Starting phenix.real_space_refine on Thu Jun 5 10:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dir_46916/06_2025/9dir_46916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dir_46916/06_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_46916/06_2025/9dir_46916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dir_46916/06_2025/9dir_46916.map" model { file = "/net/cci-nas-00/data/ceres_data/9dir_46916/06_2025/9dir_46916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dir_46916/06_2025/9dir_46916.cif" } resolution = 2.97 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= 0.072 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.80, per 1000 atoms: 0.65 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: 1.42 Conformation dependent library (CDL) restraints added in 881.0 milliseconds 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: 0.63 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: 1.96 Time building geometry restraints manager: 1.71 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: 1.340 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- 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 : 10.18 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 (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: 0.24 (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 TRP 0.004 0.001 TRP B 439 HIS 0.002 0.001 HIS B 94 PHE 0.011 0.001 PHE B 414 TYR 0.017 0.001 TYR B 119 ARG 0.007 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.18364 ( 320) hydrogen bonds : angle 8.64246 ( 903) covalent geometry : bond 0.00375 ( 6003) covalent geometry : angle 0.57522 ( 8116) *********************** 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 : 0.650 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: 0.6553 (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: 0.6956 (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: 0.9152 time to fit residues: 142.4811 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 : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.167152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137700 restraints weight = 5406.413| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.56 r_work: 0.3414 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6003 Z= 0.324 Angle : 0.755 7.700 8116 Z= 0.407 Chirality : 0.049 0.159 873 Planarity : 0.006 0.066 1068 Dihedral : 5.075 40.096 827 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 9.95 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.31), residues: 750 helix: 0.85 (0.40), residues: 135 sheet: -0.48 (0.28), residues: 349 loop : -0.05 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 390 HIS 0.005 0.001 HIS B 333 PHE 0.021 0.003 PHE B 478 TYR 0.022 0.002 TYR B 485 ARG 0.009 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 320) hydrogen bonds : angle 6.52318 ( 903) covalent geometry : bond 0.00696 ( 6003) covalent geometry : angle 0.75477 ( 8116) *********************** 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 137 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.579 Fit side-chains REVERT: A 5 LYS cc_start: 0.6713 (pttp) cc_final: 0.6158 (ptmm) REVERT: A 8 LYS cc_start: 0.6401 (ttpp) cc_final: 0.5978 (ttpt) REVERT: A 45 LYS cc_start: 0.6047 (mmtt) cc_final: 0.5697 (tttm) REVERT: A 84 LYS cc_start: 0.7605 (ttpp) cc_final: 0.7141 (ttpt) REVERT: A 86 MET cc_start: 0.7336 (mmm) cc_final: 0.6962 (mmm) REVERT: A 111 MET cc_start: 0.7538 (ptm) cc_final: 0.6884 (ptt) REVERT: A 126 MET cc_start: 0.7047 (ppp) cc_final: 0.4647 (ttm) REVERT: B 45 SER cc_start: 0.8432 (m) cc_final: 0.7953 (t) REVERT: B 86 ILE cc_start: 0.8370 (mt) cc_final: 0.8036 (mt) REVERT: B 92 THR cc_start: 0.8189 (p) cc_final: 0.7829 (t) REVERT: B 118 LEU cc_start: 0.8767 (mt) cc_final: 0.8508 (mt) REVERT: B 140 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7621 (mm-40) REVERT: B 158 HIS cc_start: 0.7868 (m90) cc_final: 0.7653 (m90) REVERT: B 186 ASP cc_start: 0.7093 (m-30) cc_final: 0.6662 (m-30) REVERT: B 200 SER cc_start: 0.8284 (t) cc_final: 0.7929 (m) REVERT: B 212 ILE cc_start: 0.8465 (mt) cc_final: 0.8250 (mt) REVERT: B 270 TRP cc_start: 0.7742 (p-90) cc_final: 0.7382 (p90) REVERT: B 277 ILE cc_start: 0.8624 (mt) cc_final: 0.8024 (pt) REVERT: B 287 GLN cc_start: 0.5949 (mm-40) cc_final: 0.5422 (pt0) REVERT: B 311 LEU cc_start: 0.8252 (mt) cc_final: 0.7907 (mp) REVERT: B 343 GLN