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130100 restraints weight = 5408.655| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.62 r_work: 0.3406 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6003 Z= 0.129 Angle : 0.515 7.576 8116 Z= 0.270 Chirality : 0.041 0.125 873 Planarity : 0.004 0.072 1068 Dihedral : 4.175 31.498 827 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.33 % Allowed : 20.39 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.31), residues: 750 helix: 1.65 (0.41), residues: 134 sheet: -0.87 (0.28), residues: 343 loop : 0.04 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 77 TYR 0.011 0.001 TYR B 423 PHE 0.016 0.001 PHE B 147 TRP 0.008 0.001 TRP B 352 HIS 0.001 0.000 HIS B 428 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6003) covalent geometry : angle 0.51499 ( 8116) hydrogen bonds : bond 0.03123 ( 320) hydrogen bonds : angle 5.53361 ( 903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5057 (ttpp) REVERT: A 86 MET cc_start: 0.7476 (mmm) cc_final: 0.7030 (mmm) REVERT: A 106 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5865 (mm-30) REVERT: A 111 MET cc_start: 0.7648 (ptm) cc_final: 0.7244 (ptt) REVERT: A 120 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 51 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.5873 (mtt90) REVERT: B 67 GLN cc_start: 0.8221 (tt0) cc_final: 0.7620 (tt0) REVERT: B 94 HIS cc_start: 0.7874 (m170) cc_final: 0.7366 (m170) REVERT: B 107 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7212 (ttt90) REVERT: B 200 SER cc_start: 0.8085 (t) cc_final: 0.7686 (m) REVERT: B 233 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7371 (mmmm) REVERT: B 252 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8239 (t) REVERT: B 270 TRP cc_start: 0.7788 (p-90) cc_final: 0.7456 (p90) REVERT: B 277 ILE cc_start: 0.8687 (mt) cc_final: 0.8193 (mp) REVERT: B 281 GLU cc_start: 0.8348 (tt0) cc_final: 0.7988 (tt0) REVERT: B 343 GLN cc_start: 0.8288 (tt0) cc_final: 0.7341 (tm130) REVERT: B 376 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.7236 (mpp-170) REVERT: B 396 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8610 (ttt) REVERT: B 426 SER cc_start: 0.8464 (p) cc_final: 0.8067 (m) REVERT: B 451 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6886 (pt0) REVERT: B 481 LYS cc_start: 0.7802 (ttmt) cc_final: 0.6816 (mtmm) REVERT: B 498 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7953 (ptp) REVERT: B 583 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6098 (tmmt) outliers start: 27 outliers final: 15 residues processed: 113 average time/residue: 0.5531 time to fit residues: 65.5595 Evaluate side-chains 116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.0570 chunk 2 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 140 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 545 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.158622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128889 restraints weight = 5459.953| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.64 r_work: 0.3377 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.8094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6003 Z= 0.149 Angle : 0.528 7.059 8116 Z= 0.278 Chirality : 0.042 0.128 873 Planarity : 0.004 0.073 1068 Dihedral : 4.183 32.424 827 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.85 % Allowed : 21.51 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.31), residues: 750 helix: 1.70 (0.41), residues: 134 sheet: -0.88 (0.28), residues: 343 loop : 0.06 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.013 0.001 TYR B 619 PHE 0.015 0.002 PHE B 147 TRP 0.009 0.001 TRP B 439 HIS 0.001 0.000 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6003) covalent geometry : angle 0.52789 ( 8116) hydrogen bonds : bond 0.03189 ( 320) hydrogen bonds : angle 5.49226 ( 903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.5730 (OUTLIER) cc_final: 0.4963 (ttpp) REVERT: A 86 MET cc_start: 0.7414 (mmm) cc_final: 0.6975 (mmm) REVERT: A 106 GLU cc_start: 0.6679 (mm-30) cc_final: 0.5881 (mm-30) REVERT: A 111 MET cc_start: 0.7625 (ptm) cc_final: 0.7236 (ptt) REVERT: A 120 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7210 (mt-10) REVERT: B 45 SER cc_start: 0.8189 (m) cc_final: 0.7595 (t) REVERT: B 51 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.5874 (mtt90) REVERT: B 67 GLN cc_start: 0.8173 (tt0) cc_final: 0.7524 (tt0) REVERT: B 94 HIS cc_start: 0.7976 (m170) cc_final: 0.7471 (m170) REVERT: B 200 SER cc_start: 0.8048 (t) cc_final: 0.7613 (m) REVERT: B 233 LYS cc_start: 0.7640 (mtpt) cc_final: 0.7255 (mmmm) REVERT: B 252 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8211 (t) REVERT: B 270 TRP cc_start: 0.7753 (p-90) cc_final: 0.7406 (p90) REVERT: B 277 ILE cc_start: 0.8657 (mt) cc_final: 0.8160 (mp) REVERT: B 281 GLU cc_start: 0.8365 (tt0) cc_final: 0.7981 (tt0) REVERT: B 343 GLN cc_start: 0.8343 (tt0) cc_final: 0.7443 (tm-30) REVERT: B 376 ARG cc_start: 0.7882 (mtp-110) cc_final: 0.7112 (mpp-170) REVERT: B 396 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8622 (ttt) REVERT: B 426 SER cc_start: 0.8533 (p) cc_final: 0.8084 (m) REVERT: B 451 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6985 (pt0) REVERT: B 481 LYS cc_start: 0.7742 (ttmt) cc_final: 0.6763 (mtmm) REVERT: B 498 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7885 (ptp) REVERT: B 583 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6343 (tmmt) outliers start: 24 outliers final: 15 residues processed: 112 average time/residue: 0.5559 time to fit residues: 65.2221 Evaluate side-chains 119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127556 restraints weight = 5355.498| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.69 r_work: 0.3343 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.8146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6003 Z= 0.147 Angle : 0.537 7.691 8116 Z= 0.282 Chirality : 0.042 0.129 873 Planarity : 0.004 0.073 1068 Dihedral : 4.151 32.060 827 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.01 % Allowed : 21.83 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.31), residues: 750 helix: 1.65 (0.41), residues: 134 sheet: -0.92 (0.28), residues: 344 loop : 0.09 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 415 TYR 0.013 0.001 TYR B 619 PHE 0.016 0.002 PHE B 147 TRP 0.008 0.001 TRP B 439 HIS 0.001 0.000 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6003) covalent geometry : angle 0.53749 ( 8116) hydrogen bonds : bond 0.03203 ( 320) hydrogen bonds : angle 5.48733 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.93 seconds wall clock time: 40 minutes 7.29 seconds (2407.29 seconds total)