cc_start: 0.8411 (tt0) cc_final: 0.7505 (tm130) REVERT: B 376 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7223 (mpp-170) REVERT: B 451 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: B 460 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7698 (ttp80) REVERT: B 479 ASP cc_start: 0.8505 (t0) cc_final: 0.8286 (t70) REVERT: B 481 LYS cc_start: 0.7567 (ttmt) cc_final: 0.6694 (mtmt) REVERT: B 529 ARG cc_start: 0.8494 (ttm170) cc_final: 0.8289 (ttm170) REVERT: B 590 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8769 (m-40) REVERT: B 603 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7597 (mmmt) REVERT: B 627 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7907 (mm110) outliers start: 19 outliers final: 9 residues processed: 134 average time/residue: 0.9557 time to fit residues: 135.2683 Evaluate side-chains 104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 285 ASN 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 590 ASN Chi-restraints excluded: chain B residue 625 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN B 19 ASN B 67 GLN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144594 restraints weight = 5419.383| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.60 r_work: 0.3404 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.6819 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= 0.174 Angle : 0.556 6.011 8116 Z= 0.298 Chirality : 0.043 0.155 873 Planarity : 0.005 0.069 1068 Dihedral : 4.517 33.213 827 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.49 % Allowed : 13.48 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.31), residues: 750 helix: 1.44 (0.40), residues: 135 sheet: -0.71 (0.27), residues: 355 loop : 0.06 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 390 HIS 0.002 0.001 HIS B 319 PHE 0.015 0.002 PHE B 457 TYR 0.019 0.002 TYR B 423 ARG 0.007 0.001 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 320) hydrogen bonds : angle 6.02049 ( 903) covalent geometry : bond 0.00358 ( 6003) covalent geometry : angle 0.55620 ( 8116) *********************** 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 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.632 Fit side-chains REVERT: A 21 GLU cc_start: 0.6358 (tt0) cc_final: 0.5974 (pt0) REVERT: A 84 LYS cc_start: 0.7456 (ttpp) cc_final: 0.7029 (ttpt) REVERT: A 86 MET cc_start: 0.7266 (mmm) cc_final: 0.6881 (mmm) REVERT: A 111 MET cc_start: 0.7624 (ptm) cc_final: 0.7028 (ptt) REVERT: B 41 GLN cc_start: 0.7984 (mt0) cc_final: 0.7614 (mt0) REVERT: B 45 SER cc_start: 0.8536 (m) cc_final: 0.7925 (t) REVERT: B 47 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7706 (p) REVERT: B 67 GLN cc_start: 0.8409 (tt0) cc_final: 0.7854 (tt0) REVERT: B 86 ILE cc_start: 0.8114 (mt) cc_final: 0.7757 (mt) REVERT: B 200 SER cc_start: 0.8192 (t) cc_final: 0.7845 (m) REVERT: B 233 LYS cc_start: 0.7266 (ttmm) cc_final: 0.6701 (tptt) REVERT: B 270 TRP cc_start: 0.7752 (p-90) cc_final: 0.7456 (p90) REVERT: B 311 LEU cc_start: 0.8119 (mt) cc_final: 0.7850 (mp) REVERT: B 343 GLN cc_start: 0.8350 (tt0) cc_final: 0.7289 (tm130) REVERT: B 360 ARG cc_start: 0.8271 (tmm-80) cc_final: 0.7964 (ttp-170) REVERT: B 376 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7285 (mpp-170) REVERT: B 426 SER cc_start: 0.8837 (p) cc_final: 0.8270 (m) REVERT: B 451 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6773 (pt0) REVERT: B 452 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8141 (m) REVERT: B 529 ARG cc_start: 0.8453 (ttm170) cc_final: 0.8248 (ttm170) REVERT: B 590 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8713 (m110) REVERT: B 603 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7473 (mmmt) outliers start: 28 outliers final: 14 residues processed: 114 average time/residue: 1.0941 time to fit residues: 131.7484 Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 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 160 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN B 88 GLN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 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 = 0.3965 r_free = 0.3965 target = 0.173220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144715 restraints weight = 5554.644| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.58 r_work: 0.3379 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6003 Z= 0.178 Angle : 0.537 7.662 8116 Z= 0.284 Chirality : 0.043 0.148 873 Planarity : 0.004 0.069 1068 Dihedral : 4.370 33.874 827 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.17 % Allowed : 15.57 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.31), residues: 750 helix: 1.60 (0.40), residues: 135 sheet: -0.84 (0.27), residues: 345 loop : -0.11 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 352 HIS 0.001 0.001 HIS B 94 PHE 0.012 0.002 PHE B 615 TYR 0.011 0.001 TYR B 328 ARG 0.003 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 320) hydrogen bonds : angle 5.83984 ( 903) covalent geometry : bond 0.00373 ( 6003) covalent geometry : angle 0.53707 ( 8116) *********************** 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 129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.690 Fit side-chains REVERT: A 84 LYS cc_start: 0.7507 (ttpp) cc_final: 0.7019 (ttpt) REVERT: A 86 MET cc_start: 0.7388 (mmm) cc_final: 0.6964 (mmm) REVERT: A 111 MET cc_start: 0.7745 (ptm) cc_final: 0.7223 (ptt) REVERT: B 41 GLN cc_start: 0.8028 (mt0) cc_final: 0.7673 (mt0) REVERT: B 45 SER cc_start: 0.8565 (m) cc_final: 0.7953 (t) REVERT: B 67 GLN cc_start: 0.8393 (tt0) cc_final: 0.7808 (tt0) REVERT: B 86 ILE cc_start: 0.8202 (mt) cc_final: 0.7824 (mt) REVERT: B 200 SER cc_start: 0.8264 (t) cc_final: 0.7907 (m) REVERT: B 270 TRP cc_start: 0.7824 (p-90) cc_final: 0.7549 (p90) REVERT: B 281 GLU cc_start: 0.8419 (tt0) cc_final: 0.8063 (tt0) REVERT: B 331 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 343 GLN cc_start: 0.8411 (tt0) cc_final: 0.7402 (tm130) REVERT: B 360 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.8013 (ttp-170) REVERT: B 376 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7283 (mpp-170) REVERT: B 426 SER cc_start: 0.8839 (p) cc_final: 0.8299 (m) REVERT: B 451 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: B 590 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8810 (m110) REVERT: B 603 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7522 (mmmt) outliers start: 26 outliers final: 15 residues processed: 117 average time/residue: 1.0235 time to fit residues: 126.3820 Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 606 THR 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 10 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146253 restraints weight = 5399.999| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.63 r_work: 0.3400 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.7354 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= 0.143 Angle : 0.508 7.225 8116 Z= 0.269 Chirality : 0.042 0.133 873 Planarity : 0.004 0.067 1068 Dihedral : 4.235 31.214 827 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.98 % Allowed : 15.89 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.31), residues: 750 helix: 1.70 (0.41), residues: 135 sheet: -0.94 (0.27), residues: 343 loop : -0.11 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 352 HIS 0.001 0.000 HIS B 94 PHE 0.011 0.001 PHE B 407 TYR 0.010 0.001 TYR B 328 ARG 0.007 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 320) hydrogen bonds : angle 5.64555 ( 903) covalent geometry : bond 0.00297 ( 6003) covalent geometry : angle 0.50810 ( 8116) *********************** 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 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.668 Fit side-chains REVERT: A 84 LYS cc_start: 0.7514 (ttpp) cc_final: 0.7302 (ttpp) REVERT: A 86 MET cc_start: 0.7388 (mmm) cc_final: 0.6994 (mmm) REVERT: A 111 MET cc_start: 0.7726 (ptm) cc_final: 0.7201 (ptt) REVERT: A 122 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4789 (mptt) REVERT: B 45 SER cc_start: 0.8334 (m) cc_final: 0.7733 (t) REVERT: B 67 GLN cc_start: 0.8253 (tt0) cc_final: 0.7761 (tt0) REVERT: B 86 ILE cc_start: 0.8092 (mt) cc_final: 0.7661 (mt) REVERT: B 200 SER cc_start: 0.8166 (t) cc_final: 0.7835 (m) REVERT: B 233 LYS cc_start: 0.7667 (mmmt) cc_final: 0.6702 (tptt) REVERT: B 252 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8409 (t) REVERT: B 270 TRP cc_start: 0.7852 (p-90) cc_final: 0.7554 (p90) REVERT: B 331 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 343 GLN cc_start: 0.8363 (tt0) cc_final: 0.7334 (tm130) REVERT: B 360 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8032 (ttp-170) REVERT: B 376 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7250 (mpp-170) REVERT: B 396 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8641 (ttt) REVERT: B 426 SER cc_start: 0.8767 (p) cc_final: 0.8253 (m) REVERT: B 451 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6932 (pt0) REVERT: B 590 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: B 603 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7486 (mmmt) outliers start: 31 outliers final: 15 residues processed: 108 average time/residue: 1.0515 time to fit residues: 120.0001 Evaluate side-chains 108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS 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 360 ARG 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 405 MET Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 606 THR 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 30 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.155987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124374 restraints weight = 5394.080| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.71 r_work: 0.3302 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6003 Z= 0.207 Angle : 0.549 7.287 8116 Z= 0.290 Chirality : 0.043 0.146 873 Planarity : 0.004 0.068 1068 Dihedral : 4.369 35.220 827 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.49 % Allowed : 16.85 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.31), residues: 750 helix: 1.62 (0.42), residues: 134 sheet: -1.01 (0.27), residues: 345 loop : -0.09 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 439 HIS 0.002 0.001 HIS B 333 PHE 0.012 0.002 PHE B 407 TYR 0.012 0.002 TYR B 328 ARG 0.006 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 320) hydrogen bonds : angle 5.76607 ( 903) covalent geometry : bond 0.00448 ( 6003) covalent geometry : angle 0.54897 ( 8116) *********************** 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 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7208 (ttpp) cc_final: 0.6943 (ttpp) REVERT: A 86 MET cc_start: 0.7032 (mmm) cc_final: 0.6643 (mmm) REVERT: A 111 MET cc_start: 0.7421 (ptm) cc_final: 0.6904 (ptt) REVERT: B 45 SER cc_start: 0.8204 (m) cc_final: 0.7547 (t) REVERT: B 51 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.5914 (mtt90) REVERT: B 67 GLN cc_start: 0.8131 (tt0) cc_final: 0.7493 (tt0) REVERT: B 69 VAL cc_start: 0.8423 (t) cc_final: 0.8184 (p) REVERT: B 86 ILE cc_start: 0.7745 (mt) cc_final: 0.7412 (mt) REVERT: B 200 SER cc_start: 0.7993 (t) cc_final: 0.7538 (m) REVERT: B 233 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6369 (tptt) REVERT: B 270 TRP cc_start: 0.7573 (p-90) cc_final: 0.7264 (p90) REVERT: B 277 ILE cc_start: 0.8527 (mt) cc_final: 0.8270 (mm) REVERT: B 281 GLU cc_start: 0.8304 (tt0) cc_final: 0.7838 (tt0) REVERT: B 331 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7563 (mt-10) REVERT: B 343 GLN cc_start: 0.8298 (tt0) cc_final: 0.7025 (tm130) REVERT: B 360 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7787 (ttp-170) REVERT: B 376 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.6983 (mpp-170) REVERT: B 396 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8623 (ttt) REVERT: B 426 SER cc_start: 0.8550 (p) cc_final: 0.8025 (m) REVERT: B 451 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: B 457 PHE cc_start: 0.8655 (p90) cc_final: 0.8265 (p90) REVERT: B 459 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 583 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6003 (tmmt) REVERT: B 603 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7163 (mmmt) outliers start: 28 outliers final: 13 residues processed: 110 average time/residue: 1.1224 time to fit residues: 130.0387 Evaluate side-chains 113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 233 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 360 ARG 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 459 LEU 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 606 THR 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 38 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125917 restraints weight = 5447.325| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.77 r_work: 0.3321 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.7708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6003 Z= 0.161 Angle : 0.535 8.422 8116 Z= 0.281 Chirality : 0.042 0.132 873 Planarity : 0.004 0.070 1068 Dihedral : 4.267 32.940 827 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.85 % Allowed : 19.58 % 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 (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: -0.49 (0.31), residues: 750 helix: 1.55 (0.42), residues: 134 sheet: -1.03 (0.27), residues: 346 loop : -0.00 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 403 HIS 0.001 0.000 HIS B 94 PHE 0.012 0.002 PHE B 407 TYR 0.013 0.001 TYR B 619 ARG 0.005 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 320) hydrogen bonds : angle 5.68567 ( 903) covalent geometry : bond 0.00342 ( 6003) covalent geometry : angle 0.53532 ( 8116) *********************** 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 117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.7042 (mmm) cc_final: 0.6591 (mmm) REVERT: A 111 MET cc_start: 0.7396 (ptm) cc_final: 0.6896 (ptt) REVERT: B 45 SER cc_start: 0.8155 (m) cc_final: 0.7522 (t) REVERT: B 51 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.5901 (mtt90) REVERT: B 67 GLN cc_start: 0.8098 (tt0) cc_final: 0.7459 (tt0) REVERT: B 200 SER cc_start: 0.7920 (t) cc_final: 0.7503 (m) REVERT: B 233 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6412 (tptt) REVERT: B 252 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8165 (t) REVERT: B 270 TRP cc_start: 0.7547 (p-90) cc_final: 0.7222 (p90) REVERT: B 277 ILE cc_start: 0.8514 (mt) cc_final: 0.7982 (mp) REVERT: B 281 GLU cc_start: 0.8275 (tt0) cc_final: 0.7917 (tt0) REVERT: B 331 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7502 (mt-10) REVERT: B 343 GLN cc_start: 0.8292 (tt0) cc_final: 0.7001 (tm130) REVERT: B 360 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7789 (ttp-170) REVERT: B 376 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.6956 (mpp-170) REVERT: B 426 SER cc_start: 0.8485 (p) cc_final: 0.7996 (m) REVERT: B 451 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: B 459 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7900 (mt) REVERT: B 583 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.5970 (tmmt) REVERT: B 603 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7420 (tptp) outliers start: 24 outliers final: 13 residues processed: 105 average time/residue: 1.0466 time to fit residues: 115.9663 Evaluate side-chains 109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 233 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 360 ARG 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 459 LEU 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 606 THR 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 46 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** B 203 ASN ** 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 = 0.3722 r_free = 0.3722 target = 0.156419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125067 restraints weight = 5344.371| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3310 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.7875 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= 0.174 Angle : 0.542 8.123 8116 Z= 0.284 Chirality : 0.043 0.139 873 Planarity : 0.004 0.072 1068 Dihedral : 4.274 33.513 827 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.69 % Allowed : 19.74 % 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 (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: -0.52 (0.31), residues: 750 helix: 1.51 (0.42), residues: 134 sheet: -1.06 (0.27), residues: 346 loop : -0.00 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 403 HIS 0.002 0.001 HIS B 333 PHE 0.012 0.002 PHE B 407 TYR 0.011 0.002 TYR B 619 ARG 0.005 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 320) hydrogen bonds : angle 5.69630 ( 903) covalent geometry : bond 0.00373 ( 6003) covalent geometry : angle 0.54171 ( 8116) *********************** 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 121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.7047 (mmm) cc_final: 0.6647 (mmm) REVERT: A 111 MET cc_start: 0.7425 (ptm) cc_final: 0.6958 (ptt) REVERT: B 45 SER cc_start: 0.8070 (m) cc_final: 0.7423 (t) REVERT: B 51 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.5934 (mtt90) REVERT: B 67 GLN cc_start: 0.8101 (tt0) cc_final: 0.7475 (tt0) REVERT: B 69 VAL cc_start: 0.8274 (t) cc_final: 0.8054 (p) REVERT: B 200 SER cc_start: 0.7929 (t) cc_final: 0.7481 (m) REVERT: B 233 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6394 (tptt) REVERT: B 270 TRP cc_start: 0.7542 (p-90) cc_final: 0.7203 (p90) REVERT: B 281 GLU cc_start: 0.8222 (tt0) cc_final: 0.7834 (tt0) REVERT: B 331 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 343 GLN cc_start: 0.8355 (tt0) cc_final: 0.7079 (tm130) REVERT: B 360 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7783 (ttp-170) REVERT: B 376 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.6924 (mpp-170) REVERT: B 426 SER cc_start: 0.8471 (p) cc_final: 0.7974 (m) REVERT: B 451 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: B 481 LYS cc_start: 0.7474 (ttmt) cc_final: 0.6463 (mtmm) REVERT: B 583 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6215 (tmmt) REVERT: B 603 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7467 (tptp) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 1.3309 time to fit residues: 153.9566 Evaluate side-chains 112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 233 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 360 ARG 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 537 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ILE 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 72 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124497 restraints weight = 5364.298| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.69 r_work: 0.3305 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.8041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6003 Z= 0.185 Angle : 0.560 7.664 8116 Z= 0.294 Chirality : 0.043 0.133 873 Planarity : 0.004 0.073 1068 Dihedral : 4.339 33.926 827 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.05 % Allowed : 21.03 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.31), residues: 750 helix: 1.51 (0.41), residues: 134 sheet: -1.10 (0.27), residues: 346 loop : -0.01 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 439 HIS 0.002 0.001 HIS B 94 PHE 0.016 0.002 PHE B 147 TYR 0.012 0.002 TYR B 328 ARG 0.005 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 320) hydrogen bonds : angle 5.73560 ( 903) covalent geometry : bond 0.00401 ( 6003) covalent geometry : angle 0.55979 ( 8116) *********************** 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 117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.6251 (mt-10) cc_final: 0.6007 (mt-10) REVERT: A 86 MET cc_start: 0.7120 (mmm) cc_final: 0.6738 (mmm) REVERT: A 107 GLU cc_start: 0.6455 (tm-30) cc_final: 0.5814 (tp30) REVERT: A 111 MET cc_start: 0.7434 (ptm) cc_final: 0.7122 (ptt) REVERT: A 120 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6995 (mt-10) REVERT: B 45 SER cc_start: 0.8093 (m) cc_final: 0.7449 (t) REVERT: B 51 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.5902 (mtt90) REVERT: B 67 GLN cc_start: 0.8095 (tt0) cc_final: 0.7468 (tt0) REVERT: B 200 SER cc_start: 0.7961 (t) cc_final: 0.7500 (m) REVERT: B 233 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6477 (tptt) REVERT: B 262 LYS cc_start: 0.8017 (tttp) cc_final: 0.7735 (tttm) REVERT: B 270 TRP cc_start: 0.7604 (p-90) cc_final: 0.7259 (p90) REVERT: B 277 ILE cc_start: 0.8569 (mt) cc_final: 0.8050 (mp) REVERT: B 281 GLU cc_start: 0.8241 (tt0) cc_final: 0.7871 (tt0) REVERT: B 331 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 343 GLN cc_start: 0.8373 (tt0) cc_final: 0.7345 (tm-30) REVERT: B 360 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7794 (ttp-170) REVERT: B 376 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.6954 (mpp-170) REVERT: B 426 SER cc_start: 0.8505 (p) cc_final: 0.8013 (m) REVERT: B 451 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6594 (pt0) REVERT: B 481 LYS cc_start: 0.7539 (ttmt) cc_final: 0.6479 (mtmm) REVERT: B 583 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6172 (tmmt) REVERT: B 603 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7563 (tptp) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 1.1846 time to fit residues: 135.2324 Evaluate side-chains 116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 233 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 360 ARG 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 537 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 606 THR 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 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN ** B 203 ASN ** 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 = 0.3697 r_free = 0.3697 target = 0.153759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122515 restraints weight = 5417.149| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.69 r_work: 0.3278 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.8151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6003 Z= 0.218 Angle : 0.599 7.842 8116 Z= 0.312 Chirality : 0.044 0.150 873 Planarity : 0.004 0.074 1068 Dihedral : 4.461 36.165 827 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.37 % Allowed : 20.71 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.31), residues: 750 helix: 1.39 (0.41), residues: 134 sheet: -1.22 (0.27), residues: 350 loop : 0.03 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 439 HIS 0.002 0.001 HIS B 94 PHE 0.013 0.002 PHE B 407 TYR 0.013 0.002 TYR B 328 ARG 0.005 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 320) hydrogen bonds : angle 5.83001 ( 903) covalent geometry : bond 0.00478 ( 6003) covalent geometry : angle 0.59906 ( 8116) ********************** 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 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.595 Fit side-chains REVERT: A 55 LYS cc_start: 0.6552 (ptpt) cc_final: 0.5779 (mptt) REVERT: A 56 GLU cc_start: 0.6505 (mt-10) cc_final: 0.6073 (mt-10) REVERT: A 86 MET cc_start: 0.7229 (mmm) cc_final: 0.6899 (mmm) REVERT: A 111 MET cc_start: 0.7426 (ptm) cc_final: 0.6964 (ptt) REVERT: A 120 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7055 (mt-10) REVERT: B 45 SER cc_start: 0.8125 (m) cc_final: 0.7478 (t) REVERT: B 51 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.5799 (mtt90) REVERT: B 67 GLN cc_start: 0.8126 (tt0) cc_final: 0.7478 (tt0) REVERT: B 69 VAL cc_start: 0.8303 (t) cc_final: 0.8089 (p) REVERT: B 200 SER cc_start: 0.7964 (t) cc_final: 0.7458 (m) REVERT: B 233 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6478 (tptt) REVERT: B 262 LYS cc_start: 0.7965 (tttp) cc_final: 0.7678 (tttm) REVERT: B 270 TRP cc_start: 0.7590 (p-90) cc_final: 0.7255 (p90) REVERT: B 277 ILE cc_start: 0.8537 (mt) cc_final: 0.8007 (mp) REVERT: B 281 GLU cc_start: 0.8245 (tt0) cc_final: 0.7834 (tt0) REVERT: B 331 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 343 GLN cc_start: 0.8437 (tt0) cc_final: 0.7427 (tm-30) REVERT: B 360 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7383 (ttp-170) REVERT: B 376 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.6978 (mpp-170) REVERT: B 426 SER cc_start: 0.8523 (p) cc_final: 0.8040 (m) REVERT: B 451 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6678 (pt0) REVERT: B 481 LYS cc_start: 0.7588 (ttmt) cc_final: 0.6476 (mtmm) REVERT: B 506 LYS cc_start: 0.7481 (tptt) cc_final: 0.6793 (ttpp) REVERT: B 583 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6218 (tmmt) REVERT: B 603 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7489 (tptp) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 1.2847 time to fit residues: 152.4187 Evaluate side-chains 119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 121 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 360 ARG 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 537 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 606 THR 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 14 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN B 189 GLN ** B 203 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 = 0.3728 r_free = 0.3728 target = 0.156783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125429 restraints weight = 5418.406| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.71 r_work: 0.3315 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.8204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6003 Z= 0.156 Angle : 0.562 8.079 8116 Z= 0.293 Chirality : 0.043 0.133 873 Planarity : 0.004 0.072 1068 Dihedral : 4.290 31.393 827 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.21 % Allowed : 21.35 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.31), residues: 750 helix: 1.51 (0.41), residues: 134 sheet: -1.18 (0.27), residues: 344 loop : 0.01 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 439 HIS 0.001 0.000 HIS B 94 PHE 0.016 0.002 PHE B 147 TYR 0.012 0.001 TYR B 619 ARG 0.005 0.000 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 320) hydrogen bonds : angle 5.65273 ( 903) covalent geometry : bond 0.00335 ( 6003) covalent geometry : angle 0.56211 ( 8116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4876.31 seconds wall clock time: 85 minutes 26.71 seconds (5126.71 seconds total)